NUCLEIC ACID AND CORRESPONDING PROTEIN ENTITLED 151P3D4 USEFUL IN TREATMENT AND DETECTION OF CANCER

Abstract

A novel gene (designated 151P3D4) and its encoded protein, and variants thereof, are described wherein 151P3D4 exhibits tissue specific expression in normal adult tissue, and is aberrantly expressed in the cancers listed in Table I. Consequently, 151P3D4 provides a diagnostic, prognostic, prophylactic and/or therapeutic target for cancer. The 151P3D4 gene or fragment thereof, or its encoded protein, or variants thereof, or a fragment thereof, can be used to elicit a humoral or cellular immune response; antibodies or T cells reactive with 151P3D4 can be used in active or passive immunization.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. Ser. No. 12/687,768, filed Jan. 14, 2010, now allowed, which is a divisional of U.S. Ser. No. 11/833,918, filed Aug. 3, 2007, now U.S. Pat. No. 7,667,015, issued Feb. 23, 2010, which is a divisional of U.S. Ser. No. 10/120,907 filed Apr. 9, 2002, now abandoned, which claims priority from U.S. Ser. No. 60/282,739 filed Apr. 10, 2001, and U.S. Ser. No. 60/286,630 filed Apr. 25, 2001. The contents of these applications are hereby incorporated by reference herein in their entirety.

STATEMENT OF RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH

Not applicable.

REFERENCE TO SEQUENCE LISTING SUBMITTED VIA EFS WEB

This application is being filed electronically via the USPTO EFS-WEB server, as authorized and set forth in MPEP §1730 II.B.2(a)(A), and this electronic filing includes an electronically submitted sequence (SEQ ID) listing. The entire content of this sequence listing is herein incorporated by reference for all purposes. The sequence listing is identified on the electronically filed .txt file as follows:

	File Name	Date of Creation	Size (bytes)
	511582006902Seqlist.txt	Jan. 6, 2011	210,387 bytes

FIELD OF THE INVENTION

The invention described herein relates to a gene and its encoded protein, termed 151P3D4, expressed in certain cancers, and to diagnostic and therapeutic methods and compositions useful in the management of cancers that express 151P3D4.

BACKGROUND OF THE INVENTION

Cancer is the second leading cause of human death next to coronary disease. Worldwide, millions of people die from cancer every year. In the United States alone, as reported by the American Cancer Society, cancer causes the death of well over a half-million people annually, with over 1.2 million new cases diagnosed per year. While deaths from heart disease have been declining significantly, those resulting from cancer generally are on the rise. In the early part of the next century, cancer is predicted to become the leading cause of death.

Worldwide, several cancers stand out as the leading killers. In particular, carcinomas of the lung, prostate, breast, colon, pancreas, and ovary represent the primary causes of cancer death. These and virtually all other carcinomas share a common lethal feature. With very few exceptions, metastatic disease from a carcinoma is fatal. Moreover, even for those cancer patients who initially survive their primary cancers, common experience has shown that their lives are dramatically altered. Many cancer patients experience strong anxieties driven by the awareness of the potential for recurrence or treatment failure. Many cancer patients experience physical debilitations following treatment. Furthermore, many cancer patients experience a recurrence.

Worldwide, prostate cancer is the fourth most prevalent cancer in men. In North America and Northern Europe, it is by far the most common cancer in males and is the second leading cause of cancer death in men. In the United States alone, well over 30,000 men die annually of this disease—second only to lung cancer. Despite the magnitude of these figures, there is still no effective treatment for metastatic prostate cancer. Surgical prostatectomy, radiation therapy, hormone ablation therapy, surgical castration and chemotherapy continue to be the main treatment modalities. Unfortunately, these treatments are ineffective for many and are often associated with undesirable consequences.

On the diagnostic front, the lack of a prostate tumor marker that can accurately detect early-stage, localized tumors remains a significant limitation in the diagnosis and management of this disease. Although the serum prostate specific antigen (PSA) assay has been a very useful tool, however its specificity and general utility is widely regarded as lacking in several important respects.

Progress in identifying additional specific markers for prostate cancer has been improved by the generation of prostate cancer xenografts that can recapitulate different stages of the disease in mice. The LAPC (Los Angeles Prostate Cancer) xenografts are prostate cancer xenografts that have survived passage in severe combined immune deficient (SCID) mice and have exhibited the capacity to mimic the transition from androgen dependence to androgen independence (Klein et al., 1997, Nat. Med. 3:402). More recently identified prostate cancer markers include PCTA-1 (Su et al., 1996, Proc. Natl. Acad. Sci. USA 93: 7252), prostate-specific membrane (PSM) antigen (Pinto et al., Clin Cancer Res 1996 September 2 (9): 1445-51), STEAP (Hubert, et al., Proc Natl Acad Sci USA. 1999 Dec. 7; 96(25): 14523-8) and prostate stem cell antigen (PSCA) (Reiter et al., 1998, Proc. Natl. Acad. Sci. USA 95: 1735).

While previously identified markers such as PSA, PSM, PCTA and PSCA have facilitated efforts to diagnose and treat prostate cancer, there is need for the identification of additional markers and therapeutic targets for prostate and related cancers in order to further improve diagnosis and therapy.

Renal cell carcinoma (RCC) accounts for approximately 3 percent of adult malignancies. Once adenomas reach a diameter of 2 to 3 cm, malignant potential exists. In the adult, the two principal malignant renal tumors are renal cell adenocarcinoma and transitional cell carcinoma of the renal pelvis or ureter. The incidence of renal cell adenocarcinoma is estimated at more than 29,000 cases in the United States, and more than 11,600 patients died of this disease in 1998. Transitional cell carcinoma is less frequent, with an incidence of approximately 500 cases per year in the United States.

Surgery has been the primary therapy for renal cell adenocarcinoma for many decades. Until recently, metastatic disease has been refractory to any systemic therapy. With recent developments in systemic therapies, particularly immunotherapies, metastatic renal cell carcinoma may be approached aggressively in appropriate patients with a possibility of durable responses. Nevertheless, there is a remaining need for effective therapies for these patients.

Of all new cases of cancer in the United States, bladder cancer represents approximately 5 percent in men (fifth most common neoplasm) and 3 percent in women (eighth most common neoplasm). The incidence is increasing slowly, concurrent with an increasing older population. In 1998, there was an estimated 54,500 cases, including 39,500 in men and 15,000 in women. The age-adjusted incidence in the United States is 32 per 100,000 for men and 8 per 100,000 in women. The historic male/female ratio of 3:1 may be decreasing related to smoking patterns in women. There were an estimated 11,000 deaths from bladder cancer in 1998 (7,800 in men and 3,900 in women). Bladder cancer incidence and mortality strongly increase with age and will be an increasing problem as the population becomes more elderly.

Most bladder cancers recur in the bladder. Bladder cancer is managed with a combination of transurethral resection of the bladder (TUR) and intravesical chemotherapy or immunotherapy. The multifocal and recurrent nature of bladder cancer points out the limitations of TUR. Most muscle-invasive cancers are not cured by TUR alone. Radical cystectomy and urinary diversion is the most effective means to eliminate the cancer but carry an undeniable impact on urinary and sexual function. There continues to be a significant need for treatment modalities that are beneficial for bladder cancer patients.

An estimated 130,200 cases of colorectal cancer occurred in 2000 in the United States, including 93,800 cases of colon cancer and 36,400 of rectal cancer. Colorectal cancers are the third most common cancers in men and women. Incidence rates declined significantly during 1992-1996 (−2.1% per year). Research suggests that these declines have been due to increased screening and polyp removal, preventing progression of polyps to invasive cancers. There were an estimated 56,300 deaths (47,700 from colon cancer, 8,600 from rectal cancer) in 2000, accounting for about 11% of all U.S. cancer deaths.

At present, surgery is the most common form of therapy for colorectal cancer, and for cancers that have not spread, it is frequently curative. Chemotherapy, or chemotherapy plus radiation, is given before or after surgery to most patients whose cancer has deeply perforated the bowel wall or has spread to the lymph nodes. A permanent colostomy (creation of an abdominal opening for elimination of body wastes) is occasionally needed for colon cancer and is infrequently required for rectal cancer. There continues to be a need for effective diagnostic and treatment modalities for colorectal cancer.

There were an estimated 164,100 new cases of lung and bronchial cancer in 2000, accounting for 14% of all U.S. cancer diagnoses. The incidence rate of lung and bronchial cancer is declining significantly in men, from a high of 86.5 per 100,000 in 1984 to 70.0 in 1996. In the 1990s, the rate of increase among women began to slow. In 1996, the incidence rate in women was 42.3 per 100,000.

Lung and bronchial cancer caused an estimated 156,900 deaths in 2000, accounting for 28% of all cancer deaths. During 1992-1996, mortality from lung cancer declined significantly among men (−1.7% per year) while rates for women were still significantly increasing (0.9% per year). Since 1987, more women have died each year of lung cancer than breast cancer, which, for over 40 years, was the major cause of cancer death in women. Decreasing lung cancer incidence and mortality rates most likely resulted from decreased smoking rates over the previous 30 years; however, decreasing smoking patterns among women lag behind those of men. Of concern, although the declines in adult tobacco use have slowed, tobacco use in youth is increasing again.

Treatment options for lung and bronchial cancer are determined by the type and stage of the cancer and include surgery, radiation therapy, and chemotherapy. For many localized cancers, surgery is usually the treatment of choice. Because the disease has usually spread by the time it is discovered, radiation therapy and chemotherapy are often needed in combination with surgery. Chemotherapy alone or combined with radiation is the treatment of choice for small cell lung cancer; on this regimen, a large percentage of patients experience remission, which in some cases is long lasting. There is however, an ongoing need for effective treatment and diagnostic approaches for lung and bronchial cancers.

An estimated 182,800 new invasive cases of breast cancer were expected to occur among women in the United States during 2000. Additionally, about 1,400 new cases of breast cancer were expected to be diagnosed in men in 2000. After increasing about 4% per year in the 1980s, breast cancer incidence rates in women have leveled off in the 1990s to about 110.6 cases per 100,000.

In the U.S. alone, there were an estimated 41,200 deaths (40,800 women, 400 men) in 2000 due to breast cancer. Breast cancer ranks second among cancer deaths in women. According to the most recent data, mortality rates declined significantly during 1992-1996 with the largest decreases in younger women, both white and black. These decreases were probably the result of earlier detection and improved treatment.

Taking into account the medical circumstances and the patient's preferences, treatment of breast cancer may involve lumpectomy (local removal of the tumor) and removal of the lymph nodes under the arm; mastectomy (surgical removal of the breast) and removal of the lymph nodes under the arm; radiation therapy; chemotherapy; or hormone therapy. Often, two or more methods are used in combination. Numerous studies have shown that, for early stage disease, long-term survival rates after lumpectomy plus radiotherapy are similar to survival rates after modified radical mastectomy. Significant advances in reconstruction techniques provide several options for breast reconstruction after mastectomy. Recently, such reconstruction has been done at the same time as the mastectomy.

Local excision of ductal carcinoma in situ (DCIS) with adequate amounts of surrounding normal breast tissue may prevent the local recurrence of the DCIS. Radiation to the breast and/or tamoxifen may reduce the chance of DCIS occurring in the remaining breast tissue. This is important because DCIS, if left untreated, may develop into invasive breast cancer. Nevertheless, there are serious side effects or sequelae to these treatments. There is, therefore, a need for efficacious breast cancer treatments.

There were an estimated 23,100 new cases of ovarian cancer in the United States in 2000. It accounts for 4% of all cancers among women and ranks second among gynecologic cancers. During 1992-1996, ovarian cancer incidence rates were significantly declining. Consequent to ovarian cancer, there were an estimated 14,000 deaths in 2000. Ovarian cancer causes more deaths than any other cancer of the female reproductive system.

Surgery, radiation therapy, and chemotherapy are treatment options for ovarian cancer. Surgery usually includes the removal of one or both ovaries, the fallopian tubes (salpingo-oophorectomy), and the uterus (hysterectomy). In some very early tumors, only the involved ovary will be removed, especially in young women who wish to have children. In advanced disease, an attempt is made to remove all intra-abdominal disease to enhance the effect of chemotherapy. There continues to be an important need for effective treatment options for ovarian cancer.

There were an estimated 28,300 new cases of pancreatic cancer in the United States in 2000. Over the past 20 years, rates of pancreatic cancer have declined in men. Rates among women have remained approximately constant but may be beginning to decline. Pancreatic cancer caused an estimated 28,200 deaths in 2000 in the United States. Over the past 20 years, there has been a slight but significant decrease in mortality rates among men (about −0.9% per year) while rates have increased slightly among women.

Surgery, radiation therapy, and chemotherapy are treatment options for pancreatic cancer. These treatment options can extend survival and/or relieve symptoms in many patients but are not likely to produce a cure for most. There is a significant need for additional therapeutic and diagnostic options for pancreatic cancer.

SUMMARY OF THE INVENTION

The present invention relates to a gene, designated 151P3D4, that has now been found to be over-expressed in the cancer(s) listed in Table I. Northern blot expression analysis of 151P3D4 gene expression in normal tissues shows a restricted expression pattern in adult tissues. The nucleotide (FIG. 2) and amino acid (FIG. 2, and FIG. 3) sequences of 151P3D4 are provided. The tissue-related profile of 151P3D4 in normal adult tissues, combined with the over-expression observed in the tissues listed in Table I, shows that 151P3D4 is aberrantly over-expressed in at least some cancers, and thus serves as a useful diagnostic, prophylactic, prognostic, and/or therapeutic target for cancers of the tissue(s) such as those listed in Table I.

The invention provides polynucleotides corresponding or complementary to all or part of the 151P3D4 genes, mRNAs, and/or coding sequences, preferably in isolated form, including polynucleotides encoding 151P3D4-related proteins and fragments of 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more than 25 contiguous amino acids; at least 30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 85, 90, 95, 100 or more than 100 contiguous amino acids of a 151P3D4-related protein, as well as the peptides/proteins themselves; DNA, RNA, DNA/RNA hybrids, and related molecules, polynucleotides or oligonucleotides complementary or having at least a 90% homology to the 151P3D4 genes or mRNA sequences or parts thereof, and polynucleotides or oligonucleotides that hybridize to the 151P3D4 genes, mRNAs, or to 151P3D4-encoding polynucleotides. Also provided are means for isolating cDNAs and the genes encoding 151P3D4. Recombinant DNA molecules containing 151P3D4 polynucleotides, cells transformed or transduced with such molecules, and host-vector systems for the expression of 151P3D4 gene products are also provided. The invention further provides antibodies that bind to 151P3D4 proteins and polypeptide fragments thereof, including polyclonal and monoclonal antibodies, murine and other mammalian antibodies, chimeric antibodies, humanized and fully human antibodies, and antibodies labeled with a detectable marker or therapeutic agent. In certain embodiments there is a proviso that the entire nucleic acid sequence of FIG. 2 is not encoded and/or the entire amino acid sequence of FIG. 2 is not prepared. In certain embodiments, the entire nucleic acid sequence of FIG. 2 is encoded and/or the entire amino acid sequence of FIG. 2 is prepared, either of which are in respective human unit dose forms.

The invention further provides methods for detecting the presence and status of 151P3D4 polynucleotides and proteins in various biological samples, as well as methods for identifying cells that express 151P3D4. A typical embodiment of this invention provides methods for monitoring 151P3D4 gene products in a tissue or hematology sample having or suspected of having some form of growth dysregulation such as cancer.

The invention further provides various immunogenic or therapeutic compositions and strategies for treating cancers that express 151P3D4 such as cancers of tissues listed in Table I, including therapies aimed at inhibiting the transcription, translation, processing or function of 151P3D4 as well as cancer vaccines. In one aspect, the invention provides compositions, and methods comprising them, for treating a cancer that expresses 151P3D4 in a human subject wherein the composition comprises a carrier suitable for human use and a human unit dose of one or more than one agent that inhibits the production or function of 151P3D4. Preferably, the carrier is a uniquely human carrier. In another aspect of the invention, the agent is a moiety that is immunoreactive with 151P3D4 protein. Non-limiting examples of such moieties include, but are not limited to, antibodies (such as single chain, monoclonal, polyclonal, humanized, chimeric, or human antibodies), functional equivalents thereof (whether naturally occurring or synthetic), and combinations thereof. The antibodies can be conjugated to a diagnostic or therapeutic moiety. In another aspect, the agent is a small molecule as defined herein.

In another aspect, the agent comprises one or more than one peptide which comprises a cytotoxic T lymphocyte (CTL) epitope that binds an HLA class I molecule in a human to elicit a CTL response to 151P3D4 and/or one or more than one peptide which comprises a helper T lymphocyte (HTL) epitope which binds an HLA class II molecule in a human to elicit an HTL response. The peptides of the invention may be on the same or on one or more separate polypeptide molecules. In a further aspect of the invention, the agent comprises one or more than one nucleic acid molecule that expresses one or more than one of the CTL or HTL response stimulating peptides as described above. In yet another aspect of the invention, the one or more than one nucleic acid molecule may express a moiety that is immunologically reactive with 151P3D4 as described above. The one or more than one nucleic acid molecule may also be, or encodes, a molecule that inhibits production of 151P3D4. Non-limiting examples of such molecules include, but are not limited to, those complementary to a nucleotide sequence essential for production of 151P3D4 (e.g. antisense sequences or molecules that form a triple helix with a nucleotide double helix essential for 151P3D4 production) or a ribozyme effective to lyse 151P3D4 mRNA.

Another embodiment of the invention is antibody epitopes which comprise a peptide regions, or an oligonucleotide encoding the peptide region, that has one two, three, four, or five of the following characteristics:

i) a peptide region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Hydrophilicity profile of FIG. 5;

ii) a peptide region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or less than 0.5, 0.4, 0.3, 0.2, 0.1, or having a value equal to 0.0, in the Hydropathicity profile of FIG. 6;

iii) a peptide region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Percent Accessible Residues profile of FIG. 7;

iv) a peptide region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Average Flexibility profile of FIG. 8; or

v) a peptide region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Beta-turn profile of FIG. 9.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. The 151P3D4 SSH sequence of 417 nucleotides.

FIG. 2. The cDNA and amino acid sequence of 151P3D4 v.1 clone 1-placenta (also called “151P3D4 v.1” or “151P3D4 variant 1”) is shown in FIG. 2A. The start methionine is underlined. The open reading frame extends from nucleic acid 316-1380 including the stop codon. The cDNA and amino acid sequence of 151P3D4 variant 2 (also called “151P3D4 v.2”) is shown in FIG. 2B. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 1-2166 including the stop codon. The cDNA and amino acid sequence of 151P3D4 variant 3 (also called “151P3D4 v.3”) is shown in FIG. 2C. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 316-1380 including the stop codon. The cDNA and amino acid sequence of 151P3D4 variant 4 (also called “151P3D4 v.4”) is shown in FIG. 2D. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 316-1380 including the stop codon. The cDNA and amino acid sequence of 151P3D4 variant 5 (also called “151P3D4 v.5”) is shown in FIG. 2E. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 316-1380 including the stop codon. The cDNA and amino acid sequence of 151P3D4 variant 6 (also called “151P3D4 v.6”) is shown in FIG. 2F. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 316-1380 including the stop codon. The cDNA and amino acid sequence of 151P3D4 variant 7 (also called “151P3D4 v.7”) is shown in FIG. 2G. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 316-1380 including the stop codon. The cDNA and amino acid sequence of 151P3D4 variant 8 (also called “151P3D4 v.8”) is shown in FIG. 2H. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 316-1380 including the stop codon. The cDNA and amino acid sequence of 151P3D4 variant 9 (also called “151P3D4 v.9”) is shown in FIG. 2I. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 316-1380 including the stop codon. The cDNA and amino acid sequence of 151P3D4 variant 10 (also called “151P3D4 v.10”) is shown in FIG. 2J. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 316-1380 including the stop codon. The cDNA and amino acid sequence of 151P3D4 variant 11 (also called “151P3D4 v.11”) is shown in FIG. 2K. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 316-1380 including the stop codon. As used herein, a reference to 151P3D4 includes all variants thereof, including those shown in FIGS. 10 and 12.

FIG. 3. Amino acid sequence of 151P3D4 v.1 is shown in FIG. 3A; it has 354 amino acids. The amino acid sequence of 151P3D4 v.2 is shown in FIG. 3B; it has 721 amino acids. As used herein, a reference to 151P3D4 includes all variants thereof, including those shown in FIGS. 11 and 12.

FIG. 4. The nucleic acid sequence alignment of 151P3D4 v.1 with the mRNA for human cartilage link protein is shown in FIG. 4A. The amino acid sequence alignments of 151P3D4 v.1 with human cartilage link protein (consensus sequence=SEQ ID NO:68) (4B), mouse cartilage link protein (consensus sequences=SEQ ID NOS:69-78) (4C), 151P3D4 v.2 (consensus sequence=SEQ ID NO:79) (4D), hypothetical protein XP_—094318 (consensus sequence=SEQ ID NO:80) (4E), bovine cartilage link protein (consensus sequences=SEQ ID NOS:81-94) (4F), and rat cartilage link protein (consensus sequences=SEQ ID NOS:95-105) (4G) are shown in FIGS. 4B-4G. The amino acid sequence alignments of 151P3D4 v.2 with human cartilage link protein is shown in FIG. 4H (consensus sequence=SEQ ID NO:106). The clustal alignment of 151P3D4 v.1 and 151P3D4 v.2 is shown in FIG. 41.

FIG. 5. Hydrophilicity amino acid profile of A) 151P3D4 v.1 and B) 151P3D4 v.2, determined by computer algorithm sequence analysis using the method of Hopp and Woods (Hopp T. P., Woods K. R., 1981. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828) accessed on the Protscale Internet website (expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server.

FIG. 6. Hydropathicity amino acid profile of A) 151P3D4 v.1 and B) 151P3D4 v.2, determined by computer algorithm sequence analysis using the method of Kyte and Doolittle (Kyte J., Doolittle R. F., 1982. J. Mol. Biol. 157:105-132) accessed on the ProtScale Internet website (expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server.

FIG. 7. Percent accessible residues amino acid profile of A) 151P3D4 v.1 and B) 151P3D4 v.2, determined by computer algorithm sequence analysis using the method of Janin (Janin J., 1979 Nature 277:491-492) accessed on the ProtScale Internet website (expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server.

FIG. 8. Average flexibility amino acid profile of A) 151P3D4 v.1 and B) 151P3D4 v.2, determined by computer algorithm sequence analysis using the method of Bhaskaran and Ponnuswamy (Bhaskaran R., and Ponnuswamy P. K., 1988. Int. J. Pept. Protein Res. 32:242-255) accessed on the ProtScale Internet website (expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server.

FIG. 9. Beta-turn amino acid profile of A) 151P3D4 v.1 and B) 151P3D4 v.2, determined by computer algorithm sequence analysis using the method of Deleage and Roux (Deleage, G., Roux B. 1987 Protein Engineering 1:289-294) accessed on the ProtScale Internet website (expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server.

FIG. 10. Schematic display of nucleotide variants of 151P3D4. Schematic alignment of Single Nucleotide Polymorphism (SNP) variants of 151P3D4. Variants 151P3D4 v.3 through v.11 are variants with single nucleotide differences. Though these SNP variants are shown separately, they could also occur in any combinations and in any one of the transcript variants that contains the base pairs. Numbers correspond to those of 151P3D4 v.1. The black boxes show the same sequence as 151P3D4 v.1. SNPs are indicated above the boxes.

FIG. 11. Schematic alignment of protein variants of 151P3D4. Nucleotide variants 151P3D4 v.2 through v.9 in FIG. 10 code for the same protein as 151P3D4 v.1. Variants 151P3D4 v.2 codes for a protein that shares 321 aa with 151P3D4 v.1. Boxes with the same fill pattern represent the same sequence. Numbers in “( )” underneath the boxes correspond to 151P3D4 v.1.

FIG. 12. Schematic alignment of transcript variants of 151P3D4. Variant 151P3D4 v.2 is an alternative transcript, which shares the last three exons with 151P3D4 v.1. The first two exons of 151P3D4 v.1 are located in the sixth intron (between exons 6 and 7) of 151P3D4 v.2. Numbers in “( )” underneath the boxes correspond to those of 151P3D4 v.2. Boxes with the same fill pattern represent the same sequence.

FIG. 13. Secondary structure prediction for 151P3D4 protein variants. The secondary structure of 151P3D4 protein variants 1 and 2 (FIGS. A (SEQ ID NO. 66) and B (SEQ ID NO. 67), respectively) were predicted using the HNN—Hierarchical Neural Network method (Guermeur, 1997, located on the World Wide Web at: pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_nn.html), accessed from the ExPasy molecular biology server from Internet website (expasy.ch/tools/). This method predicts the presence and location of alpha helices, extended strands, and random coils from the primary protein sequence. The percent of the protein in a given secondary structure is also listed.

FIG. 14. Expression of 151P3D4 by RT-PCR. First strand cDNA was prepared from vital pool 1 (liver, lung and kidney), vital pool 2 (pancreas, colon and stomach), bladder cancer pool, kidney cancer pool, colon cancer pool, lung cancer pool, ovary cancer pool, breast cancer pool, and cancer metastasis pool. Normalization was performed by PCR using primers to actin and GAPDH. Semi-quantitative PCR, using primers to 151P3D4, was performed at 26 and 30 cycles of amplification. Results show strong expression of 151P3D4 in ovary cancer pool. Expression of 151P3D4 was also detected in bladder cancer pool, kidney cancer pool, colon cancer pool, lung cancer pool, breast cancer pool, cancer metastasis pool, vital pool 2, but not in vital pool 1.

FIG. 15. Expression of 151P3D4 in normal tissues. Two multiple tissue northern blots (Clontech) both with 2 μg of mRNA/lane were probed with the 151P3D4 sequence. Size standards in kilobases (kb) are indicated on the side. Results show expression of 151P3D4 in small intestine and placenta. Lower level expression was also detected in heart and colon, but not in the other normal tissues tested.

FIG. 16. Expression of 151P3D4 in bladder cancer patient tissues. RNA was extracted from normal bladder (NB), bladder cancer cell lines (CL: UM-UC-3, J82, SCaBER), bladder cancer patient tumors (T) and normal adjacent tissue (NAT). Northern blots with 10 μg of total RNA were probed with the 151P3D4 SSH sequence. Size standards in kilobases are indicated on the side. Results show expression of 151P3D4 in patient bladder cancer tissues, and in UM-UC-3 bladder cancer cell lines, but not in normal bladder nor in the other bladder cancer cell lines tested.

FIG. 17. Expression of 151P3D4 in kidney cancer patient tissues. RNA was extracted from kidney cancer cell lines (CL: 769-P, A498, SW839), normal kidney (NK), kidney cancer patient tumors (T) and their normal adjacent tissues (NAT). Northern blots with 10 μg of total RNA were probed with the 151P3D4 SSH sequence. Size standards in kilobases are on the side. Results show expression of 151P3D4 in patient kidney tumor tissues, but not in normal kidney, nor in the cell lines tested.

FIG. 18. Expression of 151P3D4 in ovary cancer patient tissues. RNA was extracted from ovary and cervical cancer cell lines (CL), normal ovary (N), and ovary cancer patient tumor (T). Northern blots with 10 μg of total RNA were probed with the 151P3D4 SSH sequence. Size standards in kilobases are on the side. Results show strong expression of 151P3D4 in patient ovary cancer tissues, but not in normal ovary nor in the ovary and cervical cancer cell lines.

FIG. 19. Expression of 151P3D4 in stomach and uterus human cancer specimens. Expression of 151P3D4 was assayed in a panel of human stomach and uterus cancers (T) and their respective matched normal tissues (N) on RNA dot blots. 151P3D4 expression was seen in both stomach and uterus cancers.

FIG. 20. 151P3D4 expression in 293T cells following transfection. 293T cells were transfected with either 151P3D4 .pcDNA3.1/mychis or pcDNA3.1/mychis vector control. Forty hours later, cell lysates were collected. Samples were run on an SDS-PAGE acrylamide gel, blotted and stained with anti-his antibody. The blot was developed using the ECL chemiluminescence kit and visualized by autoradiography. Results show expression of 151P3D4 from the 151P3D4 .pcDNA3.1/mychis mammalian expression construct in the lysates of 151P3D4 .pcDNA3.1/mychis transfected cells, but not from the control pcDNA3.1/mychis vector.

DETAILED DESCRIPTION OF THE INVENTION

Definitions

Unless otherwise defined, all terms of art, notations and other scientific terms or terminology used herein are intended to have the meanings commonly understood by those of skill in the art to which this invention pertains. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what is generally understood in the art. Many of the techniques and procedures described or referenced herein are well understood and commonly employed using conventional methodology by those skilled in the art, such as, for example, the widely utilized molecular cloning methodologies described in Sambrook et al., Molecular Cloning: A Laboratory Manual 2nd. edition (1989) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. As appropriate, procedures involving the use of commercially available kits and reagents are generally carried out in accordance with manufacturer defined protocols and/or parameters unless otherwise noted.

The terms “advanced prostate cancer”, “locally advanced prostate cancer”, “advanced disease” and “locally advanced disease” mean prostate cancers that have extended through the prostate capsule, and are meant to include stage C disease under the American Urological Association (AUA) system, stage C₁-C₂ disease under the Whitmore-Jewett system, and stage T3-T4 and N+ disease under the TNM (tumor, node, metastasis) system. In general, surgery is not recommended for patients with locally advanced disease, and these patients have substantially less favorable outcomes compared to patients having clinically localized (organ-confined) prostate cancer. Locally advanced disease is clinically identified by palpable evidence of induration beyond the lateral border of the prostate, or asymmetry or induration above the prostate base. Locally advanced prostate cancer is presently diagnosed pathologically following radical prostatectomy if the tumor invades or penetrates the prostatic capsule, extends into the surgical margin, or invades the seminal vesicles.

“Altering the native glycosylation pattern” is intended for purposes herein to mean deleting one or more carbohydrate moieties found in native sequence 151P3D4 (either by removing the underlying glycosylation site or by deleting the glycosylation by chemical and/or enzymatic means), and/or adding one or more glycosylation sites that are not present in the native sequence 151P3D4. In addition, the phrase includes qualitative changes in the glycosylation of the native proteins, involving a change in the nature and proportions of the various carbohydrate moieties present.

The term “analog” refers to a molecule which is structurally similar or shares similar or corresponding attributes with another molecule (e.g. a 151P3D4-related protein). For example an analog of a 151P3D4 protein can be specifically bound by an antibody or T cell that specifically binds to 151P3D4.

The term “antibody” is used in the broadest sense. Therefore an “antibody” can be naturally occurring or man-made such as monoclonal antibodies produced by conventional hybridoma technology. Anti-151P3D4 antibodies comprise monoclonal and polyclonal antibodies as well as fragments containing the antigen-binding domain and/or one or more complementarity determining regions of these antibodies.

An “antibody fragment” is defined as at least a portion of the variable region of the immunoglobulin molecule that binds to its target, i.e., the antigen-binding region. In one embodiment it specifically covers single anti-151P3D4 antibodies and clones thereof (including agonist, antagonist and neutralizing antibodies) and anti-151P3D4 antibody compositions with polyepitopic specificity.

The term “codon optimized sequences” refers to nucleotide sequences that have been optimized for a particular host species by replacing any codons having a usage frequency of less than about 20%. Nucleotide sequences that have been optimized for expression in a given host species by elimination of spurious polyadenylation sequences, elimination of exon/intron splicing signals, elimination of transposon-like repeats and/or optimization of GC content in addition to codon optimization are referred to herein as an “expression enhanced sequences.”

The term “cytotoxic agent” refers to a substance that inhibits or prevents the expression activity of cells, function of cells and/or causes destruction of cells. The term is intended to include radioactive isotopes chemotherapeutic agents, and toxins such as small molecule toxins or enzymatically active toxins of bacterial, fungal, plant or animal origin, including fragments and/or variants thereof. Examples of cytotoxic agents include, but are not limited to maytansinoids, yttrium, bismuth, ricin, ricin A-chain, doxorubicin, daunorubicin, taxol, ethidium bromide, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicine, dihydroxy anthracin dione, actinomycin, diphtheria toxin, Pseudomonas exotoxin (PE) A, PE40, abrin, abrin A chain, modeccin A chain, alpha-sarcin, gelonin, mitogellin, retstrictocin, phenomycin, enomycin, curicin, crotin, calicheamicin, sapaonaria officinalis inhibitor, and glucocorticoid and other chemotherapeutic agents, as well as radioisotopes such as At²¹¹, I¹³¹, I¹²⁵, Y⁹⁰, Re¹⁸⁶, Re¹⁸⁸, Sm¹⁵³, Bi²¹², P³² and radioactive isotopes of Lu. Antibodies may also be conjugated to an anti-cancer pro-drug activating enzyme capable of converting the pro-drug to its active form.

The term “homolog” refers to a molecule which exhibits homology to another molecule, by for example, having sequences of chemical residues that are the same or similar at corresponding positions.

“Human Leukocyte Antigen” or “HLA” is a human class I or class II Major Histocompatibility Complex (MHC) protein (see, e.g., Stites, et al., IMMUNOLOGY, 8^TH ED., Lange Publishing, Los Altos, Calif. (1994).

The terms “hybridize”, “hybridizing”, “hybridizes” and the like, used in the context of polynucleotides, are meant to refer to conventional hybridization conditions, preferably such as hybridization in 50% formamide/6×SSC/0.1% SDS/100 μg/ml ssDNA, in which temperatures for hybridization are above 37° C. and temperatures for washing in 0.1×SSC/0.1% SDS are above 55° C.

The phrases “isolated” or “biologically pure” refer to material which is substantially or essentially free from components which normally accompany the material as it is found in its native state. Thus, isolated peptides in accordance with the invention preferably do not contain materials normally associated with the peptides in their in situ environment. For example, a polynucleotide is said to be “isolated” when it is substantially separated from contaminant polynucleotides that correspond or are complementary to genes other than the 151P3D4 genes or that encode polypeptides other than 151P3D4 gene product or fragments thereof. A skilled artisan can readily employ nucleic acid isolation procedures to obtain an isolated 151P3D4 polynucleotide. A protein is said to be “isolated,” for example, when physical, mechanical or chemical methods are employed to remove the 151P3D4 proteins from cellular constituents that are normally associated with the protein. A skilled artisan can readily employ standard purification methods to obtain an isolated 151P3D4 protein. Alternatively, an isolated protein can be prepared by chemical means.

The term “mammal” refers to any organism classified as a mammal, including mice, rats, rabbits, dogs, cats, cows, horses and humans. In one embodiment of the invention, the mammal is a mouse. In another embodiment of the invention, the mammal is a human.

The terms “metastatic prostate cancer” and “metastatic disease” mean prostate cancers that have spread to regional lymph nodes or to distant sites, and are meant to include stage D disease under the AUA system and stage T×N×M+ under the TNM system. As is the case with locally advanced prostate cancer, surgery is generally not indicated for patients with metastatic disease, and hormonal (androgen ablation) therapy is a preferred treatment modality. Patients with metastatic prostate cancer eventually develop an androgen-refractory state within 12 to 18 months of treatment initiation. Approximately half of these androgen-refractory patients die within 6 months after developing that status. The most common site for prostate cancer metastasis is bone. Prostate cancer bone metastases are often osteoblastic rather than osteolytic (i.e., resulting in net bone formation). Bone metastases are found most frequently in the spine, followed by the femur, pelvis, rib cage, skull and humerus. Other common sites for metastasis include lymph nodes, lung, liver and brain. Metastatic prostate cancer is typically diagnosed by open or laparoscopic pelvic lymphadenectomy, whole body radionuclide scans, skeletal radiography, and/or bone lesion biopsy.

The term “monoclonal antibody” refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the antibodies comprising the population are identical except for possible naturally occurring mutations that are present in minor amounts.

A “motif”, as in biological motif of a 151P3D4-related protein, refers to any pattern of amino acids forming part of the primary sequence of a protein, that is associated with a particular function (e.g. protein-protein interaction, protein-DNA interaction, etc) or modification (e.g. that is phosphorylated, glycosylated or amidated), or localization (e.g. secretory sequence, nuclear localization sequence, etc.) or a sequence that is correlated with being immunogenic, either humorally or cellularly. A motif can be either contiguous or capable of being aligned to certain positions that are generally correlated with a certain function or property. In the context of HLA motifs, “motif” refers to the pattern of residues in a peptide of defined length, usually a peptide of from about 8 to about 13 amino acids for a class I HLA motif and from about 6 to about 25 amino acids for a class II HLA motif, which is recognized by a particular HLA molecule. Peptide motifs for HLA binding are typically different for each protein encoded by each human HLA allele and differ in the pattern of the primary and secondary anchor residues.

A “pharmaceutical excipient” comprises a material such as an adjuvant, a carrier, pH-adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservative, and the like.

“Pharmaceutically acceptable” refers to a non-toxic, inert, and/or composition that is physiologically compatible with humans or other mammals.

The term “polynucleotide” means a polymeric form of nucleotides of at least 10 bases or base pairs in length, either ribonucleotides or deoxynucleotides or a modified form of either type of nucleotide, and is meant to include single and double stranded forms of DNA and/or RNA. In the art, this term if often used interchangeably with “oligonucleotide”. A polynucleotide can comprise a nucleotide sequence disclosed herein wherein thymidine (T), as shown for example in FIG. 2, can also be uracil (U); this definition pertains to the differences between the chemical structures of DNA and RNA, in particular the observation that one of the four major bases in RNA is uracil (U) instead of thymidine (T).

The term “polypeptide” means a polymer of at least about 4, 5, 6, 7, or 8 amino acids. Throughout the specification, standard three letter or single letter designations for amino acids are used. In the art, this term is often used interchangeably with “peptide” or “protein”.

An HLA “primary anchor residue” is an amino acid at a specific position along a peptide sequence which is understood to provide a contact point between the immunogenic peptide and the HLA molecule. One to three, usually two, primary anchor residues within a peptide of defined length generally defines a “motif” for an immunogenic peptide. These residues are understood to fit in close contact with peptide binding groove of an HLA molecule, with their side chains buried in specific pockets of the binding groove. In one embodiment, for example, the primary anchor residues for an HLA class 1 molecule are located at position 2 (from the amino terminal position) and at the carboxyl terminal position of a 8, 9, 10, 11, or 12 residue peptide epitope in accordance with the invention. In another embodiment, for example, the primary anchor residues of a peptide that will bind an HLA class II molecule are spaced relative to each other, rather than to the termini of a peptide, where the peptide is generally of at least 9 amino acids in length. The primary anchor positions for each motif and supermotif are set forth in Table IV. For example, analog peptides can be created by altering the presence or absence of particular residues in the primary and/or secondary anchor positions shown in Table IV. Such analogs are used to modulate the binding affinity and/or population coverage of a peptide comprising a particular HLA motif or supermotif.

A “recombinant” DNA or RNA molecule is a DNA or RNA molecule that has been subjected to molecular manipulation in vitro.

Non-limiting examples of small molecules include compounds that bind or interact with 151P3D4, ligands including hormones, neuropeptides, chemokines, odorants, phospholipids, and functional equivalents thereof that bind and preferably inhibit 151P3D4 protein function. Such non-limiting small molecules preferably have a molecular weight of less than about 10 kDa, more preferably below about 9, about 8, about 7, about 6, about 5 or about 4 kDa. In certain embodiments, small molecules physically associate with, or bind, 151P3D4 protein; are not found in naturally occurring metabolic pathways; and/or are more soluble in aqueous than non-aqueous solutions

“Stringency” of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends on the ability of denatured nucleic acid sequences to reanneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature that can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see Ausubel et al., Current Protocols in Molecular Biology, Wiley Interscience Publishers, (1995).

“Stringent conditions” or “high stringency conditions”, as defined herein, are identified by, but not limited to, those that: (1) employ low ionic strength and high temperature for washing, for example 0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 50° C.; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42° C.; or (3) employ 50% formamide, 5×SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5×Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 42° C. in 0.2×SSC (sodium chloride/sodium. citrate) and 50% formamide at 55° C., followed by a high-stringency wash consisting of 0.1×SSC containing EDTA at 55° C. “Moderately stringent conditions” are described by, but not limited to, those in Sambrook et al., Molecular Cloning: A Laboratory Manual, New York: Cold Spring Harbor Press, 1989, and include the use of washing solution and hybridization conditions (e.g., temperature, ionic strength and % SDS) less stringent than those described above. An example of moderately stringent conditions is overnight incubation at 37° C. in a solution comprising: 20% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 mg/mL denatured sheared salmon sperm DNA, followed by washing the filters in 1×SSC at about 37-50° C. The skilled artisan will recognize how to adjust the temperature, ionic strength, etc. as necessary to accommodate factors such as probe length and the like.

An HLA “supermotif” is a peptide binding specificity shared by HLA molecules encoded by two or more HLA alleles.

As used herein “to treat” or “therapeutic” and grammatically related terms, refer to any improvement of any consequence of disease, such as prolonged survival, less morbidity, and/or a lessening of side effects which are the byproducts of an alternative therapeutic modality; full eradication of disease is not required.

A “transgenic animal” (e.g., a mouse or rat) is an animal having cells that contain a transgene, which transgene was introduced into the animal or an ancestor of the animal at a prenatal, e.g., an embryonic stage. A “transgene” is a DNA that is integrated into the genome of a cell from which a transgenic animal develops.

As used herein, an HLA or cellular immune response “vaccine” is a composition that contains or encodes one or more peptides of the invention. There are numerous embodiments of such vaccines, such as a cocktail of one or more individual peptides; one or more peptides of the invention comprised by a polyepitopic peptide; or nucleic acids that encode such individual peptides or polypeptides, e.g., a minigene that encodes a polyepitopic peptide. The “one or more peptides” can include any whole unit integer from 1-150 or more, e.g., at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, or 150 or more peptides of the invention. The peptides or polypeptides can optionally be modified, such as by lipidation, addition of targeting or other sequences. HLA class I peptides of the invention can be admixed with, or linked to, HLA class II peptides, to facilitate activation of both cytotoxic T lymphocytes and helper T lymphocytes. HLA vaccines can also comprise peptide-pulsed antigen presenting cells, e.g., dendritic cells.

The term “variant” refers to a molecule that exhibits a variation from a described type or norm, such as a protein that has one or more different amino acid residues in the corresponding position(s) of a specifically described protein (e.g. the 151P3D4 protein shown in FIG. 2 or FIG. 3. An analog is an example of a variant protein. Splice isoforms and single nucleotides polymorphisms (SNPs) are further examples of variants.

The “151P3D4-related proteins” of the invention include those specifically identified herein, as well as allelic variants, conservative substitution variants, analogs and homologs that can be isolated/generated and characterized without undue experimentation following the methods outlined herein or readily available in the art. Fusion proteins that combine parts of different 151P3D4 proteins or fragments thereof, as well as fusion proteins of a 151P3D4 protein and a heterologous polypeptide are also included. Such 151P3D4 proteins are collectively referred to as the 151P3D4-related proteins, the proteins of the invention, or 151P3D4. The term “151P3D4-related protein” refers to a polypeptide fragment or a 151P3D4 protein sequence of 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more than 25 amino acids; or, at least 30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 225, 250, 275, 300, 325, 350, or 354 or more amino acids.

151P3D4 Polynucleotides

One aspect of the invention provides polynucleotides corresponding or complementary to all or part of a 151P3D4 gene, mRNA, and/or coding sequence, preferably in isolated form, including polynucleotides encoding a 151P3D4-related protein and fragments thereof, DNA, RNA, DNA/RNA hybrid, and related molecules, polynucleotides or oligonucleotides complementary to a 151P3D4 gene or mRNA sequence or a part thereof, and polynucleotides or oligonucleotides that hybridize to a 151P3D4 gene, mRNA, or to a 151P3D4 encoding polynucleotide (collectively, “151P3D4 polynucleotides”). In all instances when referred to in this section, T can also be U in FIG. 2.

Embodiments of a 151P3D4 polynucleotide include: a 151P3D4 polynucleotide having the sequence shown in FIG. 2, the nucleotide sequence of 151P3D4 as shown in FIG. 2 wherein T is U; at least 10 contiguous nucleotides of a polynucleotide having the sequence as shown in FIG. 2; or, at least 10 contiguous nucleotides of a polynucleotide having the sequence as shown in FIG. 2 where T is U. For example, embodiments of 151P3D4 nucleotides comprise, without limitation:

(I) a polynucleotide comprising, consisting essentially of, or consisting of a sequence as shown in FIG. 2, wherein T can also be U;

(II) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2A, from nucleotide residue number 316 through nucleotide residue number 1380, including the stop codon, wherein T can also be U;

(III) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2B, from nucleotide residue number 1 through nucleotide residue number 2166, including the stop codon, wherein T can also be U;

(IV) a polynucleotide comprising, consisting essentially of, or consisting of the sequences as shown in FIGS. 2C-2K, from nucleotide residue number 316 through nucleotide residue number 1380, including the a stop codon, wherein T can also be U;

(V) a polynucleotide that encodes a 151P3D4-related protein that is at least 90% homologous to an entire amino acid sequence shown in FIG. 2A-K;

(VI) a polynucleotide that encodes a 151P3D4-related protein that is at least 90% identical to an entire amino acid sequence shown in FIG. 2A-K;

(VII) a polynucleotide that encodes at least one peptide set forth in Tables V-XVIII and XXII-LI;

(VIII) a polynucleotide that encodes a peptide region of at least 5 amino acids of a peptide of FIG. 3A in any whole number increment up to 354 that includes an amino acid position having a value greater than 0.5 in the Hydrophilicity profile of FIG. 5A; or of FIG. 3B in any whole number increment up to 721 that includes an amino acid position having a value greater than 0.5 in the Hydrophilicity profile of FIG. 5B;

(XIX) a polynucleotide that encodes a peptide region of at least 5 amino acids of a peptide of FIG. 3A in any whole number increment up to 354 that includes an amino acid position having a value less than 0.5 in the Hydropathicity profile of FIG. 6A; or of FIG. 3B in any whole number increment up to 721 that includes an amino acid position having a value less than 0.5 in the Hydropathicity profile of FIG. 6B;

(X) a polynucleotide that encodes a peptide region of at least 5 amino acids of a peptide of FIG. 3A in any whole number increment up to 354 that includes an amino acid position having a value greater than 0.5 in the Percent Accessible Residues profile of FIG. 7A; or of FIG. 3B in any whole number increment up to 721 that includes an amino acid position having a value greater than 0.5 in the Percent Accessible Residues profile of FIG. 7B;

(XII) a polynucleotide that encodes a peptide region of at least 5 amino acids of a peptide of FIG. 3A in any whole number increment up to 354 that includes an amino acid position having a value greater than 0.5 in the Average Flexibility profile of FIG. 8A; or of FIG. 3B in any whole number increment up to 721 that includes an amino acid position having a value greater than 0.5 in the Average Flexibility profile of FIG. 8B;

(XIII) a polynucleotide that encodes a peptide region of at least 5 amino acids of a peptide of FIG. 3A in any whole number increment up to 354 that includes an amino acid position having a value greater than 0.5 in the Beta-turn profile of FIG. 9A; or of FIG. 3B in any whole number increment up to 721 that includes an amino acid position having a value greater than 0.5 in the Beta-turn profile of FIG. 9B;

(XIV) a polynucleotide that is fully complementary to a polynucleotide of any one of (I)-(XIII).

(XV) a peptide that is encoded by any of (I)-(XIV); and

(XVI) a polynucleotide of any of (I)-(XIV) or peptide of (XV) together with a pharmaceutical excipient and/or in a human unit dose form.

As used herein, a range is understood to specifically disclose all whole unit positions thereof.

Typical embodiments of the invention disclosed herein include 151P3D4 polynucleotides that encode specific portions of 151P3D4 mRNA sequences (and those which are complementary to such sequences) such as those that encode the proteins and/or fragments thereof, for example:

(a) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 225, 250, 275, 300, 325, 350, or 354 or more contiguous amino acids of 151P3D4.

(b) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700, or 721 or more contiguous amino acids of 151P3D4 variant 2.

For example, representative embodiments of the invention disclosed herein include: polynucleotides and their encoded peptides themselves encoding about amino acid 1 to about amino acid 10 of the 151P3D4 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 10 to about amino acid 20 of the 151P3D4 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 20 to about amino acid 30 of the 151P3D4 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 30 to about amino acid 40 of the 151P3D4 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 40 to about amino acid 50 of the 151P3D4 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 50 to about amino acid 60 of the 151P3D4 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 60 to about amino acid 70 of the 151P3D4 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 70 to about amino acid 80 of the 151P3D4 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 80 to about amino acid 90 of the 151P3D4 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 90 to about amino acid 100 of the 151P3D4 protein shown in FIG. 2 or FIG. 3, in increments of about 10 amino acids, ending at the carboxyl terminal amino acid set forth in FIG. 2 or FIG. 3. Accordingly polynucleotides encoding portions of the amino acid sequence (of about 10 amino acids), of amino acids 100 through the carboxyl terminal amino acid of the 151P3D4 protein are embodiments of the invention. Wherein it is understood that each particular amino acid position discloses that position plus or minus five amino acid residues.

Polynucleotides encoding relatively long portions of a 151P3D4 protein are also within the scope of the invention. For example, polynucleotides encoding from about amino acid 1 (or 20 or 30 or 40 etc.) to about amino acid 20, (or 30, or 40 or 50 etc.) of the 151P3D4 protein “or variant” shown in FIG. 2 or FIG. 3 can be generated by a variety of techniques well known in the art. These polynucleotide fragments can include any portion of the 151P3D4 sequence as shown in FIG. 2.

One embodiment of the invention comprises an HLA peptide, that occurs at least twice in Tables V-XVIII and XXII to LI collectively, or an oligonucleotide that encodes the HLA peptide. Another embodiment of the invention comprises an HLA peptide that occurs at least once in Tables V-XVIII and at least once in tables XXII to LI, or an oligonucleotide that encodes the HLA peptide. In another embodiment of the invention, typical polynucleotide fragments can encode one or more of the 151P3D4 protein or variant N-glycosylation sites, cAMP and cGMP-dependent protein kinase phosphorylation sites, casein kinase II phosphorylation sites or N-myristoylation site and amidation sites.

Uses of 151P3D4 Polynucleotides

Monitoring of Genetic Abnormalities

The polynucleotides of the preceding paragraphs have a number of different specific uses. The human 151P3D4 gene maps to the chromosomal location set forth in the Example entitled “Chromosomal Mapping of 151P3D4.” For example, because the 151P3D4 gene maps to this chromosome, polynucleotides that encode different regions of the 151P3D4 proteins are used to characterize cytogenetic abnormalities of this chromosomal locale, such as abnormalities that are identified as being associated with various cancers. In certain genes, a variety of chromosomal abnormalities including rearrangements have been identified as frequent cytogenetic abnormalities in a number of different cancers (see e.g. Krajinovic et al., Mutat. Res. 382(3-4): 81-83 (1998); Johansson et al., Blood 86(10): 3905-3914 (1995) and Finger et al., P.N.A.S. 85(23): 9158-9162 (1988)). Thus, polynucleotides encoding specific regions of the 151P3D4 proteins provide new tools that can be used to delineate, with greater precision than previously possible, cytogenetic abnormalities in the chromosomal region that encodes 151P3D4 that may contribute to the malignant phenotype. In this context, these polynucleotides satisfy a need in the art for expanding the sensitivity of chromosomal screening in order to identify more subtle and less common chromosomal abnormalities (see e.g. Evans et al., Am. J. Obstet. Gynecol 171(4): 1055-1057 (1994)).

Furthermore, as 151P3D4 was shown to be highly expressed in bladder and other cancers, 151P3D4 polynucleotides are used in methods assessing the status of 151P3D4 gene products in normal versus cancerous tissues. Typically, polynucleotides that encode specific regions of the 151P3D4 proteins are used to assess the presence of perturbations (such as deletions, insertions, point mutations, or alterations resulting in a loss of an antigen etc.) in specific regions of the 151P3D4 gene, such as regions containing one or more motifs. Exemplary assays include both RT-PCR assays as well as single-strand conformation polymorphism (SSCP) analysis (see, e.g., Marrogi et al., J. Cutan. Pathol. 26(8): 369-378 (1999), both of which utilize polynucleotides encoding specific regions of a protein to examine these regions within the protein.

Antisense Embodiments

Other specifically contemplated nucleic acid related embodiments of the invention disclosed herein are genomic DNA, cDNAs, ribozymes, and antisense molecules, as well as nucleic acid molecules based on an alternative backbone, or including alternative bases, whether derived from natural sources or synthesized, and include molecules capable of inhibiting the RNA or protein expression of 151P3D4. For example, antisense molecules can be RNAs or other molecules, including peptide nucleic acids (PNAs) or non-nucleic acid molecules such as phosphorothioate derivatives, that specifically bind DNA or RNA in a base pair-dependent manner. A skilled artisan can readily obtain these classes of nucleic acid molecules using the 151P3D4 polynucleotides and polynucleotide sequences disclosed herein.

Antisense technology entails the administration of exogenous oligonucleotides that bind to a target polynucleotide located within the cells. The term “antisense” refers to the fact that such oligonucleotides are complementary to their intracellular targets, e.g., 151P3D4. See for example, Jack Cohen, Oligodeoxynucleotides, Antisense Inhibitors of Gene Expression, CRC Press, 1989; and Synthesis 1:1-5 (1988). The 151P3D4 antisense oligonucleotides of the present invention include derivatives such as S-oligonucleotides (phosphorothioate derivatives or S-oligos, see, Jack Cohen, supra), which exhibit enhanced cancer cell growth inhibitory action. S-oligos (nucleoside phosphorothioates) are isoelectronic analogs of an oligonucleotide (O-oligo) in which a nonbridging oxygen atom of the phosphate group is replaced by a sulfur atom. The S-oligos of the present invention can be prepared by treatment of the corresponding O-oligos with 3H-1,2-benzodithiol-3-one-1,1-dioxide, which is a sulfur transfer reagent. See, e.g., Iyer, R. P. et al., J. Org. Chem. 55:4693-4698 (1990); and Iyer, R. P. et al., J. Am. Chem. Soc. 112:1253-1254 (1990). Additional 151P3D4 antisense oligonucleotides of the present invention include morpholino antisense oligonucleotides known in the art (see, e.g., Partridge et al., 1996, Antisense & Nucleic Acid Drug Development 6: 169-175).

The 151P3D4 antisense oligonucleotides of the present invention typically can be RNA or DNA that is complementary to and stably hybridizes with the first 100 5′ codons or last 100 3′ codons of a 151P3D4 genomic sequence or the corresponding mRNA. Absolute complementarity is not required, although high degrees of complementarity are preferred. Use of an oligonucleotide complementary to this region allows for the selective hybridization to 151P3D4 mRNA and not to mRNA specifying other regulatory subunits of protein kinase. In one embodiment, 151P3D4 antisense oligonucleotides of the present invention are 15 to 30-mer fragments of the antisense DNA molecule that have a sequence that hybridizes to 151P3D4 mRNA. Optionally, 151P3D4 antisense oligonucleotide is a 30-mer oligonucleotide that is complementary to a region in the first 10 5′ codons or last 10 3′ codons of 151P3D4. Alternatively, the antisense molecules are modified to employ ribozymes in the inhibition of 151P3D4 expression, see, e.g., L. A. Couture & D. T. Stinchcomb; Trends Genet. 12: 510-515 (1996).

Primers and Primer Pairs

Further specific embodiments of this nucleotides of the invention include primers and primer pairs, which allow the specific amplification of polynucleotides of the invention or of any specific parts thereof, and probes that selectively or specifically hybridize to nucleic acid molecules of the invention or to any part thereof. Probes can be labeled with a detectable marker, such as, for example, a radioisotope, fluorescent compound, bioluminescent compound, a chemiluminescent compound, metal chelator or enzyme. Such probes and primers are used to detect the presence of a 151P3D4 polynucleotide in a sample and as a means for detecting a cell expressing a 151P3D4 protein.

Examples of such probes include polypeptides comprising all or part of the human 151P3D4 cDNA sequence shown in FIG. 2. Examples of primer pairs capable of specifically amplifying 151P3D4 mRNAs are also described in the Examples. As will be understood by the skilled artisan, a great many different primers and probes can be prepared based on the sequences provided herein and used effectively to amplify and/or detect a 151P3D4 mRNA.

The 151P3D4 polynucleotides of the invention are useful for a variety of purposes, including but not limited to their use as probes and primers for the amplification and/or detection of the 151P3D4 gene(s), mRNA(s), or fragments thereof; as reagents for the diagnosis and/or prognosis of prostate cancer and other cancers; as coding sequences capable of directing the expression of 151P3D4 polypeptides; as tools for modulating or inhibiting the expression of the 151P3D4 gene(s) and/or translation of the 151P3D4 transcript(s); and as therapeutic agents.

The present invention includes the use of any probe as described herein to identify and isolate a 151P3D4 or 151P3D4 related nucleic acid sequence from a naturally occurring source, such as humans or other mammals, as well as the isolated nucleic acid sequence per se, which would comprise all or most of the sequences found in the probe used.

Isolation of 151P3D4-Encoding Nucleic Acid Molecules

The 151P3D4 cDNA sequences described herein enable the isolation of other polynucleotides encoding 151P3D4 gene product(s), as well as the isolation of polynucleotides encoding 151P3D4 gene product homologs, alternatively spliced isoforms, allelic variants, and mutant forms of a 151P3D4 gene product as well as polynucleotides that encode analogs of 151P3D4-related proteins. Various molecular cloning methods that can be employed to isolate full length cDNAs encoding a 151P3D4 gene are well known (see, for example, Sambrook, J. et al., Molecular Cloning: A Laboratory Manual, 2d edition, Cold Spring Harbor Press, New York, 1989; Current Protocols in Molecular Biology. Ausubel et al., Eds., Wiley and Sons, 1995). For example, lambda phage cloning methodologies can be conveniently employed, using commercially available cloning systems (e.g., Lambda ZAP Express, Stratagene). Phage clones containing 151P3D4 gene cDNAs can be identified by probing with a labeled 151P3D4 cDNA or a fragment thereof. For example, in one embodiment, a 151P3D4 cDNA (e.g., FIG. 2) or a portion thereof can be synthesized and used as a probe to retrieve overlapping and full-length cDNAs corresponding to a 151P3D4 gene. A 151P3D4 gene itself can be isolated by screening genomic DNA libraries, bacterial artificial chromosome libraries (BACs), yeast artificial chromosome libraries (YACs), and the like, with 151P3D4 DNA probes or primers.

Recombinant Nucleic Acid Molecules and Host-Vector Systems

The invention also provides recombinant DNA or RNA molecules containing a 151P3D4 polynucleotide, a fragment, analog or homologue thereof, including but not limited to phages, plasmids, phagemids, cosmids, YACs, BACs, as well as various viral and non-viral vectors well known in the art, and cells transformed or transfected with such recombinant DNA or RNA molecules. Methods for generating such molecules are well known (see, for example, Sambrook et al., 1989, supra).

The invention further provides a host-vector system comprising a recombinant DNA molecule containing a 151P3D4 polynucleotide, fragment, analog or homologue thereof within a suitable prokaryotic or eukaryotic host cell. Examples of suitable eukaryotic host cells include a yeast cell, a plant cell, or an animal cell, such as a mammalian cell or an insect cell (e.g., a baculovirus-infectible cell such as an Sf9 or HighFive cell). Examples of suitable mammalian cells include various prostate cancer cell lines such as DU145 and TsuPr1, other transfectable or transducible prostate cancer cell lines, primary cells (PrEC), as well as a number of mammalian cells routinely used for the expression of recombinant proteins (e.g., COS, CHO, 293, 293T cells). More particularly, a polynucleotide comprising the coding sequence of 151P3D4 or a fragment, analog or homolog thereof can be used to generate 151P3D4 proteins or fragments thereof using any number of host-vector systems routinely used and widely known in the art.

A wide range of host-vector systems suitable for the expression of 151P3D4 proteins or fragments thereof are available, see for example, Sambrook et al., 1989, supra; Current Protocols in Molecular Biology, 1995, supra). Preferred vectors for mammalian expression include but are not limited to pcDNA 3.1 myc-His-tag (Invitrogen) and the retroviral vector pSRαtkneo (Muller et al., 1991, MCB 11:1785). Using these expression vectors, 151P3D4 can be expressed in several prostate cancer and non-prostate cell lines, including for example 293, 293T, rat-1, NIH 3T3 and TsuPr1. The host-vector systems of the invention are useful for the production of a 151P3D4 protein or fragment thereof. Such host-vector systems can be employed to study the functional properties of 151P3D4 and 151P3D4 mutations or analogs.

Recombinant human 151P3D4 protein or an analog or homolog or fragment thereof can be produced by mammalian cells transfected with a construct encoding a 151P3D4-related nucleotide. For example, 293T cells can be transfected with an expression plasmid encoding 151P3D4 or fragment, analog or homolog thereof, a 151P3D4-related protein is expressed in the 293T cells, and the recombinant 151P3D4 protein is isolated using standard purification methods (e.g., affinity purification using anti-151P3D4 antibodies). In another embodiment, a 151P3D4 coding sequence is subcloned into the retroviral vector pSRαMSVtkneo and used to infect various mammalian cell lines, such as NIH 3T3, TsuPr1, 293 and rat-1 in order to establish 151P3D4 expressing cell lines. Various other expression systems well known in the art can also be employed. Expression constructs encoding a leader peptide joined in frame to a 151P3D4 coding sequence can be used for the generation of a secreted form of recombinant 151P3D4 protein.

As discussed herein, redundancy in the genetic code permits variation in 151P3D4 gene sequences. In particular, it is known in the art that specific host species often have specific codon preferences, and thus one can adapt the disclosed sequence as preferred for a desired host. For example, preferred analog codon sequences typically have rare codons (i.e., codons having a usage frequency of less than about 20% in known sequences of the desired host) replaced with higher frequency codons. Codon preferences for a specific species are calculated, for example, by utilizing codon usage tables available on the Internet such as at URL dna.affrc.go.jp/˜nakamura/codon.html.

Additional sequence modifications are known to enhance protein expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon/intron splice site signals, transposon-like repeats, and/or other such well-characterized sequences that are deleterious to gene expression. The GC content of the sequence is adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. Where possible, the sequence is modified to avoid predicted hairpin secondary mRNA structures. Other useful modifications include the addition of a translational initiation consensus sequence at the start of the open reading frame, as described in Kozak, Mol. Cell. Biol., 9:5073-5080 (1989) Skilled artisans understand that the general rule that eukaryotic ribosomes initiate translation exclusively at the 5′ proximal AUG codon is abrogated only under rare conditions (see, e.g., Kozak PNAS 92(7): 2662-2666, (1995) and Kozak NAR 15(20): 8125-8148 (1987)).

151P3D4-Related Proteins

Another aspect of the present invention provides 151P3D4-related proteins. Specific embodiments of 151P3D4 proteins comprise a polypeptide having all or part of the amino acid sequence of human 151P3D4 as shown in FIG. 2 or FIG. 3. Alternatively, embodiments of 151P3D4 proteins comprise variant, homolog or analog polypeptides that have alterations in the amino acid sequence of 151P3D4 shown in FIG. 2 or FIG. 3.

In general, naturally occurring allelic variants of human 151P3D4 share a high degree of structural identity and homology (e.g., 90% or more homology). Typically, allelic variants of a 151P3D4 protein contain conservative amino acid substitutions within the 151P3D4 sequences described herein or contain a substitution of an amino acid from a corresponding position in a homologue of 151P3D4. One class of 151P3D4 allelic variants are proteins that share a high degree of homology with at least a small region of a particular 151P3D4 amino acid sequence, but further contain a radical departure from the sequence, such as a non-conservative substitution, truncation, insertion or frame shift. In comparisons of protein sequences, the terms, similarity, identity, and homology each have a distinct meaning as appreciated in the field of genetics. Moreover, orthology and paralogy can be important concepts describing the relationship of members of a given protein family in one organism to the members of the same family in other organisms.

Amino acid abbreviations are provided in Table II. Conservative amino acid substitutions can frequently be made in a protein without altering either the conformation or the function of the protein. Proteins of the invention can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 conservative substitutions. Such changes include substituting any of isoleucine (I), valine (V), and leucine (L) for any other of these hydrophobic amino acids; aspartic acid (D) for glutamic acid (E) and vice versa; glutamine (Q) for asparagine (N) and vice versa; and serine (S) for threonine (T) and vice versa. Other substitutions can also be considered conservative, depending on the environment of the particular amino acid and its role in the three-dimensional structure of the protein. For example, glycine (G) and alanine (A) can frequently be interchangeable, as can alanine (A) and valine (V). Methionine (M), which is relatively hydrophobic, can frequently be interchanged with leucine and isoleucine, and sometimes with valine. Lysine (K) and arginine (R) are frequently interchangeable in locations in which the significant feature of the amino acid residue is its charge and the differing pK's of these two amino acid residues are not significant. Still other changes can be considered “conservative” in particular environments (see, e.g. Table III herein; pages 13-15 “Biochemistry” 2^nd ED. Lubert Stryer ed (Stanford University); Henikoff et al., PNAS 1992 Vol 89 10915-10919; Lei et al., J Biol Chem 1995 May 19; 270(20):11882-6).

Embodiments of the invention disclosed herein include a wide variety of art-accepted variants or analogs of 151P3D4 proteins such as polypeptides having amino acid insertions, deletions and substitutions. 151P3D4 variants can be made using methods known in the art such as site-directed mutagenesis, alanine scanning, and PCR mutagenesis. Site-directed mutagenesis (Carter et al., Nucl. Acids Res., 13:4331 (1986); Zoller et al., Nucl. Acids Res., 10:6487 (1987)), cassette mutagenesis (Wells et al., Gene, 34:315 (1985)), restriction selection mutagenesis (Wells et al., Philos. Trans. R. Soc. London SerA, 317:415 (1986)) or other known techniques can be performed on the cloned DNA to produce the 151P3D4 variant DNA.

Scanning amino acid analysis can also be employed to identify one or more amino acids along a contiguous sequence that is involved in a specific biological activity such as a protein-protein interaction. Among the preferred scanning amino acids are relatively small, neutral amino acids. Such amino acids include alanine, glycine, serine, and cysteine. Alanine is typically a preferred scanning amino acid among this group because it eliminates the side-chain beyond the beta-carbon and is less likely to alter the main-chain conformation of the variant. Alanine is also typically preferred because it is the most common amino acid. Further, it is frequently found in both buried and exposed positions (Creighton, The Proteins, (W.H. Freeman & Co., N.Y.); Chothia, J. Mol. Biol., 150:1 (1976)). If alanine substitution does not yield adequate amounts of variant, an isosteric amino acid can be used.

As defined herein, 151P3D4 variants, analogs or homologs, have the distinguishing attribute of having at least one epitope that is “cross reactive” with a 151P3D4 protein having an amino acid sequence of FIG. 3. As used in this sentence, “cross reactive” means that an antibody or T cell that specifically binds to a 151P3D4 variant also specifically binds to a 151P3D4 protein having an amino acid sequence set forth in FIG. 3. A polypeptide ceases to be a variant of a protein shown in FIG. 3, when it no longer contains any epitope capable of being recognized by an antibody or T cell that specifically binds to the starting 151P3D4 protein. Those skilled in the art understand that antibodies that recognize proteins bind to epitopes of varying size, and a grouping of the order of about four or five amino acids, contiguous or not, is regarded as a typical number of amino acids in a minimal epitope. See, e.g., Nair et al., J. Immunol. 2000 165(12): 6949-6955; Hebbes et al., Mol Immunol (1989) 26(9):865-73; Schwartz et al., J Immunol (1985) 135(4):2598-608.

Other classes of 151P3D4-related protein variants share 70%, 75%, 80%, 85% or 90% or more similarity with an amino acid sequence of FIG. 3, or a fragment thereof. Another specific class of 151P3D4 protein variants or analogs comprise one or more of the 151P3D4 biological motifs described herein or presently known in the art. Thus, encompassed by the present invention are analogs of 151P3D4 fragments (nucleic or amino acid) that have altered functional (e.g. immunogenic) properties relative to the starting fragment. It is to be appreciated that motifs now or which become part of the art are to be applied to the nucleic or amino acid sequences of FIG. 2 or FIG. 3.

As discussed herein, embodiments of the claimed invention include polypeptides containing less than the full amino acid sequence of a 151P3D4 protein shown in FIG. 2 or FIG. 3. For example, representative embodiments of the invention comprise peptides/proteins having any 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more contiguous amino acids of a 151P3D4 protein shown in FIG. 2 or FIG. 3.

Moreover, representative embodiments of the invention disclosed herein include polypeptides consisting of about amino acid 1 to about amino acid 10 of a 151P3D4 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 10 to about amino acid 20 of a 151P3D4 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 20 to about amino acid 30 of a 151P3D4 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 30 to about amino acid 40 of a 151P3D4 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 40 to about amino acid 50 of a 151P3D4 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 50 to about amino acid 60 of a 151P3D4 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 60 to about amino acid 70 of a 151P3D4 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 70 to about amino acid 80 of a 151P3D4 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 80 to about amino acid 90 of a 151P3D4 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 90 to about amino acid 100 of a 151P3D4 protein shown in FIG. 2 or FIG. 3, etc. throughout the entirety of a 151P3D4 amino acid sequence. Moreover, polypeptides consisting of about amino acid 1 (or 20 or 30 or 40 etc.) to about amino acid 20, (or 130, or 140 or 150 etc.) of a 151P3D4 protein shown in FIG. 2 or FIG. 3 are embodiments of the invention. It is to be appreciated that the starting and stopping positions in this paragraph refer to the specified position as well as that position plus or minus 5 residues.

151P3D4-related proteins are generated using standard peptide synthesis technology or using chemical cleavage methods well known in the art. Alternatively, recombinant methods can be used to generate nucleic acid molecules that encode a 151P3D4-related protein. In one embodiment, nucleic acid molecules provide a means to generate defined fragments of a 151P3D4 protein (or variants, homologs or analogs thereof).

Motif-Bearing Protein Embodiments

Additional illustrative embodiments of the invention disclosed herein include 151P3D4 polypeptides comprising the amino acid residues of one or more of the biological motifs contained within a 151P3D4 polypeptide sequence set forth in FIG. 2 or FIG. 3. Various motifs are known in the art, and a protein can be evaluated for the presence of such motifs by a number of publicly available Internet sites (see, e.g., URL addresses: pfam.wustl.edu/; searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html; psort.ims.u-tokyo.ac.jp/; cbs.dtu.dk; ebi.ac.uk/interpro/scan.html; expasy.ch/tools/scnpsit1.html; Epimatrix™ and Epimer™, Brown University, brown.edu/Research/TB-HIV_Lab/epimatrix/epimatrix.html; and BIMAS, bimas.dcrt.nih.gov/).

Motif bearing subsequences of all 151P3D4 variant proteins are set forth and identified in Tables V-XVIII and XXII-LII.

Table XIX sets forth several frequently occurring motifs based on pfam searches (see URL address pfam.wustl.edu/). The columns of Table XIX list (1) motif name abbreviation, (2) percent identity found amongst the different member of the motif family, (3) motif name or description and (4) most common function; location information is included if the motif is relevant for location.

Polypeptides comprising one or more of the 151P3D4 motifs discussed above are useful in elucidating the specific characteristics of a malignant phenotype in view of the observation that the 151P3D4 motifs discussed above are associated with growth dysregulation and because 151P3D4 is overexpressed in certain cancers (See, e.g., Table I). Casein kinase II, cAMP and camp-dependent protein kinase, and Protein Kinase C, for example, are enzymes known to be associated with the development of the malignant phenotype (see e.g. Chen et al., Lab Invest., 78(2): 165-174 (1998); Gaiddon et al., Endocrinology 136(10): 4331-4338 (1995); Hall et al., Nucleic Acids Research 24(6): 1119-1126 (1996); Peterziel et al., Oncogene 18(46): 6322-6329 (1999) and O′Brian, Oncol. Rep. 5(2): 305-309 (1998)). Moreover, both glycosylation and myristoylation are protein modifications also associated with cancer and cancer progression (see e.g. Dennis et al., Biochem. Biophys. Acta 1473(1):21-34 (1999); Raju et al., Exp. Cell Res. 235(1): 145-154 (1997)). Amidation is another protein modification also associated with cancer and cancer progression (see e.g. Treston et al., J. Natl. Cancer Inst. Monogr. (13): 169-175 (1992)).

In another embodiment, proteins of the invention comprise one or more of the immunoreactive epitopes identified in accordance with art-accepted methods, such as the peptides set forth in Tables V-XVIII and XXII-LI. CTL epitopes can be determined using specific algorithms to identify peptides within a 151P3D4 protein that are capable of optimally binding to specified HLA alleles (e.g., Table IV; Epimatrix™ and Epimer™, Brown University, Internet URL brown.edu/Research/TB-HIV_Lab/epimatrix/epimatrix.html; and BIMAS, URL bimas.dcrt.nih.gov/.) Moreover, processes for identifying peptides that have sufficient binding affinity for HLA molecules and which are correlated with being immunogenic epitopes, are well known in the art, and are carried out without undue experimentation. In addition, processes for identifying peptides that are immunogenic epitopes, are well known in the art, and are carried out without undue experimentation either in vitro or in vivo.

Also known in the art are principles for creating analogs of such epitopes in order to modulate immunogenicity. For example, one begins with an epitope that bears a CTL or HTL motif (see, e.g., the HLA Class I and HLA Class II motifs/supermotifs of Table IV). The epitope is analoged by substituting out an amino acid at one of the specified positions, and replacing it with another amino acid specified for that position. For example, one can substitute out a deleterious residue in favor of any other residue, such as a preferred residue as defined in Table IV; substitute a less-preferred residue with a preferred residue as defined in Table IV; or substitute an originally-occurring preferred residue with another preferred residue as defined in Table IV. Substitutions can occur at primary anchor positions or at other positions in a peptide; see, e.g., Table IV.

A variety of references reflect the art regarding the identification and generation of epitopes in a protein of interest as well as analogs thereof. See, for example, WO 97/33602 to Chesnut et al.; Sette, Immunogenetics 1999 50(3-4): 201-212; Sette et al., J. Immunol. 2001 166(2): 1389-1397; Sidney et al., Hum. Immunol. 1997 58(1): 12-20; Kondo et al., Immunogenetics 1997 45(4): 249-258; Sidney et al., J. Immunol. 1996 157(8): 3480-90; and Falk et al., Nature 351: 290-6 (1991); Hunt et al., Science 255:1261-3 (1992); Parker et al., J. Immunol. 149: 3580-7 (1992); Parker et al., J. Immunol. 152:163-75 (1994)); Kast et al., 1994 152(8): 3904-12; Borras-Cuesta et al., Hum. Immunol. 2000 61(3): 266-278; Alexander et al., J. Immunol. 2000 164(3); 164(3): 1625-1633; Alexander et al., PMID: 7895164, UI: 95202582; O'Sullivan et al., J. Immunol. 1991 147(8): 2663-2669; Alexander et al., Immunity 1994 1(9): 751-761 and Alexander et al., Immunol. Res. 1998 18(2): 79-92.

Related embodiments of the invention include polypeptides comprising combinations of the different motifs set forth in Table XX, and/or, one or more of the predicted CTL epitopes of Tables V-XVII and XXII-XLVII, and/or, one or more of the predicted HTL epitopes of Tables XLVIII-LI, and/or, one or more of the T cell binding motifs known in the art. Preferred embodiments contain no insertions, deletions or substitutions either within the motifs or the intervening sequences of the polypeptides. In addition, embodiments which include a number of either N-terminal and/or C-terminal amino acid residues on either side of these motifs may be desirable (to, for example, include a greater portion of the polypeptide architecture in which the motif is located). Typically the number of N-terminal and/or C-terminal amino acid residues on either side of a motif is between about 1 to about 100 amino acid residues, preferably 5 to about 50 amino acid residues.

151P3D4-related proteins are embodied in many forms, preferably in isolated form. A purified 151P3D4 protein molecule will be substantially free of other proteins or molecules that impair the binding of 151P3D4 to antibody, T cell or other ligand. The nature and degree of isolation and purification will depend on the intended use. Embodiments of a 151P3D4-related proteins include purified 151P3D4-related proteins and functional, soluble 151P3D4-related proteins. In one embodiment, a functional, soluble 151P3D4 protein or fragment thereof retains the ability to be bound by antibody, T cell or other ligand.

The invention also provides 151P3D4 proteins comprising biologically active fragments of a 151P3D4 amino acid sequence shown in FIG. 2 or FIG. 3. Such proteins exhibit properties of the starting 151P3D4 protein, such as the ability to elicit the generation of antibodies that specifically bind an epitope associated with the starting 151P3D4 protein; to be bound by such antibodies; to elicit the activation of HTL or CTL; and/or, to be recognized by HTL or CTL that also specifically bind to the starting protein.

151P3D4-related polypeptides that contain particularly interesting structures can be predicted and/or identified using various analytical techniques well known in the art, including, for example, the methods of Chou-Fasman, Garnier-Robson, Kyte-Doolittle, Eisenberg, Karplus-Schultz or Jameson-Wolf analysis, or on the basis of immunogenicity. Fragments that contain such structures are particularly useful in generating subunit-specific anti-151P3D4 antibodies, or T cells or in identifying cellular factors that bind to 151P3D4. For example, hydrophilicity profiles can be generated, and immunogenic peptide fragments identified, using the method of Hopp, T. P. and Woods, K. R., 1981, Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828. Hydropathicity profiles can be generated, and immunogenic peptide fragments identified, using the method of Kyte, J. and Doolittle, R. F., 1982, J. Mol. Biol. 157:105-132. Percent (%) Accessible Residues profiles can be generated, and immunogenic peptide fragments identified, using the method of Janin J., 1979, Nature 277:491-492. Average Flexibility profiles can be generated, and immunogenic peptide fragments identified, using the method of Bhaskaran R., Ponnuswamy P. K., 1988, Int. J. Pept. Protein Res. 32:242-255. Beta-turn profiles can be generated, and immunogenic peptide fragments identified, using the method of Deleage, G., Roux B., 1987, Protein Engineering 1:289-294.

CTL epitopes can be determined using specific algorithms to identify peptides within a 151P3D4 protein that are capable of optimally binding to specified HLA alleles (e.g., by using the SYFPEITHI site at World Wide Web URL syfpeithi.bmi-heidelberg.com/; the listings in Table IV(A)-(E); Epimatrix™ and Epimer™, Brown University, Internet URL (brown.edu/Research/TB-HIV_Lab/epimatrix/epimatrix.html); and BIMAS, URL bimas.dcrt.nih.gov/). Illustrating this, peptide epitopes from 151P3D4 that are presented in the context of human MHC Class I molecules, e.g., HLA-A1, A2, A3, A11, A24, B7 and B35 were predicted (see, e.g., Tables V-XVIII, XXII-LI). Specifically, the complete amino acid sequence of the 151P3D4 protein and relevant portions of other variants, i.e., for HLA Class I predictions 9 flanking residues on either side of a point mutation, and for HLA Class II predictions 14 flanking residues on either side of a point mutation, were entered into the HLA Peptide Motif Search algorithm found in the Bioinformatics and Molecular Analysis Section (BIMAS) web site listed above; in addition to the site SYFPEITHI, at URL syfpeithi.bmi-heidelberg.com/.

The HLA peptide motif search algorithm was developed by Dr. Ken Parker based on binding of specific peptide sequences in the groove of HLA Class I molecules, in particular HLA-A2 (see, e.g., Falk et al., Nature 351: 290-6 (1991); Hunt et al., Science 255:1261-3 (1992); Parker et al., J. Immunol. 149:3580-7 (1992); Parker et al., J. Immunol. 152:163-75 (1994)). This algorithm allows location and ranking of 8-mer, 9-mer, and 10-mer peptides from a complete protein sequence for predicted binding to HLA-A2 as well as numerous other HLA Class I molecules. Many HLA class I binding peptides are 8-, 9-, 10 or 11-mers. For example, for Class I HLA-A2, the epitopes preferably contain a leucine (L) or methionine (M) at position 2 and a valine (V) or leucine (L) at the C-terminus (see, e.g., Parker et al., J. Immunol. 149:3580-7 (1992)). Selected results of 151P3D4 predicted binding peptides are shown in Tables V-XVIII and XXII-LI herein. In Tables V-XVIII and XXII-XLVII, selected candidates, 9-mers and 10-mers, for each family member are shown along with their location, the amino acid sequence of each specific peptide, and an estimated binding score. In Tables XLVIII-LI, selected candidates, 15-mers, for each family member are shown along with their location, the amino acid sequence of each specific peptide, and an estimated binding score. The binding score corresponds to the estimated half time of dissociation of complexes containing the peptide at 37° C. at pH 6.5. Peptides with the highest binding score are predicted to be the most tightly bound to HLA Class I on the cell surface for the greatest period of time and thus represent the best immunogenic targets for T-cell recognition.

Actual binding of peptides to an HLA allele can be evaluated by stabilization of HLA expression on the antigen-processing defective cell line T2 (see, e.g., Xue et al., Prostate 30:73-8 (1997) and Peshwa et al., Prostate 36:129-38 (1998)). Immunogenicity of specific peptides can be evaluated in vitro by stimulation of CD8+ cytotoxic T lymphocytes (CTL) in the presence of antigen presenting cells such as dendritic cells.

It is to be appreciated that every epitope predicted by the BIMAS site, Epimer™ and Epimatrix™ sites, or specified by the HLA class I or class II motifs available in the art or which become part of the art such as set forth in Table IV (or determined using World Wide Web site URL syfpeithi.bmi-heidelberg.com/, or BIMAS, bimas.dcrt.nih.gov/) are to be “applied” to a 151P3D4 protein in accordance with the invention. As used in this context “applied” means that a 151P3D4 protein is evaluated, e.g., visually or by computer-based patterns finding methods, as appreciated by those of skill in the relevant art. Every subsequence of a 151P3D4 protein of 8, 9, 10, or 11 amino acid residues that bears an HLA Class I motif, or a subsequence of 9 or more amino acid residues that bear an HLA Class II motif are within the scope of the invention.

Expression of 151P3D4-Related Proteins

In an embodiment described in the examples that follow, 151P3D4 can be conveniently expressed in cells (such as 293T cells) transfected with a commercially available expression vector such as a CMV-driven expression vector encoding 151P3D4 with a C-terminal 6× His and MYC tag (pcDNA3.1/mycHIS, Invitrogen or Tag5, GenHunter Corporation, Nashville Tenn.). The Tag5 vector provides an IgGK secretion signal that can be used to facilitate the production of a secreted 151P3D4 protein in transfected cells. The secreted HIS-tagged 151P3D4 in the culture media can be purified, e.g., using a nickel column using standard techniques.

Modifications of 151P3D4-Related Proteins

Modifications of 151P3D4-related proteins such as covalent modifications are included within the scope of this invention. One type of covalent modification includes reacting targeted amino acid residues of a 151P3D4 polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C-terminal residues of a 151P3D4 protein. Another type of covalent modification of a 151P3D4 polypeptide included within the scope of this invention comprises altering the native glycosylation pattern of a protein of the invention. Another type of covalent modification of 151P3D4 comprises linking a 151P3D4 polypeptide to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol (PEG), polypropylene glycol, or polyoxyalkylenes, in the manner set forth in U.S. Pat. No. 4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or 4,179,337.

The 151P3D4-related proteins of the present invention can also be modified to form a chimeric molecule comprising 151P3D4 fused to another, heterologous polypeptide or amino acid sequence. Such a chimeric molecule can be synthesized chemically or recombinantly. A chimeric molecule can have a protein of the invention fused to another tumor-associated antigen or fragment thereof. Alternatively, a protein in accordance with the invention can comprise a fusion of fragments of a 151P3D4 sequence (amino or nucleic acid) such that a molecule is created that is not, through its length, directly homologous to the amino or nucleic acid sequences shown in FIG. 2 or FIG. 3. Such a chimeric molecule can comprise multiples of the same subsequence of 151P3D4. A chimeric molecule can comprise a fusion of a 151P3D4-related protein with a polyhistidine epitope tag, which provides an epitope to which immobilized nickel can selectively bind, with cytokines or with growth factors. The epitope tag is generally placed at the amino- or carboxyl-terminus of a 151P3D4 protein. In an alternative embodiment, the chimeric molecule can comprise a fusion of a 151P3D4-related protein with an immunoglobulin or a particular region of an immunoglobulin. For a bivalent form of the chimeric molecule (also referred to as an “immunoadhesin”), such a fusion could be to the Fc region of an IgG molecule. The Ig fusions preferably include the substitution of a soluble (transmembrane domain deleted or inactivated) form of a 151P3D4 polypeptide in place of at least one variable region within an Ig molecule. In a preferred embodiment, the immunoglobulin fusion includes the hinge, CH2 and CH3, or the hinge, CHI, CH2 and CH3 regions of an IgGI molecule. For the production of immunoglobulin fusions see, e.g., U.S. Pat. No. 5,428,130 issued Jun. 27, 1995.

Uses of 151P3D4-Related Proteins

The proteins of the invention have a number of different specific uses. As 151P3D4 is highly expressed in prostate and other cancers, 151P3D4-related proteins are used in methods that assess the status of 151P3D4 gene products in normal versus cancerous tissues, thereby elucidating the malignant phenotype. Typically, polypeptides from specific regions of a 151P3D4 protein are used to assess the presence of perturbations (such as deletions, insertions, point mutations etc.) in those regions (such as regions containing one or more motifs). Exemplary assays utilize antibodies or T cells targeting 151P3D4-related proteins comprising the amino acid residues of one or more of the biological motifs contained within a 151P3D4 polypeptide sequence in order to evaluate the characteristics of this region in normal versus cancerous tissues or to elicit an immune response to the epitope. Alternatively, 151P3D4-related proteins that contain the amino acid residues of one or more of the biological motifs in a 151P3D4 protein are used to screen for factors that interact with that region of 151P3D4.

151P3D4 protein fragments/subsequences are particularly useful in generating and characterizing domain-specific antibodies (e.g., antibodies recognizing an extracellular or intracellular epitope of a 151P3D4 protein), for identifying agents or cellular factors that bind to 151P3D4 or a particular structural domain thereof, and in various therapeutic and diagnostic contexts, including but not limited to diagnostic assays, cancer vaccines and methods of preparing such vaccines.

Proteins encoded by the 151P3D4 genes, or by analogs, homologs or fragments thereof, have a variety of uses, including but not limited to generating antibodies and in methods for identifying ligands and other agents and cellular constituents that bind to a 151P3D4 gene product. Antibodies raised against a 151P3D4 protein or fragment thereof are useful in diagnostic and prognostic assays, and imaging methodologies in the management of human cancers characterized by expression of 151P3D4 protein, such as those listed in Table I. Such antibodies can be expressed intracellularly and used in methods of treating patients with such cancers. 151P3D4-related nucleic acids or proteins are also used in generating HTL or CTL responses.

Various immunological assays useful for the detection of 151P3D4 proteins are used, including but not limited to various types of radioimmunoassays, enzyme-linked immunosorbent assays (ELISA), enzyme-linked immunofluorescent assays (ELIFA), immunocytochemical methods, and the like. Antibodies can be labeled and used as immunological imaging reagents capable of detecting 151P3D4-expressing cells (e.g., in radioscintigraphic imaging methods). 151P3D4 proteins are also particularly useful in generating cancer vaccines, as further described herein.

151P3D4 Antibodies

Another aspect of the invention provides antibodies that bind to 151P3D4-related proteins. Preferred antibodies specifically bind to a 151P3D4-related protein and do not bind (or bind weakly) to peptides or proteins that are not 151P3D4-related proteins. For example, antibodies that bind 151P3D4 can bind 151P3D4-related proteins such as the homologs or analogs thereof.

151P3D4 antibodies of the invention are particularly useful in cancer (see, e.g., Table I) diagnostic and prognostic assays, and imaging methodologies. Similarly, such antibodies are useful in the treatment, diagnosis, and/or prognosis of other cancers, to the extent 151P3D4 is also expressed or overexpressed in these other cancers. Moreover, intracellularly expressed antibodies (e.g., single chain antibodies) are therapeutically useful in treating cancers in which the expression of 151P3D4 is involved, such as advanced or metastatic prostate cancers.

The invention also provides various immunological assays useful for the detection and quantification of 151P3D4 and mutant 151P3D4-related proteins. Such assays can comprise one or more 151P3D4 antibodies capable of recognizing and binding a 151P3D4-related protein, as appropriate. These assays are performed within various immunological assay formats well known in the art, including but not limited to various types of radioimmunoassays, enzyme-linked immunosorbent assays (ELISA), enzyme-linked immunofluorescent assays (ELIFA), and the like.

Immunological non-antibody assays of the invention also comprise T cell immunogenicity assays (inhibitory or stimulatory) as well as major histocompatibility complex (MHC) binding assays.

In addition, immunological imaging methods capable of detecting prostate cancer and other cancers expressing 151P3D4 are also provided by the invention, including but not limited to radioscintigraphic imaging methods using labeled 151P3D4 antibodies. Such assays are clinically useful in the detection, monitoring, and prognosis of 151P3D4 expressing cancers such as prostate cancer.

151P3D4 antibodies are also used in methods for purifying a 151P3D4-related protein and for isolating 151P3D4 homologues and related molecules. For example, a method of purifying a 151P3D4-related protein comprises incubating a 151P3D4 antibody, which has been coupled to a solid matrix, with a lysate or other solution containing a 151P3D4-related protein under conditions that permit the 151P3D4 antibody to bind to the 151P3D4-related protein; washing the solid matrix to eliminate impurities; and eluting the 151P3D4-related protein from the coupled antibody. Other uses of 151P3D4 antibodies in accordance with the invention include generating anti-idiotypic antibodies that mimic a 151P3D4 protein.

Various methods for the preparation of antibodies are well known in the art. For example, antibodies can be prepared by immunizing a suitable mammalian host using a 151P3D4-related protein, peptide, or fragment, in isolated or immunoconjugated form (Antibodies: A Laboratory Manual, CSH Press, Eds., Harlow, and Lane (1988); Harlow, Antibodies, Cold Spring Harbor Press, NY (1989)). In addition, fusion proteins of 151P3D4 can also be used, such as a 151P3D4 GST-fusion protein. In a particular embodiment, a GST fusion protein comprising all or most of the amino acid sequence of FIG. 2 or FIG. 3 is produced, then used as an immunogen to generate appropriate antibodies. In another embodiment, a 151P3D4-related protein is synthesized and used as an immunogen.

In addition, naked DNA immunization techniques known in the art are used (with or without purified 151P3D4-related protein or 151P3D4 expressing cells) to generate an immune response to the encoded immunogen (for review, see Donnelly et al., 1997, Ann. Rev. Immunol. 15: 617-648).

The amino acid sequence of a 151P3D4 protein as shown in FIG. 2 or FIG. 3 can be analyzed to select specific regions of the 151P3D4 protein for generating antibodies. For example, hydrophobicity and hydrophilicity analyses of a 151P3D4 amino acid sequence are used to identify hydrophilic regions in the 151P3D4 structure. Regions of a 151P3D4 protein that show immunogenic structure, as well as other regions and domains, can readily be identified using various other methods known in the art, such as Chou-Fasman, Garnier-Robson, Kyte-Doolittle, Eisenberg, Karplus-Schultz or Jameson-Wolf analysis. Hydrophilicity profiles can be generated using the method of Hopp, T. P. and Woods, K. R., 1981, Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828. Hydropathicity profiles can be generated using the method of Kyte, J. and Doolittle, R. F., 1982, J. Mol. Biol. 157:105-132. Percent (%) Accessible Residues profiles can be generated using the method of Janin J., 1979, Nature 277:491-492. Average Flexibility profiles can be generated using the method of Bhaskaran R., Ponnuswamy P. K., 1988, Int. J. Pept. Protein Res. 32:242-255. Beta-turn profiles can be generated using the method of Deleage, G., Roux B., 1987, Protein Engineering 1:289-294. Thus, each region identified by any of these programs or methods is within the scope of the present invention. Methods for the generation of 151P3D4 antibodies are further illustrated by way of the examples provided herein. Methods for preparing a protein or polypeptide for use as an immunogen are well known in the art. Also well known in the art are methods for preparing immunogenic conjugates of a protein with a carrier, such as BSA, KLH or other carrier protein. In some circumstances, direct conjugation using, for example, carbodiimide reagents are used; in other instances linking reagents such as those supplied by Pierce Chemical Co., Rockford, Ill., are effective. Administration of a 151P3D4 immunogen is often conducted by injection over a suitable time period and with use of a suitable adjuvant, as is understood in the art. During the immunization schedule, titers of antibodies can be taken to determine adequacy of antibody formation.

151P3D4 monoclonal antibodies can be produced by various means well known in the art. For example, immortalized cell lines that secrete a desired monoclonal antibody are prepared using the standard hybridoma technology of Kohler and Milstein or modifications that immortalize antibody-producing B cells, as is generally known. Immortalized cell lines that secrete the desired antibodies are screened by immunoassay in which the antigen is a 151P3D4-related protein. When the appropriate immortalized cell culture is identified, the cells can be expanded and antibodies produced either from in vitro cultures or from ascites fluid.

The antibodies or fragments of the invention can also be produced, by recombinant means. Regions that bind specifically to the desired regions of a 151P3D4 protein can also be produced in the context of chimeric or complementarity determining region (CDR) grafted antibodies of multiple species origin. Humanized or human 151P3D4 antibodies can also be produced, and are preferred for use in therapeutic contexts. Methods for humanizing murine and other non-human antibodies, by substituting one or more of the non-human antibody CDRs for corresponding human antibody sequences, are well known (see for example, Jones et al., 1986, Nature 321: 522-525; Riechmann et al., 1988, Nature 332: 323-327; Verhoeyen et al., 1988, Science 239: 1534-1536). See also, Carter et al., 1993, Proc. Natl. Acad. Sci. USA 89: 4285 and Sims et al., 1993, J. Immunol. 151: 2296.

Methods for producing fully human monoclonal antibodies include phage display and transgenic methods (for review, see Vaughan et al., 1998, Nature Biotechnology 16: 535-539). Fully human 151P3D4 monoclonal antibodies can be generated using cloning technologies employing large human Ig gene combinatorial libraries (i.e., phage display) (Griffiths and Hoogenboom, Building an in vitro immune system: human antibodies from phage display libraries. In: Protein Engineering of Antibody Molecules for Prophylactic and Therapeutic Applications in Man, Clark, M. (Ed.), Nottingham Academic, pp 45-64 (1993); Burton and Barbas, Human Antibodies from combinatorial libraries. Id., pp 65-82). Fully human 151P3D4 monoclonal antibodies can also be produced using transgenic mice engineered to contain human immunoglobulin gene loci as described in PCT Patent Application WO98/24893, Kucherlapati and Jakobovits et al., published Dec. 3, 1997 (see also, Jakobovits, 1998, Exp. Opin. Invest. Drugs 7(4): 607-614; U.S. Pat. Nos. 6,162,963 issued 19 Dec. 2000; 6,150,584 issued 12 Nov. 2000; and, 6,114,598 issued 5 Sep. 2000). This method avoids the in vitro manipulation required with phage display technology and efficiently produces high affinity authentic human antibodies.

Reactivity of 151P3D4 antibodies with a 151P3D4-related protein can be established by a number of well known means, including Western blot, immunoprecipitation, ELISA, and FACS analyses using, as appropriate, 151P3D4-related proteins, 151P3D4-expressing cells or extracts thereof. A 151P3D4 antibody or fragment thereof can be labeled with a detectable marker or conjugated to a second molecule. Suitable detectable markers include, but are not limited to, a radioisotope, a fluorescent compound, a bioluminescent compound, chemiluminescent compound, a metal chelator or an enzyme. Further, bi-specific antibodies specific for two or more 151P3D4 epitopes are generated using methods generally known in the art. Homodimeric antibodies can also be generated by cross-linking techniques known in the art (e.g., Wolff et al., Cancer Res. 53: 2560-2565).

151P3D4 Cellular Immune Responses

The mechanism by which T cells recognize antigens has been delineated. Efficacious peptide epitope vaccine compositions of the invention induce a therapeutic or prophylactic immune responses in very broad segments of the world-wide population. For an understanding of the value and efficacy of compositions of the invention that induce cellular immune responses, a brief review of immunology-related technology is provided.

A complex of an HLA molecule and a peptidic antigen acts as the ligand recognized by HLA-restricted T cells (Buus, S. et al., Cell 47:1071, 1986; Babbitt, B. P. et al., Nature 317:359, 1985; Townsend, A. and Bodmer, H., Annu. Rev. Immunol. 7:601, 1989; Germain, R. N., Annu. Rev. Immunol. 11:403, 1993). Through the study of single amino acid substituted antigen analogs and the sequencing of endogenously bound, naturally processed peptides, critical residues that correspond to motifs required for specific binding to HLA antigen molecules have been identified and are set forth in Table IV (see also, e.g., Southwood, et al., J. Immunol. 160:3363, 1998; Rammensee, et al., Immunogenetics 41:178, 1995; Rammensee et al., SYFPEITHI, access via World Wide Web at URL syfpeithi.bmi-heidelberg.com/; Sette, A. and Sidney, J. Curr. Opin. Immunol. 10:478, 1998; Engelhard, V. H., Curr. Opin. Immunol. 6:13, 1994; Sette, A. and Grey, H. M., Curr. Opin. Immunol. 4:79, 1992; Sinigaglia, F. and Hammer, J. Curr. Biol. 6:52, 1994; Ruppert et al., Cell 74:929-937, 1993; Kondo et al., J. Immunol. 155:4307-4312, 1995; Sidney et al., J. Immunol. 157:3480-3490, 1996; Sidney et al., Human Immunol. 45:79-93, 1996; Sette, A. and Sidney, J. Immunogenetics 1999 November; 50(3-4):201-12, Review).

Furthermore, x-ray crystallographic analyses of HLA-peptide complexes have revealed pockets within the peptide binding cleft/groove of HLA molecules which accommodate, in an allele-specific mode, residues borne by peptide ligands; these residues in turn determine the HLA binding capacity of the peptides in which they are present. (See, e.g., Madden, D. R. Annu. Rev. Immunol. 13:587, 1995; Smith, et al., Immunity 4:203, 1996; Fremont et al., Immunity 8:305, 1998; Stern et al., Structure 2:245, 1994; Jones, E. Y. Curr. Opin. Immunol. 9:75, 1997; Brown, J. H. et al., Nature 364:33, 1993; Guo, H. C. et al., Proc. Natl. Acad. Sci. USA 90:8053, 1993; Guo, H. C. et al., Nature 360:364, 1992; Silver, M. L. et al., Nature 360:367, 1992; Matsumura, M. et al., Science 257:927, 1992; Madden et al., Cell 70:1035, 1992; Fremont, D. H. et al., Science 257:919, 1992; Saper, M. A., Bjorkman, P. J. and Wiley, D.C., J. Mol. Biol. 219:277, 1991.)

Accordingly, the definition of class I and class II allele-specific HLA binding motifs, or class I or class II supermotifs allows identification of regions within a protein that are correlated with binding to particular HLA antigen(s).

Thus, by a process of HLA motif identification, candidates for epitope-based vaccines have been identified; such candidates can be further evaluated by HLA-peptide binding assays to determine binding affinity and/or the time period of association of the epitope and its corresponding HLA molecule. Additional confirmatory work can be performed to select, amongst these vaccine candidates, epitopes with preferred characteristics in terms of population coverage, and/or immunogenicity.

Various strategies can be utilized to evaluate cellular immunogenicity, including:

1) Evaluation of primary T cell cultures from normal individuals (see, e.g., Wentworth, P. A. et al., Mol. Immunol. 32:603, 1995; Celis, E. et al., Proc. Natl. Acad. Sci. USA 91:2105, 1994; Tsai, V. et al., J. Immunol. 158:1796, 1997; Kawashima, I. et al., Human Immunol. 59:1, 1998). This procedure involves the stimulation of peripheral blood lymphocytes (PBL) from normal subjects with a test peptide in the presence of antigen presenting cells in vitro over a period of several weeks. T cells specific for the peptide become activated during this time and are detected using, e.g., a lymphokine- or ⁵¹Cr-release assay involving peptide sensitized target cells.

2) Immunization of HLA transgenic mice (see, e.g., Wentworth, P. A. et al., J. Immunol. 26:97, 1996; Wentworth, P. A. et al., Int. Immunol. 8:651, 1996; Alexander, J. et al., J. Immunol. 159:4753, 1997). For example, in such methods peptides in incomplete Freund's adjuvant are administered subcutaneously to HLA transgenic mice. Several weeks following immunization, splenocytes are removed and cultured in vitro in the presence of test peptide for approximately one week. Peptide-specific T cells are detected using, e.g., a ⁵¹Cr-release assay involving peptide sensitized target cells and target cells expressing endogenously generated antigen.

3) Demonstration of recall T cell responses from immune individuals who have been either effectively vaccinated and/or from chronically ill patients (see, e.g., Rehermann, B. et al., J. Exp. Med. 181:1047, 1995; Doolan, D. L. et al., Immunity 7:97, 1997; Bertoni, R. et al., J. Clin. Invest. 100:503, 1997; Threlkeld, S. C. et al., J. Immunol. 159:1648, 1997; Diepolder, H. M. et al., J. Virol. 71:6011, 1997). Accordingly, recall responses are detected by culturing PBL from subjects that have been exposed to the antigen due to disease and thus have generated an immune response “naturally”, or from patients who were vaccinated against the antigen. PBL from subjects are cultured in vitro for 1-2 weeks in the presence of test peptide plus antigen presenting cells (APC) to allow activation of “memory” T cells, as compared to “naive” T cells. At the end of the culture period, T cell activity is detected using assays including ⁵¹Cr release involving peptide-sensitized targets, T cell proliferation, or lymphokine release.

151P3D4 Transgenic Animals

Nucleic acids that encode a 151P3D4-related protein can also be used to generate either transgenic animals or “knock out” animals that, in turn, are useful in the development and screening of therapeutically useful reagents. In accordance with established techniques, cDNA encoding 151P3D4 can be used to clone genomic DNA that encodes 151P3D4. The cloned genomic sequences can then be used to generate transgenic animals containing cells that express DNA that encode 151P3D4. Methods for generating transgenic animals, particularly animals such as mice or rats, have become conventional in the art and are described, for example, in U.S. Pat. Nos. 4,736,866 issued 12 Apr. 1988, and 4,870,009 issued 26 Sep. 1989. Typically, particular cells would be targeted for 151P3D4 transgene incorporation with tissue-specific enhancers.

Transgenic animals that include a copy of a transgene encoding 151P3D4 can be used to examine the effect of increased expression of DNA that encodes 151P3D4. Such animals can be used as tester animals for reagents thought to confer protection from, for example, pathological conditions associated with its overexpression. In accordance with this aspect of the invention, an animal is treated with a reagent and a reduced incidence of a pathological condition, compared to untreated animals that bear the transgene, would indicate a potential therapeutic intervention for the pathological condition.

Alternatively, non-human homologues of 151P3D4 can be used to construct a 151P3D4 “knock out” animal that has a defective or altered gene encoding 151P3D4 as a result of homologous recombination between the endogenous gene encoding 151P3D4 and altered genomic DNA encoding 151P3D4 introduced into an embryonic cell of the animal. For example, cDNA that encodes 151P3D4 can be used to clone genomic DNA encoding 151P3D4 in accordance with established techniques. A portion of the genomic DNA encoding 151P3D4 can be deleted or replaced with another gene, such as a gene encoding a selectable marker that can be used to monitor integration. Typically, several kilobases of unaltered flanking DNA (both at the 5′ and 3′ ends) are included in the vector (see, e.g., Thomas and Capecchi, Cell, 51:503 (1987) for a description of homologous recombination vectors). The vector is introduced into an embryonic stem cell line (e.g., by electroporation) and cells in which the introduced DNA has homologously recombined with the endogenous DNA are selected (see, e.g., Li et al., Cell, 69:915 (1992)). The selected cells are then injected into a blastocyst of an animal (e.g., a mouse or rat) to form aggregation chimeras (see, e.g., Bradley, in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, E. J. Robertson, ed. (IRL, Oxford, 1987), pp. 113-152). A chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal, and the embryo brought to term to create a “knock out” animal. Progeny harboring the homologously recombined DNA in their germ cells can be identified by standard techniques and used to breed animals in which all cells of the animal contain the homologously recombined DNA. Knock out animals can be characterized, for example, for their ability to defend against certain pathological conditions or for their development of pathological conditions due to absence of a 151P3D4 polypeptide.

Methods for the Detection of 151P3D4

Another aspect of the present invention relates to methods for detecting 151P3D4 polynucleotides and 151P3D4-related proteins, as well as methods for identifying a cell that expresses 151P3D4. The expression profile of 151P3D4 makes it a diagnostic marker for metastasized disease. Accordingly, the status of 151P3D4 gene products provides information useful for predicting a variety of factors including susceptibility to advanced stage disease, rate of progression, and/or tumor aggressiveness. As discussed in detail herein, the status of 151P3D4 gene products in patient samples can be analyzed by a variety protocols that are well known in the art including immunohistochemical analysis, the variety of Northern blotting techniques including in situ hybridization, RT-PCR analysis (for example on laser capture micro-dissected samples), Western blot analysis and tissue array analysis.

More particularly, the invention provides assays for the detection of 151P3D4 polynucleotides in a biological sample, such as serum, bone, prostate, and other tissues, urine, semen, cell preparations, and the like. Detectable 151P3D4 polynucleotides include, for example, a 151P3D4 gene or fragment thereof, 151P3D4 mRNA, alternative splice variant 151P3D4 mRNAs, and recombinant DNA or RNA molecules that contain a 151P3D4 polynucleotide. A number of methods for amplifying and/or detecting the presence of 151P3D4 polynucleotides are well known in the art and can be employed in the practice of this aspect of the invention.

In one embodiment, a method for detecting a 151P3D4 mRNA in a biological sample comprises producing cDNA from the sample by reverse transcription using at least one primer; amplifying the cDNA so produced using a 151P3D4 polynucleotides as sense and antisense primers to amplify 151P3D4 cDNAs therein; and detecting the presence of the amplified 151P3D4 cDNA. Optionally, the sequence of the amplified 151P3D4 cDNA can be determined.

In another embodiment, a method of detecting a 151P3D4 gene in a biological sample comprises first isolating genomic DNA from the sample; amplifying the isolated genomic DNA using 151P3D4 polynucleotides as sense and antisense primers; and detecting the presence of the amplified 151P3D4 gene. Any number of appropriate sense and antisense probe combinations can be designed from a 151P3D4 nucleotide sequence (see, e.g., FIG. 2) and used for this purpose.

The invention also provides assays for detecting the presence of a 151P3D4 protein in a tissue or other biological sample such as serum, semen, bone, prostate, urine, cell preparations, and the like. Methods for detecting a 151P3D4-related protein are also well known and include, for example, immunoprecipitation, immunohistochemical analysis, Western blot analysis, molecular binding assays, ELISA, ELIFA and the like. For example, a method of detecting the presence of a 151P3D4-related protein in a biological sample comprises first contacting the sample with a 151P3D4 antibody, a 151P3D4-reactive fragment thereof, or a recombinant protein containing an antigen binding region of a 151P3D4 antibody; and then detecting the binding of 151P3D4-related protein in the sample.

Methods for identifying a cell that expresses 151P3D4 are also within the scope of the invention. In one embodiment, an assay for identifying a cell that expresses a 151P3D4 gene comprises detecting the presence of 151P3D4 mRNA in the cell. Methods for the detection of particular mRNAs in cells are well known and include, for example, hybridization assays using complementary DNA probes (such as in situ hybridization using labeled 151P3D4 riboprobes, Northern blot and related techniques) and various nucleic acid amplification assays (such as RT-PCR using complementary primers specific for 151P3D4, and other amplification type detection methods, such as, for example, branched DNA, SISBA, TMA and the like). Alternatively, an assay for identifying a cell that expresses a 151P3D4 gene comprises detecting the presence of 151P3D4-related protein in the cell or secreted by the cell. Various methods for the detection of proteins are well known in the art and are employed for the detection of 151P3D4-related proteins and cells that express 151P3D4-related proteins.

151P3D4 expression analysis is also useful as a tool for identifying and evaluating agents that modulate 151P3D4 gene expression. For example, 151P3D4 expression is significantly upregulated in prostate cancer, and is expressed in cancers of the tissues listed in Table I. Identification of a molecule or biological agent that inhibits 151P3D4 expression or over-expression in cancer cells is of therapeutic value. For example, such an agent can be identified by using a screen that quantifies 151P3D4 expression by RT-PCR, nucleic acid hybridization or antibody binding.

Methods for Monitoring the Status of 151P3D4-Related Genes and their Products

Oncogenesis is known to be a multistep process where cellular growth becomes progressively dysregulated and cells progress from a normal physiological state to precancerous and then cancerous states (see, e.g., Alers et al., Lab Invest. 77(5): 437-438 (1997) and Isaacs et al., Cancer Surv. 23: 19-32 (1995)). In this context, examining a biological sample for evidence of dysregulated cell growth (such as aberrant 151P3D4 expression in cancers) allows for early detection of such aberrant physiology, before a pathologic state such as cancer has progressed to a stage that therapeutic options are more limited and or the prognosis is worse. In such examinations, the status of 151P3D4 in a biological sample of interest can be compared, for example, to the status of 151P3D4 in a corresponding normal sample (e.g. a sample from that individual or alternatively another individual that is not affected by a pathology). An alteration in the status of 151P3D4 in the biological sample (as compared to the normal sample) provides evidence of dysregulated cellular growth. In addition to using a biological sample that is not affected by a pathology as a normal sample, one can also use a predetermined normative value such as a predetermined normal level of mRNA expression (see, e.g., Grever et al., J. Comp. Neurol. 1996 Dec. 9; 376(2): 306-14 and U.S. Pat. No. 5,837,501) to compare 151P3D4 status in a sample.

The term “status” in this context is used according to its art accepted meaning and refers to the condition or state of a gene and its products. Typically, skilled artisans use a number of parameters to evaluate the condition or state of a gene and its products. These include, but are not limited to the location of expressed gene products (including the location of 151P3D4 expressing cells) as well as the level, and biological activity of expressed gene products (such as 151P3D4 mRNA, polynucleotides and polypeptides). Typically, an alteration in the status of 151P3D4 comprises a change in the location of 151P3D4 and/or 151P3D4 expressing cells and/or an increase in 151P3D4 mRNA and/or protein expression.

151P3D4 status in a sample can be analyzed by a number of means well known in the art, including without limitation, immunohistochemical analysis, in situ hybridization, RT-PCR analysis on laser capture micro-dissected samples, Western blot analysis, and tissue array analysis. Typical protocols for evaluating the status of a 151P3D4 gene and gene products are found, for example in Ausubel et al. eds., 1995, Current Protocols In Molecular Biology, Units 2 (Northern Blotting), 4 (Southern Blotting), 15 (Immunoblotting) and 18 (PCR Analysis). Thus, the status of 151P3D4 in a biological sample is evaluated by various methods utilized by skilled artisans including, but not limited to genomic Southern analysis (to examine, for example perturbations in a 151P3D4 gene), Northern analysis and/or PCR analysis of 151P3D4 mRNA (to examine, for example alterations in the polynucleotide sequences or expression levels of 151P3D4 mRNAs), and, Western and/or immunohistochemical analysis (to examine, for example alterations in polypeptide sequences, alterations in polypeptide localization within a sample, alterations in expression levels of 151P3D4 proteins and/or associations of 151P3D4 proteins with polypeptide binding partners). Detectable 151P3D4 polynucleotides include, for example, a 151P3D4 gene or fragment thereof, 151P3D4 mRNA, alternative splice variants, 151P3D4 mRNAs, and recombinant DNA or RNA molecules containing a 151P3D4 polynucleotide.

The expression profile of 151P3D4 makes it a diagnostic marker for local and/or metastasized disease, and provides information on the growth or oncogenic potential of a biological sample. In particular, the status of 151P3D4 provides information useful for predicting susceptibility to particular disease stages, progression, and/or tumor aggressiveness. The invention provides methods and assays for determining 151P3D4 status and diagnosing cancers that express 151P3D4, such as cancers of the tissues listed in Table I. For example, because 151P3D4 mRNA is so highly expressed in prostate and other cancers relative to normal prostate tissue, assays that evaluate the levels of 151P3D4 mRNA transcripts or proteins in a biological sample can be used to diagnose a disease associated with 151P3D4 dysregulation, and can provide prognostic information useful in defining appropriate therapeutic options.

The expression status of 151P3D4 provides information including the presence, stage and location of dysplastic, precancerous and cancerous cells, predicting susceptibility to various stages of disease, and/or for gauging tumor aggressiveness. Moreover, the expression profile makes it useful as an imaging reagent for metastasized disease. Consequently, an aspect of the invention is directed to the various molecular prognostic and diagnostic methods for examining the status of 151P3D4 in biological samples such as those from individuals suffering from, or suspected of suffering from a pathology characterized by dysregulated cellular growth, such as cancer.

As described above, the status of 151P3D4 in a biological sample can be examined by a number of well-known procedures in the art. For example, the status of 151P3D4 in a biological sample taken from a specific location in the body can be examined by evaluating the sample for the presence or absence of 151P3D4 expressing cells (e.g. those that express 151P3D4 mRNAs or proteins). This examination can provide evidence of dysregulated cellular growth, for example, when 151P3D4-expressing cells are found in a biological sample that does not normally contain such cells (such as a lymph node), because such alterations in the status of 151P3D4 in a biological sample are often associated with dysregulated cellular growth. Specifically, one indicator of dysregulated cellular growth is the metastases of cancer cells from an organ of origin (such as the prostate) to a different area of the body (such as a lymph node). In this context, evidence of dysregulated cellular growth is important for example because occult lymph node metastases can be detected in a substantial proportion of patients with prostate cancer, and such metastases are associated with known predictors of disease progression (see, e.g., Murphy et al., Prostate 42(4): 315-317 (2000); Su et al., Semin. Surg. Oncol. 18(1): 17-28 (2000) and Freeman et al., J Urol 1995 August 154(2 Pt 1):474-8).

In one aspect, the invention provides methods for monitoring 151P3D4 gene products by determining the status of 151P3D4 gene products expressed by cells from an individual suspected of having a disease associated with dysregulated cell growth (such as hyperplasia or cancer) and then comparing the status so determined to the status of 151P3D4 gene products in a corresponding normal sample. The presence of aberrant 151P3D4 gene products in the test sample relative to the normal sample provides an indication of the presence of dysregulated cell growth within the cells of the individual.

In another aspect, the invention provides assays useful in determining the presence of cancer in an individual, comprising detecting a significant increase in 151P3D4 mRNA or protein expression in a test cell or tissue sample relative to expression levels in the corresponding normal cell or tissue. The presence of 151P3D4 mRNA can, for example, be evaluated in tissues including but not limited to those listed in Table I. The presence of significant 151P3D4 expression in any of these tissues is useful to indicate the emergence, presence and/or severity of a cancer, since the corresponding normal tissues do not express 151P3D4 mRNA or express it at lower levels.

In a related embodiment, 151P3D4 status is determined at the protein level rather than at the nucleic acid level. For example, such a method comprises determining the level of 151P3D4 protein expressed by cells in a test tissue sample and comparing the level so determined to the level of 151P3D4 expressed in a corresponding normal sample. In one embodiment, the presence of 151P3D4 protein is evaluated, for example, using immunohistochemical methods. 151P3D4 antibodies or binding partners capable of detecting 151P3D4 protein expression are used in a variety of assay formats well known in the art for this purpose.

In a further embodiment, one can evaluate the status of 151P3D4 nucleotide and amino acid sequences in a biological sample in order to identify perturbations in the structure of these molecules. These perturbations can include insertions, deletions, substitutions and the like. Such evaluations are useful because perturbations in the nucleotide and amino acid sequences are observed in a large number of proteins associated with a growth dysregulated phenotype (see, e.g., Marrogi et al., 1999, J. Cutan. Pathol. 26(8):369-378). For example, a mutation in the sequence of 151P3D4 may be indicative of the presence or promotion of a tumor. Such assays therefore have diagnostic and predictive value where a mutation in 151P3D4 indicates a potential loss of function or increase in tumor growth.

A wide variety of assays for observing perturbations in nucleotide and amino acid sequences are well known in the art. For example, the size and structure of nucleic acid or amino acid sequences of 151P3D4 gene products are observed by the Northern, Southern, Western, PCR and DNA sequencing protocols discussed herein. In addition, other methods for observing perturbations in nucleotide and amino acid sequences such as single strand conformation polymorphism analysis are well known in the art (see, e.g., U.S. Pat. Nos. 5,382,510 issued 7 Sep. 1999, and 5,952,170 issued 17 Jan. 1995).

Additionally, one can examine the methylation status of a 151P3D4 gene in a biological sample. Aberrant demethylation and/or hypermethylation of CpG islands in gene 5′ regulatory regions frequently occurs in immortalized and transformed cells, and can result in altered expression of various genes. For example, promoter hypermethylation of the pi-class glutathione S-transferase (a protein expressed in normal prostate but not expressed in >90% of prostate carcinomas) appears to permanently silence transcription of this gene and is the most frequently detected genomic alteration in prostate carcinomas (De Marzo et al., Am. J. Pathol. 155(6): 1985-1992 (1999)). In addition, this alteration is present in at least 70% of cases of high-grade prostatic intraepithelial neoplasia (PIN) (Brooks et al., Cancer Epidemiol. Biomarkers Prey., 1998, 7:531-536). In another example, expression of the LAGE-I tumor specific gene (which is not expressed in normal prostate but is expressed in 25-50% of prostate cancers) is induced by deoxy-azacytidine in lymphoblastoid cells, suggesting that tumoral expression is due to demethylation (Lethe et al., Int. J. Cancer 76(6): 903-908 (1998)). A variety of assays for examining methylation status of a gene are well known in the art. For example, one can utilize, in Southern hybridization approaches, methylation-sensitive restriction enzymes that cannot cleave sequences that contain methylated CpG sites to assess the methylation status of CpG islands. In addition, MSP (methylation specific PCR) can rapidly profile the methylation status of all the CpG sites present in a CpG island of a given gene. This procedure involves initial modification of DNA by sodium bisulfite (which will convert all unmethylated cytosines to uracil) followed by amplification using primers specific for methylated versus unmethylated DNA. Protocols involving methylation interference can also be found for example in Current Protocols In Molecular Biology, Unit 12, Frederick M. Ausubel et al. eds., 1995.

Gene amplification is an additional method for assessing the status of 151P3D4. Gene amplification is measured in a sample directly, for example, by conventional Southern blotting or Northern blotting to quantitate the transcription of mRNA (Thomas, 1980, Proc. Natl. Acad. Sci. USA, 77:5201-5205), dot blotting (DNA analysis), or in situ hybridization, using an appropriately labeled probe, based on the sequences provided herein. Alternatively, antibodies are employed that recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. The antibodies in turn are labeled and the assay carried out where the duplex is bound to a surface, so that upon the formation of duplex on the surface, the presence of antibody bound to the duplex can be detected.

Biopsied tissue or peripheral blood can be conveniently assayed for the presence of cancer cells using for example, Northern, dot blot or RT-PCR analysis to detect 151P3D4 expression. The presence of RT-PCR amplifiable 151P3D4 mRNA provides an indication of the presence of cancer. RT-PCR assays are well known in the art. RT-PCR detection assays for tumor cells in peripheral blood are currently being evaluated for use in the diagnosis and management of a number of human solid tumors. In the prostate cancer field, these include RT-PCR assays for the detection of cells expressing PSA and PSM (Verkaik et al., 1997, Urol. Res. 25:373-384; Ghossein et al., 1995, J. Clin. Oncol. 13:1195-2000; Heston et al., 1995, Clin. Chem. 41:1687-1688).

A further aspect of the invention is an assessment of the susceptibility that an individual has for developing cancer. In one embodiment, a method for predicting susceptibility to cancer comprises detecting 151P3D4 mRNA or 151P3D4 protein in a tissue sample, its presence indicating susceptibility to cancer, wherein the degree of 151P3D4 mRNA expression correlates to the degree of susceptibility. In a specific embodiment, the presence of 151P3D4 in prostate or other tissue is examined, with the presence of 151P3D4 in the sample providing an indication of prostate cancer susceptibility (or the emergence or existence of a prostate tumor). Similarly, one can evaluate the integrity 151P3D4 nucleotide and amino acid sequences in a biological sample, in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like. The presence of one or more perturbations in 151P3D4 gene products in the sample is an indication of cancer susceptibility (or the emergence or existence of a tumor).

The invention also comprises methods for gauging tumor aggressiveness. In one embodiment, a method for gauging aggressiveness of a tumor comprises determining the level of 151P3D4 mRNA or 151P3D4 protein expressed by tumor cells, comparing the level so determined to the level of 151P3D4 mRNA or 151P3D4 protein expressed in a corresponding normal tissue taken from the same individual or a normal tissue reference sample, wherein the degree of 151P3D4 mRNA or 151P3D4 protein expression in the tumor sample relative to the normal sample indicates the degree of aggressiveness. In a specific embodiment, aggressiveness of a tumor is evaluated by determining the extent to which 151P3D4 is expressed in the tumor cells, with higher expression levels indicating more aggressive tumors. Another embodiment is the evaluation of the integrity of 151P3D4 nucleotide and amino acid sequences in a biological sample, in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like. The presence of one or more perturbations indicates more aggressive tumors.

Another embodiment of the invention is directed to methods for observing the progression of a malignancy in an individual over time. In one embodiment, methods for observing the progression of a malignancy in an individual over time comprise determining the level of 151P3D4 mRNA or 151P3D4 protein expressed by cells in a sample of the tumor, comparing the level so determined to the level of 151P3D4 mRNA or 151P3D4 protein expressed in an equivalent tissue sample taken from the same individual at a different time, wherein the degree of 151P3D4 mRNA or 151P3D4 protein expression in the tumor sample over time provides information on the progression of the cancer. In a specific embodiment, the progression of a cancer is evaluated by determining 151P3D4 expression in the tumor cells over time, where increased expression over time indicates a progression of the cancer. Also, one can evaluate the integrity 151P3D4 nucleotide and amino acid sequences in a biological sample in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like, where the presence of one or more perturbations indicates a progression of the cancer.

The above diagnostic approaches can be combined with any one of a wide variety of prognostic and diagnostic protocols known in the art. For example, another embodiment of the invention is directed to methods for observing a coincidence between the expression of 151P3D4 gene and 151P3D4 gene products (or perturbations in 151P3D4 gene and 151P3D4 gene products) and a factor that is associated with malignancy, as a means for diagnosing and prognosticating the status of a tissue sample. A wide variety of factors associated with malignancy can be utilized, such as the expression of genes associated with malignancy (e.g. PSA, PSCA and PSM expression for prostate cancer etc.) as well as gross cytological observations (see, e.g., Bocking et al., 1984, Anal. Quant. Cytol. 6(2):74-88; Epstein, 1995, Hum. Pathol. 26(2):223-9; Thorson et al., 1998, Mod. Pathol. 11(6):543-51; Baisden et al., 1999, Am. J. Surg. Pathol. 23(8):918-24). Methods for observing a coincidence between the expression of 151P3D4 gene and 151P3D4 gene products (or perturbations in 151P3D4 gene and 151P3D4 gene products) and another factor that is associated with malignancy are useful, for example, because the presence of a set of specific factors that coincide with disease provides information crucial for diagnosing and prognosticating the status of a tissue sample.

In one embodiment, methods for observing a coincidence between the expression of 151P3D4 gene and 151P3D4 gene products (or perturbations in 151P3D4 gene and 151P3D4 gene products) and another factor associated with malignancy entails detecting the overexpression of 151P3D4 mRNA or protein in a tissue sample, detecting the overexpression of PSA mRNA or protein in a tissue sample (or PSCA or PSM expression), and observing a coincidence of 151P3D4 mRNA or protein and PSA mRNA or protein overexpression (or PSCA or PSM expression). In a specific embodiment, the expression of 151P3D4 and PSA mRNA in prostate tissue is examined, where the coincidence of 151P3D4 and PSA mRNA overexpression in the sample indicates the existence of prostate cancer, prostate cancer susceptibility or the emergence or status of a prostate tumor.

Methods for detecting and quantifying the expression of 151P3D4 mRNA or protein are described herein, and standard nucleic acid and protein detection and quantification technologies are well known in the art. Standard methods for the detection and quantification of 151P3D4 mRNA include in situ hybridization using labeled 151P3D4 riboprobes, Northern blot and related techniques using 151P3D4 polynucleotide probes, RT-PCR analysis using primers specific for 151P3D4, and other amplification type detection methods, such as, for example, branched DNA, SISBA, TMA and the like. In a specific embodiment, semi-quantitative RT-PCR is used to detect and quantify 151P3D4 mRNA expression. Any number of primers capable of amplifying 151P3D4 can be used for this purpose, including but not limited to the various primer sets specifically described herein. In a specific embodiment, polyclonal or monoclonal antibodies specifically reactive with the wild-type 151P3D4 protein can be used in an immunohistochemical assay of biopsied tissue.

Identification of Molecules that Interact with 151P3D4

The 151P3D4 protein and nucleic acid sequences disclosed herein allow a skilled artisan to identify proteins, small molecules and other agents that interact with 151P3D4, as well as pathways activated by 151P3D4 via any one of a variety of art accepted protocols. For example, one can utilize one of the so-called interaction trap systems (also referred to as the “two-hybrid assay”). In such systems, molecules interact and reconstitute a transcription factor which directs expression of a reporter gene, whereupon the expression of the reporter gene is assayed. Other systems identify protein-protein interactions in vivo through reconstitution of a eukaryotic transcriptional activator, see, e.g., U.S. Pat. Nos. 5,955,280 issued 21 Sep. 1999, 5,925,523 issued 20 Jul. 1999, 5,846,722 issued 8 Dec. 1998 and 6,004,746 issued 21 Dec. 1999. Algorithms are also available in the art for genome-based predictions of protein function (see, e.g., Marcotte, et al., Nature 402: 4 Nov. 1999, 83-86).

Alternatively one can screen peptide libraries to identify molecules that interact with 151P3D4 protein sequences. In such methods, peptides that bind to 151P3D4 are identified by screening libraries that encode a random or controlled collection of amino acids. Peptides encoded by the libraries are expressed as fusion proteins of bacteriophage coat proteins, the bacteriophage particles are then screened against the 151P3D4 protein(s).

Accordingly, peptides having a wide variety of uses, such as therapeutic, prognostic or diagnostic reagents, are thus identified without any prior information on the structure of the expected ligand or receptor molecule. Typical peptide libraries and screening methods that can be used to identify molecules that interact with 151P3D4 protein sequences are disclosed for example in U.S. Pat. Nos. 5,723,286 issued 3 Mar. 1998 and 5,733,731 issued 31 Mar. 1998.

Alternatively, cell lines that express 151P3D4 are used to identify protein-protein interactions mediated by 151P3D4. Such interactions can be examined using immunoprecipitation techniques (see, e.g., Hamilton B. J., et al. Biochem. Biophys. Res. Commun. 1999, 261:646-51). 151P3D4 protein can be immunoprecipitated from 151P3D4-expressing cell lines using anti-151P3D4 antibodies. Alternatively, antibodies against His-tag can be used in a cell line engineered to express fusions of 151P3D4 and a His-tag (vectors mentioned above). The immunoprecipitated complex can be examined for protein association by procedures such as Western blotting, ³⁵S-methionine labeling of proteins, protein microsequencing, silver staining and two-dimensional gel electrophoresis.

Small molecules and ligands that interact with 151P3D4 can be identified through related embodiments of such screening assays. For example, small molecules can be identified that interfere with protein function, including molecules that interfere with 151P3D4's ability to mediate phosphorylation and de-phosphorylation, interaction with DNA or RNA molecules as an indication of regulation of cell cycles, second messenger signaling or tumorigenesis. Similarly, small molecules that modulate 151P3D4-related ion channel, protein pump, or cell communication functions are identified and used to treat patients that have a cancer that expresses 151P3D4 (see, e.g., Hille, B., Ionic Channels of Excitable Membranes 2^nd Ed., Sinauer Assoc., Sunderland, Mass., 1992). Moreover, ligands that regulate 151P3D4 function can be identified based on their ability to bind 151P3D4 and activate a reporter construct. Typical methods are discussed for example in U.S. Pat. No. 5,928,868 issued 27 Jul. 1999, and include methods for forming hybrid ligands in which at least one ligand is a small molecule. In an illustrative embodiment, cells engineered to express a fusion protein of 151P3D4 and a DNA-binding protein are used to co-express a fusion protein of a hybrid ligand/small molecule and a cDNA library transcriptional activator protein. The cells further contain a reporter gene, the expression of which is conditioned on the proximity of the first and second fusion proteins to each other, an event that occurs only if the hybrid ligand binds to target sites on both hybrid proteins. Those cells that express the reporter gene are selected and the unknown small molecule or the unknown ligand is identified. This method provides a means of identifying modulators which activate or inhibit 151P3D4.

An embodiment of this invention comprises a method of screening for a molecule that interacts with a 151P3D4 amino acid sequence shown in FIG. 2 or FIG. 3, comprising the steps of contacting a population of molecules with a 151P3D4 amino acid sequence, allowing the population of molecules and the 151P3D4 amino acid sequence to interact under conditions that facilitate an interaction, determining the presence of a molecule that interacts with the 151P3D4 amino acid sequence, and then separating molecules that do not interact with the 151P3D4 amino acid sequence from molecules that do. In a specific embodiment, the method further comprises purifying, characterizing and identifying a molecule that interacts with the 151P3D4 amino acid sequence. The identified molecule can be used to modulate a function performed by 151P3D4. In a preferred embodiment, the 151P3D4 amino acid sequence is contacted with a library of peptides.

Therapeutic Methods and Compositions

The identification of 151P3D4 as a protein that is normally expressed in a restricted set of tissues, but which is also expressed in prostate and other cancers, opens a number of therapeutic approaches to the treatment of such cancers. As contemplated herein, 151P3D4 functions as a transcription factor involved in activating tumor-promoting genes or repressing genes that block tumorigenesis.

Accordingly, therapeutic approaches that inhibit the activity of a 151P3D4 protein are useful for patients suffering from a cancer that expresses 151P3D4. These therapeutic approaches generally fall into two classes. One class comprises various methods for inhibiting the binding or association of a 151P3D4 protein with its binding partner or with other proteins. Another class comprises a variety of methods for inhibiting the transcription of a 151P3D4 gene or translation of 151P3D4 mRNA.

Anti-Cancer Vaccines

The invention provides cancer vaccines comprising a 151P3D4-related protein or 151P3D4-related nucleic acid. In view of the expression of 151P3D4, cancer vaccines prevent and/or treat 151P3D4-expressing cancers with minimal or no effects on non-target tissues. The use of a tumor antigen in a vaccine that generates humoral and/or cell-mediated immune responses as anti-cancer therapy is well known in the art and has been employed in prostate cancer using human PSMA and rodent PAP immunogens (Hodge et al., 1995, Int. J. Cancer 63:231-237; Fong et al., 1997, J. Immunol. 159:3113-3117).

Such methods can be readily practiced by employing a 151P3D4-related protein, or a 151P3D4-encoding nucleic acid molecule and recombinant vectors capable of expressing and presenting the 151P3D4 immunogen (which typically comprises a number of antibody or T cell epitopes). Skilled artisans understand that a wide variety of vaccine systems for delivery of immunoreactive epitopes are known in the art (see, e.g., Heryln et al., Ann Med 1999 February 31(1):66-78; Maruyama et al., Cancer Immunol Immunother 2000 June 49(3):123-32) Briefly, such methods of generating an immune response (e.g. humoral and/or cell-mediated) in a mammal, comprise the steps of: exposing the mammal's immune system to an immunoreactive epitope (e.g. an epitope present in a 151P3D4 protein shown in FIG. 3 or analog or homolog thereof) so that the mammal generates an immune response that is specific for that epitope (e.g. generates antibodies that specifically recognize that epitope). In a preferred method, a 151P3D4 immunogen contains a biological motif, see e.g., Tables V-XVIII and XXII-LI, or a peptide of a size range from 151P3D4 indicated in FIG. 5, FIG. 6, FIG. 7, FIG. 8, and FIG. 9.

The entire 151P3D4 protein, immunogenic regions or epitopes thereof can be combined and delivered by various means. Such vaccine compositions can include, for example, lipopeptides (e.g., Vitiello, A. et al., J. Clin. Invest. 95:341, 1995), peptide compositions encapsulated in poly(DL-lactide-co-glycolide) (“PLG”) microspheres (see, e.g., Eldridge, et al., Molec. Immunol. 28:287-294, 1991: Alonso et al., Vaccine 12:299-306, 1994; Jones et al., Vaccine 13:675-681, 1995), peptide compositions contained in immune stimulating complexes (ISCOMS) (see, e.g., Takahashi et al., Nature 344:873-875, 1990; Hu et al., Clin Exp Immunol. 113:235-243, 1998), multiple antigen peptide systems (MAPs) (see e.g., Tam, J. P., Proc. Natl. Acad. Sci. U.S.A. 85:5409-5413, 1988; Tam, J. P., J. Immunol. Methods 196:17-32, 1996), peptides formulated as multivalent peptides; peptides for use in ballistic delivery systems, typically crystallized peptides, viral delivery vectors (Perkus, M. E. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 379, 1996; Chakrabarti, S. et al., Nature 320:535, 1986; Hu, S. L. et al., Nature 320:537, 1986; Kieny, M.-P. et al., AIDS Bio/Technology 4:790, 1986; Top, F. H. et al., J. Infect. Dis. 124:148, 1971; Chanda, P. K. et al., Virology 175:535, 1990), particles of viral or synthetic origin (e.g., Kofler, N. et al., J. Immunol. Methods. 192:25, 1996; Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993; Falo, L. D., Jr. et al., Nature Med. 7:649, 1995), adjuvants (Warren, H. S., Vogel, F. R., and Chedid, L. A. Annu. Rev. Immunol. 4:369, 1986; Gupta, R. K. et al., Vaccine 11:293, 1993), liposomes (Reddy, R. et al., J. Immunol. 148:1585, 1992; Rock, K. L., Immunol. Today 17:131, 1996), or, naked or particle absorbed cDNA (Ulmer, J. B. et al., Science 259:1745, 1993; Robinson, H. L., Hunt, L. A., and Webster, R. G., Vaccine 11:957, 1993; Shiver, J. W. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 423, 1996; Cease, K. B., and Berzofsky, J. A., Annu. Rev. Immunol. 12:923, 1994 and Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993). Toxin-targeted delivery technologies, also known as receptor mediated targeting, such as those of Avant Immunotherapeutics, Inc. (Needham, Mass.) may also be used.

In patients with 151P3D4-associated cancer, the vaccine compositions of the invention can also be used in conjunction with other treatments used for cancer, e.g., surgery, chemotherapy, drug therapies, radiation therapies, etc. including use in combination with immune adjuvants such as IL-2, IL-12, GM-CSF, and the like.

Cellular Vaccines:

CTL epitopes can be determined using specific algorithms to identify peptides within 151P3D4 protein that bind corresponding HLA alleles (see e.g., Table IV; Epimer™ and Epimatrix™, Brown University (URL located on the World Wide Web at (.brown.edu/Research/TB-HIV_Lab/epimatrix/epimatrix.html)); and, BIMAS, (URL bimas.dcrt.nih.gov/; SYFPEITHI at URL syfpeithi.bmi-heidelberg.com/). In a preferred embodiment, a 151P3D4 immunogen contains one or more amino acid sequences identified using techniques well known in the art, such as the sequences shown in Tables V-XVIII and XXII-LI or a peptide of 8, 9, 10 or 11 amino acids specified by an HLA Class I motif/supermotif (e.g., Table IV (A), Table IV (D), or Table IV (E)) and/or a peptide of at least 9 amino acids that comprises an HLA Class II motif/supermotif (e.g., Table IV (B) or Table IV (C)). As is appreciated in the art, the HLA Class I binding groove is essentially closed ended so that peptides of only a particular size range can fit into the groove and be bound, generally HLA Class I epitopes are 8, 9, 10, or 11 amino acids long. In contrast, the HLA Class II binding groove is essentially open ended; therefore a peptide of about 9 or more amino acids can be bound by an HLA Class II molecule. Due to the binding groove differences between HLA Class I and II, HLA Class I motifs are length specific, i.e., position two of a Class I motif is the second amino acid in an amino to carboxyl direction of the peptide. The amino acid positions in a Class II motif are relative only to each other, not the overall peptide, i.e., additional amino acids can be attached to the amino and/or carboxyl termini of a motif-bearing sequence. HLA Class II epitopes are often 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 amino acids long, or longer than 25 amino acids.

Antibody-Based Vaccines

A wide variety of methods for generating an immune response in a mammal are known in the art (for example as the first step in the generation of hybridomas). Methods of generating an immune response in a mammal comprise exposing the mammal's immune system to an immunogenic epitope on a protein (e.g. a 151P3D4 protein) so that an immune response is generated. A typical embodiment consists of a method for generating an immune response to 151P3D4 in a host, by contacting the host with a sufficient amount of at least one 151P3D4 B cell or cytotoxic T-cell epitope or analog thereof; and at least one periodic interval thereafter re-contacting the host with the 151P3D4 B cell or cytotoxic T-cell epitope or analog thereof. A specific embodiment consists of a method of generating an immune response against a 151P3D4-related protein or a man-made multiepitopic peptide comprising: administering 151P3D4 immunogen (e.g. a 151P3D4 protein or a peptide fragment thereof, a 151P3D4 fusion protein or analog etc.) in a vaccine preparation to a human or another mammal. Typically, such vaccine preparations further contain a suitable adjuvant (see, e.g., U.S. Pat. No. 6,146,635) or a universal helper epitope such as a PADRE™ peptide (Epimmune Inc., San Diego, Calif.; see, e.g., Alexander et al., J. Immunol. 2000 164(3); 164(3): 1625-1633; Alexander et al., Immunity 1994 1(9): 751-761 and Alexander et al., Immunol. Res. 1998 18(2): 79-92). An alternative method comprises generating an immune response in an individual against a 151P3D4 immunogen by: administering in vivo to muscle or skin of the individual's body a DNA molecule that comprises a DNA sequence that encodes a 151P3D4 immunogen, the DNA sequence operatively linked to regulatory sequences which control the expression of the DNA sequence; wherein the DNA molecule is taken up by cells, the DNA sequence is expressed in the cells and an immune response is generated against the immunogen (see, e.g., U.S. Pat. No. 5,962,428). Optionally a genetic vaccine facilitator such as anionic lipids; saponins; lectins; estrogenic compounds; hydroxylated lower alkyls; dimethyl sulfoxide; and urea is also administered. In addition, an antiidiotypic antibody can be administered that mimics 151P3D4, in order to generate a response to the target antigen.

Nucleic Acid Vaccines:

Vaccine compositions of the invention include nucleic acid-mediated modalities. DNA or RNA that encode protein(s) of the invention can be administered to a patient. Genetic immunization methods can be employed to generate prophylactic or therapeutic humoral and cellular immune responses directed against cancer cells expressing 151P3D4. Constructs comprising DNA encoding a 151P3D4-related protein/immunogen and appropriate regulatory sequences can be injected directly into muscle or skin of an individual, such that the cells of the muscle or skin take-up the construct and express the encoded 151P3D4 protein/immunogen. Alternatively, a vaccine comprises a 151P3D4-related protein. Expression of the 151P3D4-related protein immunogen results in the generation of prophylactic or therapeutic humoral and cellular immunity against cells that bear a 151P3D4 protein. Various prophylactic and therapeutic genetic immunization techniques known in the art can be used (for review, see information and references published at Internet address located on the World Wide Web at .genweb.com). Nucleic acid-based delivery is described, for instance, in Wolff et. al., Science 247:1465 (1990) as well as U.S. Pat. Nos. 5,580,859; 5,589,466; 5,804,566; 5,739,118; 5,736,524; 5,679,647; WO 98/04720. Examples of DNA-based delivery technologies include “naked DNA”, facilitated (bupivicaine, polymers, peptide-mediated) delivery, cationic lipid complexes, and particle-mediated (“gene gun”) or pressure-mediated delivery (see, e.g., U.S. Pat. No. 5,922,687).

For therapeutic or prophylactic immunization purposes, proteins of the invention can be expressed via viral or bacterial vectors. Various viral gene delivery systems that can be used in the practice of the invention include, but are not limited to, vaccinia, fowlpox, canarypox, adenovirus, influenza, poliovirus, adeno-associated virus, lentivirus, and sindbis virus (see, e.g., Restifo, 1996, Curr. Opin. Immunol. 8:658-663; Tsang et al. J. Natl. Cancer Inst. 87:982-990 (1995)). Non-viral delivery systems can also be employed by introducing naked DNA encoding a 151P3D4-related protein into the patient (e.g., intramuscularly or intradermally) to induce an anti-tumor response.

Vaccinia virus is used, for example, as a vector to express nucleotide sequences that encode the peptides of the invention. Upon introduction into a host, the recombinant vaccinia virus expresses the protein immunogenic peptide, and thereby elicits a host immune response. Vaccinia vectors and methods useful in immunization protocols are described in, e.g., U.S. Pat. No. 4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG vectors are described in Stover et al., Nature 351:456-460 (1991). A wide variety of other vectors useful for therapeutic administration or immunization of the peptides of the invention, e.g. adeno and adeno-associated virus vectors, retroviral vectors, Salmonella typhi vectors, detoxified anthrax toxin vectors, and the like, will be apparent to those skilled in the art from the description herein.

Thus, gene delivery systems are used to deliver a 151P3D4-related nucleic acid molecule. In one embodiment, the full-length human 151P3D4 cDNA is employed. In another embodiment, 151P3D4 nucleic acid molecules encoding specific cytotoxic T lymphocyte (CTL) and/or antibody epitopes are employed.

Ex Vivo Vaccines

Various ex vivo strategies can also be employed to generate an immune response. One approach involves the use of antigen presenting cells (APCs) such as dendritic cells (DC) to present 151P3D4 antigen to a patient's immune system. Dendritic cells express MHC class I and II molecules, B7 co-stimulator, and IL-12, and are thus highly specialized antigen presenting cells. In prostate cancer, autologous dendritic cells pulsed with peptides of the prostate-specific membrane antigen (PSMA) are being used in a Phase I clinical trial to stimulate prostate cancer patients' immune systems (Tjoa et al., 1996, Prostate 28:65-69; Murphy et al., 1996, Prostate 29:371-380). Thus, dendritic cells can be used to present 151P3D4 peptides to T cells in the context of MHC class I or II molecules. In one embodiment, autologous dendritic cells are pulsed with 151P3D4 peptides capable of binding to MHC class I and/or class II molecules. In another embodiment, dendritic cells are pulsed with the complete 151P3D4 protein. Yet another embodiment involves engineering the overexpression of a 151P3D4 gene in dendritic cells using various implementing vectors known in the art, such as adenovirus (Arthur et al., 1997, Cancer Gene Ther. 4:17-25), retrovirus (Henderson et al., 1996, Cancer Res. 56:3763-3770), lentivirus, adeno-associated virus, DNA transfection (Ribas et al., 1997, Cancer Res. 57:2865-2869), or tumor-derived RNA transfection (Ashley et al., 1997, J. Exp. Med. 186:1177-1182). Cells that express 151P3D4 can also be engineered to express immune modulators, such as GM-CSF, and used as immunizing agents.

151P3D4 as a Target for Antibody-Based Therapy

151P3D4 is an attractive target for antibody-based therapeutic strategies. A number of antibody strategies are known in the art for targeting both extracellular and intracellular molecules (see, e.g., complement and ADCC mediated killing as well as the use of intrabodies). Because 151P3D4 is expressed by cancer cells of various lineages relative to corresponding normal cells, systemic administration of 151P3D4-immunoreactive compositions are prepared that exhibit excellent sensitivity without toxic, non-specific and/or non-target effects caused by binding of the immunoreactive composition to non-target organs and tissues. Antibodies specifically reactive with domains of 151P3D4 are useful to treat 151P3D4-expressing cancers systemically, either as conjugates with a toxin or therapeutic agent, or as naked antibodies capable of inhibiting cell proliferation or function.

151P3D4 antibodies can be introduced into a patient such that the antibody binds to 151P3D4 and modulates a function, such as an interaction with a binding partner, and consequently mediates destruction of the tumor cells and/or inhibits the growth of the tumor cells. Mechanisms by which such antibodies exert a therapeutic effect can include complement-mediated cytolysis, antibody-dependent cellular cytotoxicity, modulation of the physiological function of 151P3D4, inhibition of ligand binding or signal transduction pathways, modulation of tumor cell differentiation, alteration of tumor angiogenesis factor profiles, and/or apoptosis.

Those skilled in the art understand that antibodies can be used to specifically target and bind immunogenic molecules such as an immunogenic region of a 151P3D4 sequence shown in FIG. 2 or FIG. 3. In addition, skilled artisans understand that it is routine to conjugate antibodies to cytotoxic agents (see, e.g., Slevers et al. Blood 93:11 3678-3684 (Jun. 1, 1999)). When cytotoxic and/or therapeutic agents are delivered directly to cells, such as by conjugating them to antibodies specific for a molecule expressed by that cell (e.g. 151P3D4), the cytotoxic agent will exert its known biological effect (i.e. cytotoxicity) on those cells.

A wide variety of compositions and methods for using antibody-cytotoxic agent conjugates to kill cells are known in the art. In the context of cancers, typical methods entail administering to an animal having a tumor a biologically effective amount of a conjugate comprising a selected cytotoxic and/or therapeutic agent linked to a targeting agent (e.g. an anti-151P3D4 antibody) that binds to a marker (e.g. 151P3D4) expressed, accessible to binding or localized on the cell surfaces. A typical embodiment is a method of delivering a cytotoxic and/or therapeutic agent to a cell expressing 151P3D4, comprising conjugating the cytotoxic agent to an antibody that immunospecifically binds to a 151P3D4 epitope, and, exposing the cell to the antibody-agent conjugate. Another illustrative embodiment is a method of treating an individual suspected of suffering from metastasized cancer, comprising a step of administering parenterally to said individual a pharmaceutical composition comprising a therapeutically effective amount of an antibody conjugated to a cytotoxic and/or therapeutic agent.

Cancer immunotherapy using anti-151P3D4 antibodies can be done in accordance with various approaches that have been successfully employed in the treatment of other types of cancer, including but not limited to colon cancer (Arlen et al., 1998, Crit. Rev. Immunol. 18:133-138), multiple myeloma (Ozaki et al., 1997, Blood 90:3179-3186, Tsunenari et al., 1997, Blood 90:2437-2444), gastric cancer (Kasprzyk et al., 1992, Cancer Res. 52:2771-2776), B-cell lymphoma (Funakoshi et al., 1996, J. Immunother. Emphasis Tumor Immunol. 19:93-101), leukemia (Zhong et al., 1996, Leuk. Res. 20:581-589), colorectal cancer (Moun et al., 1994, Cancer Res. 54:6160-6166; Velders et al., 1995, Cancer Res. 55:4398-4403), and breast cancer (Shepard et al., 1991, J. Clin. Immunol. 11:117-127). Some therapeutic approaches involve conjugation of naked antibody to a toxin or radioisotope, such as the conjugation of Y⁹¹ or I¹³¹ to anti-CD20 antibodies (e.g., Zevalin™, IDEC Pharmaceuticals Corp. or Bexxar™, Coulter Pharmaceuticals), while others involve co-administration of antibodies and other therapeutic agents, such as Herceptin™ (trastuzumab) with paclitaxel (Genentech, Inc.). The antibodies can be conjugated to a therapeutic agent. To treat prostate cancer, for example, 151P3D4 antibodies can be administered in conjunction with radiation, chemotherapy or hormone ablation. Also, antibodies can be conjugated to a toxin such as calicheamicin (e.g., Mylotarg™, Wyeth-Ayerst, Madison, N.J., a recombinant humanized IgG₄ kappa antibody conjugated to antitumor antibiotic calicheamicin) or a maytansinoid (e.g., taxane-based Tumor-Activated Prodrug, TAP, platform, ImmunoGen, Cambridge, Mass., also see e.g., U.S. Pat. No. 5,416,064).

Although 151P3D4 antibody therapy is useful for all stages of cancer, antibody therapy can be particularly appropriate in advanced or metastatic cancers. Treatment with the antibody therapy of the invention is indicated for patients who have received one or more rounds of chemotherapy. Alternatively, antibody therapy of the invention is combined with a chemotherapeutic or radiation regimen for patients who have not received chemotherapeutic treatment. Additionally, antibody therapy can enable the use of reduced dosages of concomitant chemotherapy, particularly for patients who do not tolerate the toxicity of the chemotherapeutic agent very well. Fan et al. (Cancer Res. 53:4637-4642, 1993), Prewett et al. (International J. of Onco. 9:217-224, 1996), and Hancock et al. (Cancer Res. 51:4575-4580, 1991) describe the use of various antibodies together with chemotherapeutic agents.

Although 151P3D4 antibody therapy is useful for all stages of cancer, antibody therapy can be particularly appropriate in advanced or metastatic cancers. Treatment with the antibody therapy of the invention is indicated for patients who have received one or more rounds of chemotherapy. Alternatively, antibody therapy of the invention is combined with a chemotherapeutic or radiation regimen for patients who have not received chemotherapeutic treatment. Additionally, antibody therapy can enable the use of reduced dosages of concomitant chemotherapy, particularly for patients who do not tolerate the toxicity of the chemotherapeutic agent very well.

Cancer patients can be evaluated for the presence and level of 151P3D4 expression, preferably using immunohistochemical assessments of tumor tissue, quantitative 151P3D4 imaging, or other techniques that reliably indicate the presence and degree of 151P3D4 expression. Immunohistochemical analysis of tumor biopsies or surgical specimens is preferred for this purpose. Methods for immunohistochemical analysis of tumor tissues are well known in the art.

Anti-151P3D4 monoclonal antibodies that treat prostate and other cancers include those that initiate a potent immune response against the tumor or those that are directly cytotoxic. In this regard, anti-151P3D4 monoclonal antibodies (mAbs) can elicit tumor cell lysis by either complement-mediated or antibody-dependent cell cytotoxicity (ADCC) mechanisms, both of which require an intact Fc portion of the immunoglobulin molecule for interaction with effector cell Fc receptor sites on complement proteins. In addition, anti-151P3D4 mAbs that exert a direct biological effect on tumor growth are useful to treat cancers that express 151P3D4. Mechanisms by which directly cytotoxic mAbs act include: inhibition of cell growth, modulation of cellular differentiation, modulation of tumor angiogenesis factor profiles, and the induction of apoptosis. The mechanism(s) by which a particular anti-151P3D4 mAb exerts an anti-tumor effect is evaluated using any number of in vitro assays that evaluate cell death such as ADCC, ADMMC, complement-mediated cell lysis, and so forth, as is generally known in the art.

In some patients, the use of murine or other non-human monoclonal antibodies, or human/mouse chimeric mAbs can induce moderate to strong immune responses against the non-human antibody. This can result in clearance of the antibody from circulation and reduced efficacy. In the most severe cases, such an immune response can lead to the extensive formation of immune complexes which, potentially, can cause renal failure. Accordingly, preferred monoclonal antibodies used in the therapeutic methods of the invention are those that are either fully human or humanized and that bind specifically to the target 151P3D4 antigen with high affinity but exhibit low or no antigenicity in the patient.

Therapeutic methods of the invention contemplate the administration of single anti-151P3D4 mAbs as well as combinations, or cocktails, of different mAbs. Such mAb cocktails can have certain advantages inasmuch as they contain mAbs that target different epitopes, exploit different effector mechanisms or combine directly cytotoxic mAbs with mAbs that rely on immune effector functionality. Such mAbs in combination can exhibit synergistic therapeutic effects. In addition, anti-151P3D4 mAbs can be administered concomitantly with other therapeutic modalities, including but not limited to various chemotherapeutic agents, androgen-blockers, immune modulators (e.g., IL-2, GM-CSF), surgery or radiation. The anti-151P3D4 mAbs are administered in their “naked” or unconjugated form, or can have a therapeutic agent(s) conjugated to them.

Anti-151P3D4 antibody formulations are administered via any route capable of delivering the antibodies to a tumor cell. Routes of administration include, but are not limited to, intravenous, intraperitoneal, intramuscular, intratumor, intradermal, and the like. Treatment generally involves repeated administration of the anti-151P3D4 antibody preparation, via an acceptable route of administration such as intravenous injection (IV), typically at a dose in the range of about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 mg/kg body weight. In general, doses in the range of 10-1000 mg mAb per week are effective and well tolerated.

Based on clinical experience with the Herceptin™ mAb in the treatment of metastatic breast cancer, an initial loading dose of approximately 4 mg/kg patient body weight IV, followed by weekly doses of about 2 mg/kg IV of the anti-151P3D4 mAb preparation represents an acceptable dosing regimen. Preferably, the initial loading dose is administered as a 90 minute or longer infusion. The periodic maintenance dose is administered as a 30 minute or longer infusion, provided the initial dose was well tolerated. As appreciated by those of skill in the art, various factors can influence the ideal dose regimen in a particular case. Such factors include, for example, the binding affinity and half life of the Ab or mAbs used, the degree of 151P3D4 expression in the patient, the extent of circulating shed 151P3D4 antigen, the desired steady-state antibody concentration level, frequency of treatment, and the influence of chemotherapeutic or other agents used in combination with the treatment method of the invention, as well as the health status of a particular patient.

Optionally, patients should be evaluated for the levels of 151P3D4 in a given sample (e.g. the levels of circulating 151P3D4 antigen and/or 151P3D4 expressing cells) in order to assist in the determination of the most effective dosing regimen, etc. Such evaluations are also used for monitoring purposes throughout therapy, and are useful to gauge therapeutic success in combination with the evaluation of other parameters (for example, urine cytology and/or ImmunoCyt levels in bladder cancer therapy, or by analogy, serum PSA levels in prostate cancer therapy).

Anti-idiotypic anti-151P3D4 antibodies can also be used in anti-cancer therapy as a vaccine for inducing an immune response to cells expressing a 151P3D4-related protein. In particular, the generation of anti-idiotypic antibodies is well known in the art; this methodology can readily be adapted to generate anti-idiotypic anti-151P3D4 antibodies that mimic an epitope on a 151P3D4-related protein (see, for example, Wagner et al., 1997, Hybridoma 16: 33-40; Foon et al., 1995, J. Clin. Invest. 96:334-342; Herlyn et al., 1996, Cancer Immunol. Immunother. 43:65-76). Such an anti-idiotypic antibody can be used in cancer vaccine strategies.

151P3D4 as a Target for Cellular Immune Responses

Vaccines and methods of preparing vaccines that contain an immunogenically effective amount of one or more HLA-binding peptides as described herein are further embodiments of the invention. Furthermore, vaccines in accordance with the invention encompass compositions of one or more of the claimed peptides. A peptide can be present in a vaccine individually. Alternatively, the peptide can exist as a homopolymer comprising multiple copies of the same peptide, or as a heteropolymer of various peptides. Polymers have the advantage of increased immunological reaction and, where different peptide epitopes are used to make up the polymer, the additional ability to induce antibodies and/or CTLs that react with different antigenic determinants of the pathogenic organism or tumor-related peptide targeted for an immune response. The composition can be a naturally occurring region of an antigen or can be prepared, e.g., recombinantly or by chemical synthesis.

Carriers that can be used with vaccines of the invention are well known in the art, and include, e.g., thyroglobulin, albumins such as human serum albumin, tetanus toxoid, polyamino acids such as poly L-lysine, poly L-glutamic acid, influenza, hepatitis B virus core protein, and the like. The vaccines can contain a physiologically tolerable (i.e., acceptable) diluent such as water, or saline, preferably phosphate buffered saline. The vaccines also typically include an adjuvant. Adjuvants such as incomplete Freund's adjuvant, aluminum phosphate, aluminum hydroxide, or alum are examples of materials well known in the art. Additionally, as disclosed herein, CTL responses can be primed by conjugating peptides of the invention to lipids, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P₃CSS). Moreover, an adjuvant such as a synthetic cytosine-phosphorothiolated-guanine-containing (CpG) oligonucleotides has been found to increase CTL responses 10- to 100-fold. (see, e.g. Davila and Celis, J. Immunol. 165:539-547 (2000))

Upon immunization with a peptide composition in accordance with the invention, via injection, aerosol, oral, transdermal, transmucosal, intrapleural, intrathecal, or other suitable routes, the immune system of the host responds to the vaccine by producing large amounts of CTLs and/or HTLs specific for the desired antigen. Consequently, the host becomes at least partially immune to later development of cells that express or overexpress 151P3D4 antigen, or derives at least some therapeutic benefit when the antigen was tumor-associated.

In some embodiments, it may be desirable to combine the class I peptide components with components that induce or facilitate neutralizing antibody and or helper T cell responses directed to the target antigen. A preferred embodiment of such a composition comprises class I and class II epitopes in accordance with the invention. An alternative embodiment of such a composition comprises a class I and/or class II epitope in accordance with the invention, along with a cross reactive HTL epitope such as PADRE™ (Epimmune, San Diego, Calif.) molecule (described e.g., in U.S. Pat. No. 5,736,142).

A vaccine of the invention can also include antigen-presenting cells (APC), such as dendritic cells (DC), as a vehicle to present peptides of the invention. Vaccine compositions can be created in vitro, following dendritic cell mobilization and harvesting, whereby loading of dendritic cells occurs in vitro. For example, dendritic cells are transfected, e.g., with a minigene in accordance with the invention, or are pulsed with peptides. The dendritic cell can then be administered to a patient to elicit immune responses in vivo. Vaccine compositions, either DNA- or peptide-based, can also be administered in vivo in combination with dendritic cell mobilization whereby loading of dendritic cells occurs in vivo.

Preferably, the following principles are utilized when selecting an array of epitopes for inclusion in a polyepitopic composition for use in a vaccine, or for selecting discrete epitopes to be included in a vaccine and/or to be encoded by nucleic acids such as a minigene. It is preferred that each of the following principles be balanced in order to make the selection. The multiple epitopes to be incorporated in a given vaccine composition may be, but need not be, contiguous in sequence in the native antigen from which the epitopes are derived.

1.) Epitopes are selected which, upon administration, mimic immune responses that have been observed to be correlated with tumor clearance. For HLA Class I this includes 3-4 epitopes that come from at least one tumor associated antigen (TAA). For HLA Class II a similar rationale is employed; again 3-4 epitopes are selected from at least one TAA (see, e.g., Rosenberg et al., Science 278:1447-1450). Epitopes from one TAA may be used in combination with epitopes from one or more additional TAAs to produce a vaccine that targets tumors with varying expression patterns of frequently-expressed TAAs.

2.) Epitopes are selected that have the requisite binding affinity established to be correlated with immunogenicity: for HLA Class I an IC₅₀ of 500 nM or less, often 200 nM or less; and for Class II an IC₅₀ of 1000 nM or less.

3.) Sufficient supermotif bearing-peptides, or a sufficient array of allele-specific motif-bearing peptides, are selected to give broad population coverage. For example, it is preferable to have at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art, can be employed to assess the breadth, or redundancy of, population coverage.

4.) When selecting epitopes from cancer-related antigens it is often useful to select analogs because the patient may have developed tolerance to the native epitope.

5.) Of particular relevance are epitopes referred to as “nested epitopes.” Nested epitopes occur where at least two epitopes overlap in a given peptide sequence. A nested peptide sequence can comprise B cell, HLA class I and/or HLA class II epitopes. When providing nested epitopes, a general objective is to provide the greatest number of epitopes per sequence. Thus, an aspect is to avoid providing a peptide that is any longer than the amino terminus of the amino terminal epitope and the carboxyl terminus of the carboxyl terminal epitope in the peptide. When providing a multi-epitopic sequence, such as a sequence comprising nested epitopes, it is generally important to screen the sequence in order to insure that it does not have pathological or other deleterious biological properties.

6.) If a polyepitopic protein is created, or when creating a minigene, an objective is to generate the smallest peptide that encompasses the epitopes of interest. This principle is similar, if not the same as that employed when selecting a peptide comprising nested epitopes. However, with an artificial polyepitopic peptide, the size minimization objective is balanced against the need to integrate any spacer sequences between epitopes in the polyepitopic protein. Spacer amino acid residues can, for example, be introduced to avoid junctional epitopes (an epitope recognized by the immune system, not present in the target antigen, and only created by the man-made juxtaposition of epitopes), or to facilitate cleavage between epitopes and thereby enhance epitope presentation. Junctional epitopes are generally to be avoided because the recipient may generate an immune response to that non-native epitope. Of particular concern is a junctional epitope that is a “dominant epitope.” A dominant epitope may lead to such a zealous response that immune responses to other epitopes are diminished or suppressed.

7.) Where the sequences of multiple variants of the same target protein are present, potential peptide epitopes can also be selected on the basis of their conservancy. For example, a criterion for conservancy may define that the entire sequence of an HLA class I binding peptide or the entire 9-mer core of a class II binding peptide be conserved in a designated percentage of the sequences evaluated for a specific protein antigen.

Minigene Vaccines

A number of different approaches are available which allow simultaneous delivery of multiple epitopes. Nucleic acids encoding the peptides of the invention are a particularly useful embodiment of the invention. Epitopes for inclusion in a minigene are preferably selected according to the guidelines set forth in the previous section. A preferred means of administering nucleic acids encoding the peptides of the invention uses minigene constructs encoding a peptide comprising one or multiple epitopes of the invention.

The use of multi-epitope minigenes is described below and in, Ishioka et al., J. Immunol. 162:3915-3925, 1999; An, L. and Whitton, J. L., J. Virol. 71:2292, 1997; Thomson, S. A. et al., J. Immunol. 157:822, 1996; Whitton, J. L. et al., J. Virol. 67:348, 1993; Hanke, R. et al., Vaccine 16:426, 1998. For example, a multi-epitope DNA plasmid encoding supermotif- and/or motif-bearing epitopes derived 151P3D4, the PADRE® universal helper T cell epitope or multiple HTL epitopes from 151P3D4 (see e.g., Tables V-XVIII and XXII to LI), and an endoplasmic reticulum-translocating signal sequence can be engineered. A vaccine may also comprise epitopes that are derived from other TAAs.

The immunogenicity of a multi-epitopic minigene can be confirmed in transgenic mice to evaluate the magnitude of CTL induction responses against the epitopes tested. Further, the immunogenicity of DNA-encoded epitopes in vivo can be correlated with the in vitro responses of specific CTL lines against target cells transfected with the DNA plasmid. Thus, these experiments can show that the minigene serves to both: 1.) generate a CTL response and 2.) that the induced CTLs recognized cells expressing the encoded epitopes.

For example, to create a DNA sequence encoding the selected epitopes (minigene) for expression in human cells, the amino acid sequences of the epitopes may be reverse translated. A human codon usage table can be used to guide the codon choice for each amino acid. These epitope-encoding DNA sequences may be directly adjoined, so that when translated, a continuous polypeptide sequence is created. To optimize expression and/or immunogenicity, additional elements can be incorporated into the minigene design. Examples of amino acid sequences that can be reverse translated and included in the minigene sequence include: HLA class I epitopes, HLA class II epitopes, antibody epitopes, a ubiquitination signal sequence, and/or an endoplasmic reticulum targeting signal. In addition, HLA presentation of CTL and HTL epitopes may be improved by including synthetic (e.g. poly-alanine) or naturally-occurring flanking sequences adjacent to the CTL or HTL epitopes; these larger peptides comprising the epitope(s) are within the scope of the invention.

The minigene sequence may be converted to DNA by assembling oligonucleotides that encode the plus and minus strands of the minigene. Overlapping oligonucleotides (30-100 bases long) may be synthesized, phosphorylated, purified and annealed under appropriate conditions using well known techniques. The ends of the oligonucleotides can be joined, for example, using T4 DNA ligase. This synthetic minigene, encoding the epitope polypeptide, can then be cloned into a desired expression vector.

Standard regulatory sequences well known to those of skill in the art are preferably included in the vector to ensure expression in the target cells. Several vector elements are desirable: a promoter with a down-stream cloning site for minigene insertion; a polyadenylation signal for efficient transcription termination; an E. coli origin of replication; and an E. coli selectable marker (e.g. ampicillin or kanamycin resistance). Numerous promoters can be used for this purpose, e.g., the human cytomegalovirus (hCMV) promoter. See, e.g., U.S. Pat. Nos. 5,580,859 and 5,589,466 for other suitable promoter sequences.

Additional vector modifications may be desired to optimize minigene expression and immunogenicity. In some cases, introns are required for efficient gene expression, and one or more synthetic or naturally-occurring introns could be incorporated into the transcribed region of the minigene. The inclusion of mRNA stabilization sequences and sequences for replication in mammalian cells may also be considered for increasing minigene expression.

Once an expression vector is selected, the minigene is cloned into the polylinker region downstream of the promoter. This plasmid is transformed into an appropriate E. coli strain, and DNA is prepared using standard techniques. The orientation and DNA sequence of the minigene, as well as all other elements included in the vector, are confirmed using restriction mapping and DNA sequence analysis. Bacterial cells harboring the correct plasmid can be stored as a master cell bank and a working cell bank.

In addition, immunostimulatory sequences (ISSs or CpGs) appear to play a role in the immunogenicity of DNA vaccines. These sequences may be included in the vector, outside the minigene coding sequence, if desired to enhance immunogenicity.

In some embodiments, a bi-cistronic expression vector which allows production of both the minigene-encoded epitopes and a second protein (included to enhance or decrease immunogenicity) can be used. Examples of proteins or polypeptides that could beneficially enhance the immune response if co-expressed include cytokines (e.g., IL-2, IL-12, GM-CSF), cytokine-inducing molecules (e.g., LeIF), costimulatory molecules, or for HTL responses, pan-DR binding proteins (PADRE®, Epimmune, San Diego, Calif.). Helper (HTL) epitopes can be joined to intracellular targeting signals and expressed separately from expressed CTL epitopes; this allows direction of the HTL epitopes to a cell compartment different than that of the CTL epitopes. If required, this could facilitate more efficient entry of HTL epitopes into the HLA class II pathway, thereby improving HTL induction. In contrast to HTL or CTL induction, specifically decreasing the immune response by co-expression of immunosuppressive molecules (e.g. TGF-β) may be beneficial in certain diseases.

Therapeutic quantities of plasmid DNA can be produced for example, by fermentation in E. coli, followed by purification. Aliquots from the working cell bank are used to inoculate growth medium, and grown to saturation in shaker flasks or a bioreactor according to well-known techniques. Plasmid DNA can be purified using standard bioseparation technologies such as solid phase anion-exchange resins supplied by QIAGEN, Inc. (Valencia, Calif.). If required, supercoiled DNA can be isolated from the open circular and linear forms using gel electrophoresis or other methods.

Purified plasmid DNA can be prepared for injection using a variety of formulations. The simplest of these is reconstitution of lyophilized DNA in sterile phosphate-buffer saline (PBS). This approach, known as “naked DNA,” is currently being used for intramuscular (IM) administration in clinical trials. To maximize the immunotherapeutic effects of minigene DNA vaccines, an alternative method for formulating purified plasmid DNA may be desirable. A variety of methods have been described, and new techniques may become available. Cationic lipids, glycolipids, and fusogenic liposomes can also be used in the formulation (see, e.g., as described by WO 93/24640; Mannino & Gould-Fogerite, BioTechniques 6(7): 682 (1988); U.S. Pat. No. 5,279,833; WO 91/06309; and Felgner, et al., Proc. Nat'l Acad. Sci. USA 84:7413 (1987). In addition, peptides and compounds referred to collectively as protective, interactive, non-condensing compounds (PINC) could also be complexed to purified plasmid DNA to influence variables such as stability, intramuscular dispersion, or trafficking to specific organs or cell types.

Target cell sensitization can be used as a functional assay for expression and HLA class I presentation of minigene-encoded CTL epitopes. For example, the plasmid DNA is introduced into a mammalian cell line that is suitable as a target for standard CTL chromium release assays. The transfection method used will be dependent on the final formulation. Electroporation can be used for “naked” DNA, whereas cationic lipids allow direct in vitro transfection. A plasmid expressing green fluorescent protein (GFP) can be co-transfected to allow enrichment of transfected cells using fluorescence activated cell sorting (FACS). These cells are then chromium-51 (⁵¹Cr) labeled and used as target cells for epitope-specific CTL lines; cytolysis, detected by ⁵¹Cr release, indicates both production of, and HLA presentation of, minigene-encoded CTL epitopes. Expression of HTL epitopes may be evaluated in an analogous manner using assays to assess HTL activity.

In vivo immunogenicity is a second approach for functional testing of minigene DNA formulations. Transgenic mice expressing appropriate human HLA proteins are immunized with the DNA product. The dose and route of administration are formulation dependent (e.g., IM for DNA in PBS, intraperitoneal (i.p.) for lipid-complexed DNA). Twenty-one days after immunization, splenocytes are harvested and restimulated for one week in the presence of peptides encoding each epitope being tested. Thereafter, for CTL effector cells, assays are conducted for cytolysis of peptide-loaded, ⁵¹Cr-labeled target cells using standard techniques. Lysis of target cells that were sensitized by HLA loaded with peptide epitopes, corresponding to minigene-encoded epitopes, demonstrates DNA vaccine function for in vivo induction of CTLs. Immunogenicity of HTL epitopes is confirmed in transgenic mice in an analogous manner.

Alternatively, the nucleic acids can be administered using ballistic delivery as described, for instance, in U.S. Pat. No. 5,204,253. Using this technique, particles comprised solely of DNA are administered. In a further alternative embodiment, DNA can be adhered to particles, such as gold particles.

Minigenes can also be delivered using other bacterial or viral delivery systems well known in the art, e.g., an expression construct encoding epitopes of the invention can be incorporated into a viral vector such as vaccinia.

Combinations of CTL Peptides with Helper Peptides

Vaccine compositions comprising CTL peptides of the invention can be modified, e.g., analoged, to provide desired attributes, such as improved serum half life, broadened population coverage or enhanced immunogenicity.

For instance, the ability of a peptide to induce CTL activity can be enhanced by linking the peptide to a sequence which contains at least one epitope that is capable of inducing a T helper cell response. Although a CTL peptide can be directly linked to a T helper peptide, often CTL epitope/HTL epitope conjugates are linked by a spacer molecule. The spacer is typically comprised of relatively small, neutral molecules, such as amino acids or amino acid mimetics, which are substantially uncharged under physiological conditions. The spacers are typically selected from, e.g., Ala, Gly, or other neutral spacers of nonpolar amino acids or neutral polar amino acids. It will be understood that the optionally present spacer need not be comprised of the same residues and thus may be a hetero- or homo-oligomer. When present, the spacer will usually be at least one or two residues, more usually three to six residues and sometimes 10 or more residues. The CTL peptide epitope can be linked to the T helper peptide epitope either directly or via a spacer either at the amino or carboxy terminus of the CTL peptide. The amino terminus of either the immunogenic peptide or the T helper peptide may be acylated.

In certain embodiments, the T helper peptide is one that is recognized by T helper cells present in a majority of a genetically diverse population. This can be accomplished by selecting peptides that bind to many, most, or all of the HLA class II molecules. Examples of such amino acid bind many HLA Class II molecules include sequences from antigens such as tetanus toxoid at positions 830-843 (QYIKANSKFIGITE; SEQ ID NO: 44), Plasmodium falciparum circumsporozoite (CS) protein at positions 378-398 (DIEKKIAKMEKASSVFNVVNS; SEQ ID NO: 45), and Streptococcus 18 kD protein at positions 116-131 (GAVDSILGGVATYGAA; SEQ ID NO: 46). Other examples include peptides bearing a DR 1-4-7 supermotif, or either of the DR3 motifs.

Alternatively, it is possible to prepare synthetic peptides capable of stimulating T helper lymphocytes, in a loosely HLA-restricted fashion, using amino acid sequences not found in nature (see, e.g., PCT publication WO 95/07707). These synthetic compounds called Pan-DR-binding epitopes (e.g., PADRE™, Epimmune, Inc., San Diego, Calif.) are designed to most preferably bind most HLA-DR (human HLA class II) molecules. For instance, a pan-DR-binding epitope peptide having the formula: aKXVAAWTLKAAa (SEQ ID NO: 47), where “X” is either cyclohexylalanine, phenylalanine, or tyrosine, and a is either D-alanine or L-alanine, has been found to bind to most HLA-DR alleles, and to stimulate the response of T helper lymphocytes from most individuals, regardless of their HLA type. An alternative of a pan-DR binding epitope comprises all “L” natural amino acids and can be provided in the form of nucleic acids that encode the epitope.

HTL peptide epitopes can also be modified to alter their biological properties. For example, they can be modified to include D-amino acids to increase their resistance to proteases and thus extend their serum half life, or they can be conjugated to other molecules such as lipids, proteins, carbohydrates, and the like to increase their biological activity. For example, a T helper peptide can be conjugated to one or more palmitic acid chains at either the amino or carboxyl termini.

Combinations of CTL Peptides with T Cell Priming Agents

In some embodiments it may be desirable to include in the pharmaceutical compositions of the invention at least one component which primes B lymphocytes or T lymphocytes. Lipids have been identified as agents capable of priming CTL in vivo. For example, palmitic acid residues can be attached to the ε- and α-amino groups of a lysine residue and then linked, e.g., via one or more linking residues such as Gly, Gly-Gly-, Ser, Ser-Ser, or the like, to an immunogenic peptide. The lipidated peptide can then be administered either directly in a micelle or particle, incorporated into a liposome, or emulsified in an adjuvant, e.g., incomplete Freund's adjuvant. In a preferred embodiment, a particularly effective immunogenic composition comprises palmitic acid attached to ε- and α-amino groups of Lys, which is attached via linkage, e.g., Ser-Ser, to the amino terminus of the immunogenic peptide.

As another example of lipid priming of CTL responses, E. coli lipoproteins, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P₃CSS) can be used to prime virus specific CTL when covalently attached to an appropriate peptide (see, e.g., Deres, et al., Nature 342:561, 1989). Peptides of the invention can be coupled to P₃CSS, for example, and the lipopeptide administered to an individual to specifically prime an immune response to the target antigen. Moreover, because the induction of neutralizing antibodies can also be primed with P₃CSS-conjugated epitopes, two such compositions can be combined to more effectively elicit both humoral and cell-mediated responses.

Vaccine Compositions Comprising DC Pulsed with CTL and/or HTL Peptides

An embodiment of a vaccine composition in accordance with the invention comprises ex vivo administration of a cocktail of epitope-bearing peptides to PBMC, or isolated DC therefrom, from the patient's blood. A pharmaceutical to facilitate harvesting of DC can be used, such as Progenipoietin™ (Pharmacia-Monsanto, St. Louis, Mo.) or GM-CSF/IL-4. After pulsing the DC with peptides and prior to reinfusion into patients, the DC are washed to remove unbound peptides. In this embodiment, a vaccine comprises peptide-pulsed DCs which present the pulsed peptide epitopes complexed with HLA molecules on their surfaces.

The DC can be pulsed ex vivo with a cocktail of peptides, some of which stimulate CTL responses to 151P3D4. Optionally, a helper T cell (HTL) peptide, such as a natural or artificial loosely restricted HLA Class II peptide, can be included to facilitate the CTL response. Thus, a vaccine in accordance with the invention is used to treat a cancer which expresses or overexpresses 151P3D4.

Adoptive Immunotherapy

Antigenic 151P3D4-related peptides are used to elicit a CTL and/or HTL response ex vivo, as well. The resulting CTL or HTL cells, can be used to treat tumors in patients that do not respond to other conventional forms of therapy, or will not respond to a therapeutic vaccine peptide or nucleic acid in accordance with the invention. Ex vivo CTL or HTL responses to a particular antigen are induced by incubating in tissue culture the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of antigen-presenting cells (APC), such as dendritic cells, and the appropriate immunogenic peptide. After an appropriate incubation time (typically about 7-28 days), in which the precursor cells are activated and expanded into effector cells, the cells are infused back into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cell (e.g., a tumor cell). Transfected dendritic cells may also be used as antigen presenting cells.

Administration of Vaccines for Therapeutic or Prophylactic Purposes

Pharmaceutical and vaccine compositions of the invention are typically used to treat and/or prevent a cancer that expresses or overexpresses 151P3D4. In therapeutic applications, peptide and/or nucleic acid compositions are administered to a patient in an amount sufficient to elicit an effective B cell, CTL and/or HTL response to the antigen and to cure or at least partially arrest or slow symptoms and/or complications. An amount adequate to accomplish this is defined as “therapeutically effective dose.” Amounts effective for this use will depend on, e.g., the particular composition administered, the manner of administration, the stage and severity of the disease being treated, the weight and general state of health of the patient, and the judgment of the prescribing physician.

For pharmaceutical compositions, the immunogenic peptides of the invention, or DNA encoding them, are generally administered to an individual already bearing a tumor that expresses 151P3D4. The peptides or DNA encoding them can be administered individually or as fusions of one or more peptide sequences. Patients can be treated with the immunogenic peptides separately or in conjunction with other treatments, such as surgery, as appropriate.

For therapeutic use, administration should generally begin at the first diagnosis of 151P3D4-associated cancer. This is followed by boosting doses until at least symptoms are substantially abated and for a period thereafter. The embodiment of the vaccine composition (i.e., including, but not limited to embodiments such as peptide cocktails, polyepitopic polypeptides, minigenes, or TAA-specific CTLs or pulsed dendritic cells) delivered to the patient may vary according to the stage of the disease or the patient's health status. For example, in a patient with a tumor that expresses 151P3D4, a vaccine comprising 151P3D4-specific CTL may be more efficacious in killing tumor cells in patient with advanced disease than alternative embodiments.

It is generally important to provide an amount of the peptide epitope delivered by a mode of administration sufficient to effectively stimulate a cytotoxic T cell response; compositions which stimulate helper T cell responses can also be given in accordance with this embodiment of the invention.

The dosage for an initial therapeutic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1,000 μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a human typically range from about 500 μg to about 50,000 μg per 70 kilogram patient. Boosting dosages of between about 1.0 μg to about 50,000 μg of peptide pursuant to a boosting regimen over weeks to months may be administered depending upon the patient's response and condition as determined by measuring the specific activity of CTL and HTL obtained from the patient's blood. Administration should continue until at least clinical symptoms or laboratory tests indicate that the neoplasia, has been eliminated or reduced and for a period thereafter. The dosages, routes of administration, and dose schedules are adjusted in accordance with methodologies known in the art.

In certain embodiments, the peptides and compositions of the present invention are employed in serious disease states, that is, life-threatening or potentially life threatening situations. In such cases, as a result of the minimal amounts of extraneous substances and the relative nontoxic nature of the peptides in preferred compositions of the invention, it is possible and may be felt desirable by the treating physician to administer substantial excesses of these peptide compositions relative to these stated dosage amounts.

The vaccine compositions of the invention can also be used purely as prophylactic agents. Generally the dosage for an initial prophylactic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1000 μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a human typically range from about 500 μg to about 50,000 μg per 70 kilogram patient. This is followed by boosting dosages of between about 1.0 μg to about 50,000 μg of peptide administered at defined intervals from about four weeks to six months after the initial administration of vaccine. The immunogenicity of the vaccine can be assessed by measuring the specific activity of CTL and HTL obtained from a sample of the patient's blood.

The pharmaceutical compositions for therapeutic treatment are intended for parenteral, topical, oral, nasal, intrathecal, or local (e.g. as a cream or topical ointment) administration. Preferably, the pharmaceutical compositions are administered parentally, e.g., intravenously, subcutaneously, intradermally, or intramuscularly. Thus, the invention provides compositions for parenteral administration which comprise a solution of the immunogenic peptides dissolved or suspended in an acceptable carrier, preferably an aqueous carrier.

A variety of aqueous carriers may be used, e.g., water, buffered water, 0.8% saline, 0.3% glycine, hyaluronic acid and the like. These compositions may be sterilized by conventional, well-known sterilization techniques, or may be sterile filtered. The resulting aqueous solutions may be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration.

The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH-adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservatives, and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc.

The concentration of peptides of the invention in the pharmaceutical formulations can vary widely, i.e., from less than about 0.1%, usually at or at least about 2% to as much as 20% to 50% or more by weight, and will be selected primarily by fluid volumes, viscosities, etc., in accordance with the particular mode of administration selected.

A human unit dose form of a composition is typically included in a pharmaceutical composition that comprises a human unit dose of an acceptable carrier, in one embodiment an aqueous carrier, and is administered in a volume/quantity that is known by those of skill in the art to be used for administration of such compositions to humans (see, e.g., Remington's Pharmaceutical Sciences, 17^th Edition, A. Gennaro, Editor, Mack Publishing Co., Easton, Pa., 1985). For example a peptide dose for initial immunization can be from about 1 to about 50,000 μg, generally 100-5,000 μg, for a 70 kg patient. For example, for nucleic acids an initial immunization may be performed using an expression vector in the form of naked nucleic acid administered IM (or SC or ID) in the amounts of 0.5-5 mg at multiple sites. The nucleic acid (0.1 to 1000 μg) can also be administered using a gene gun. Following an incubation period of 3-4 weeks, a booster dose is then administered. The booster can be recombinant fowlpox virus administered at a dose of 5-10⁷ to 5×10⁹ pfu.

For antibodies, a treatment generally involves repeated administration of the anti-151P3D4 antibody preparation, via an acceptable route of administration such as intravenous injection (IV), typically at a dose in the range of about 0.1 to about 10 mg/kg body weight. In general, doses in the range of 10-500 mg mAb per week are effective and well tolerated. Moreover, an initial loading dose of approximately 4 mg/kg patient body weight IV, followed by weekly doses of about 2 mg/kg IV of the anti-151P3D4 mAb preparation represents an acceptable dosing regimen. As appreciated by those of skill in the art, various factors can influence the ideal dose in a particular case. Such factors include, for example, half life of a composition, the binding affinity of an Ab, the immunogenicity of a substance, the degree of 151P3D4 expression in the patient, the extent of circulating shed 151P3D4 antigen, the desired steady-state concentration level, frequency of treatment, and the influence of chemotherapeutic or other agents used in combination with the treatment method of the invention, as well as the health status of a particular patient. Non-limiting preferred human unit doses are, for example, 500 μg-1 mg, 1 mg-50 mg, 50 mg-100 mg, 100 mg-200 mg, 200 mg-300 mg, 400 mg-500 mg, 500 mg-600 mg, 600 mg-700 mg, 700 mg-800 mg, 800 mg-900 mg, 900 mg-1 g, or 1 mg-700 mg. In certain embodiments, the dose is in a range of 2-5 mg/kg body weight, e.g., with follow on weekly doses of 1-3 mg/kg; 0.5 mg, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 mg/kg body weight followed, e.g., in two, three or four weeks by weekly doses; 0.5-10 mg/kg body weight, e.g., followed in two, three or four weeks by weekly doses; 225, 250, 275, 300, 325, 350, 375, 400 mg m² of body area weekly; 1-600 mg m² of body area weekly; 225-400 mg m² of body area weekly; these does can be followed by weekly doses for 2, 3, 4, 5, 6, 7, 8, 9, 19, 11, 12 or more weeks.

In one embodiment, human unit dose forms of polynucleotides comprise a suitable dosage range or effective amount that provides any therapeutic effect. As appreciated by one of ordinary skill in the art a therapeutic effect depends on a number of factors, including the sequence of the polynucleotide, molecular weight of the polynucleotide and route of administration. Dosages are generally selected by the physician or other health care professional in accordance with a variety of parameters known in the art, such as severity of symptoms, history of the patient and the like. Generally, for a polynucleotide of about 20 bases, a dosage range may be selected from, for example, an independently selected lower limit such as about 0.1, 0.25, 0.5, 1, 2, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400 or 500 mg/kg up to an independently selected upper limit, greater than the lower limit, of about 60, 80, 100, 200, 300, 400, 500, 750, 1000, 1500, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000 or 10,000 mg/kg. For example, a dose may be about any of the following: 0.1 to 100 mg/kg, 0.1 to 50 mg/kg, 0.1 to 25 mg/kg, 0.1 to 10 mg/kg, 1 to 500 mg/kg, 100 to 400 mg/kg, 200 to 300 mg/kg, 1 to 100 mg/kg, 100 to 200 mg/kg, 300 to 400 mg/kg, 400 to 500 mg/kg, 500 to 1000 mg/kg, 500 to 5000 mg/kg, or 500 to 10,000 mg/kg. Generally, parenteral routes of administration may require higher doses of polynucleotide compared to more direct application to the nucleotide to diseased tissue, as do polynucleotides of increasing length.

In one embodiment, human unit dose forms of T-cells comprise a suitable dosage range or effective amount that provides any therapeutic effect. As appreciated by one of ordinary skill in the art, a therapeutic effect depends on a number of factors. Dosages are generally selected by the physician or other health care professional in accordance with a variety of parameters known in the art, such as severity of symptoms, history of the patient and the like. A dose may be about 10⁴ cells to about 10⁶ cells, about 10⁶ cells to about 10⁸ cells, about 10⁸ to about 10¹¹ cells, or about 10⁸ to about 5×10¹⁰ cells. A dose may also about 10⁶ cells/m² to about 10¹⁰ cells/m², or about 10⁶ cells/m² to about 10⁸ cells/m².

Proteins(s) of the invention, and/or nucleic acids encoding the protein(s), can also be administered via liposomes, which may also serve to: 1) target the proteins(s) to a particular tissue, such as lymphoid tissue; 2) to target selectively to diseases cells; or, 3) to increase the half-life of the peptide composition. Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. In these preparations, the peptide to be delivered is incorporated as part of a liposome, alone or in conjunction with a molecule which binds to a receptor prevalent among lymphoid cells, such as monoclonal antibodies which bind to the CD45 antigen, or with other therapeutic or immunogenic compositions. Thus, liposomes either filled or decorated with a desired peptide of the invention can be directed to the site of lymphoid cells, where the liposomes then deliver the peptide compositions. Liposomes for use in accordance with the invention are formed from standard vesicle-forming lipids, which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of, e.g., liposome size, acid lability and stability of the liposomes in the blood stream. A variety of methods are available for preparing liposomes, as described in, e.g., Szoka, et al., Ann. Rev. Biophys. Bioeng. 9:467 (1980), and U.S. Pat. Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369.

For targeting cells of the immune system, a ligand to be incorporated into the liposome can include, e.g., antibodies or fragments thereof specific for cell surface determinants of the desired immune system cells. A liposome suspension containing a peptide may be administered intravenously, locally, topically, etc. in a dose which varies according to, inter alia, the manner of administration, the peptide being delivered, and the stage of the disease being treated.

For solid compositions, conventional nontoxic solid carriers may be used which include, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like. For oral administration, a pharmaceutically acceptable nontoxic composition is formed by incorporating any of the normally employed excipients, such as those carriers previously listed, and generally 10-95% of active ingredient, that is, one or more peptides of the invention, and more preferably at a concentration of 25%-75%.

For aerosol administration, immunogenic peptides are preferably supplied in finely divided form along with a surfactant and propellant. Typical percentages of peptides are about 0.01%-20% by weight, preferably about 1%-10%. The surfactant must, of course, be nontoxic, and preferably soluble in the propellant. Representative of such agents are the esters or partial esters of fatty acids containing from about 6 to 22 carbon atoms, such as caproic, octanoic, lauric, palmitic, stearic, linoleic, linolenic, olesteric and oleic acids with an aliphatic polyhydric alcohol or its cyclic anhydride. Mixed esters, such as mixed or natural glycerides may be employed. The surfactant may constitute about 0.1%-20% by weight of the composition, preferably about 0.25-5%. The balance of the composition is ordinarily propellant. A carrier can also be included, as desired, as with, e.g., lecithin for intranasal delivery.

Diagnostic and Prognostic Embodiments of 151P3D4.

As disclosed herein, 151P3D4 polynucleotides, polypeptides, reactive cytotoxic T cells (CTL), reactive helper T cells (HTL) and anti-polypeptide antibodies are used in well known diagnostic, prognostic and therapeutic assays that examine conditions associated with dysregulated cell growth such as cancer, in particular the cancers listed in Table I (see, e.g., both its specific pattern of tissue expression as well as its overexpression in certain cancers as described for example in the Example entitled “Expression analysis of 151P3D4 in normal tissues, and patient specimens”).

151P3D4 can be analogized to a prostate associated antigen PSA, the archetypal marker that has been used by medical practitioners for years to identify and monitor the presence of prostate cancer (see, e.g., Merrill et al., J. Urol. 163(2): 503-5120 (2000); Polascik et al., J. Urol. August; 162(2):293-306 (1999) and Fortier et al., J. Nat. Cancer Inst. 91(19): 1635-1640 (1999)). A variety of other diagnostic markers are also used in similar contexts including p53 and K-ras (see, e.g., Tulchinsky et al., Int J Mol Med 1999 July 4(1):99-102 and Minimoto et al., Cancer Detect Prey 2000; 24(1):1-12). Therefore, this disclosure of 151P3D4 polynucleotides and polypeptides (as well as 151P3D4 polynucleotide probes and anti-151P3D4 antibodies used to identify the presence of these molecules) and their properties allows skilled artisans to utilize these molecules in methods that are analogous to those used, for example, in a variety of diagnostic assays directed to examining conditions associated with cancer.

Typical embodiments of diagnostic methods which utilize the 151P3D4 polynucleotides, polypeptides, reactive T cells and antibodies are analogous to those methods from well-established diagnostic assays which employ, e.g., PSA polynucleotides, polypeptides, reactive T cells and antibodies. For example, just as PSA polynucleotides are used as probes (for example in Northern analysis, see, e.g., Sharief et al., Biochem. Mol. Biol. Int. 33(3):567-74 (1994)) and primers (for example in PCR analysis, see, e.g., Okegawa et al., J. Urol. 163(4): 1189-1190 (2000)) to observe the presence and/or the level of PSA mRNAs in methods of monitoring PSA overexpression or the metastasis of prostate cancers, the 151P3D4 polynucleotides described herein can be utilized in the same way to detect 151P3D4 overexpression or the metastasis of prostate and other cancers expressing this gene. Alternatively, just as PSA polypeptides are used to generate antibodies specific for PSA which can then be used to observe the presence and/or the level of PSA proteins in methods to monitor PSA protein overexpression (see, e.g., Stephan et al., Urology 55(4):560-3 (2000)) or the metastasis of prostate cells (see, e.g., Alanen et al., Pathol. Res. Pract. 192(3):233-7 (1996)), the 151P3D4 polypeptides described herein can be utilized to generate antibodies for use in detecting 151P3D4 overexpression or the metastasis of prostate cells and cells of other cancers expressing this gene.

Specifically, because metastases involves the movement of cancer cells from an organ of origin (such as the lung or prostate gland etc.) to a different area of the body (such as a lymph node), assays which examine a biological sample for the presence of cells expressing 151P3D4 polynucleotides and/or polypeptides can be used to provide evidence of metastasis. For example, when a biological sample from tissue that does not normally contain 151P3D4-expressing cells (lymph node) is found to contain 151P3D4-expressing cells such as the 151P3D4 expression seen in LAPC4 and LAPC9, xenografts isolated from lymph node and bone metastasis, respectively, this finding is indicative of metastasis.

Alternatively 151P3D4 polynucleotides and/or polypeptides can be used to provide evidence of cancer, for example, when cells in a biological sample that do not normally express 151P3D4 or express 151P3D4 at a different level are found to express 151P3D4 or have an increased expression of 151P3D4 (see, e.g., the 151P3D4 expression in the cancers listed in Table I and in patient samples etc. shown in the accompanying Figures). In such assays, artisans may further wish to generate supplementary evidence of metastasis by testing the biological sample for the presence of a second tissue restricted marker (in addition to 151P3D4) such as PSA, PSCA etc. (see, e.g., Alanen et al., Pathol. Res. Pract. 192(3): 233-237 (1996)).

Just as PSA polynucleotide fragments and polynucleotide variants are employed by skilled artisans for use in methods of monitoring PSA, 151P3D4 polynucleotide fragments and polynucleotide variants are used in an analogous manner. In particular, typical PSA polynucleotides used in methods of monitoring PSA are probes or primers which consist of fragments of the PSA cDNA sequence. Illustrating this, primers used to PCR amplify a PSA polynucleotide must include less than the whole PSA sequence to function in the polymerase chain reaction. In the context of such PCR reactions, skilled artisans generally create a variety of different polynucleotide fragments that can be used as primers in order to amplify different portions of a polynucleotide of interest or to optimize amplification reactions (see, e.g., Caetano-Anolles, G. Biotechniques 25(3): 472-476, 478-480 (1998); Robertson et al., Methods Mol. Biol. 98:121-154 (1998)). An additional illustration of the use of such fragments is provided in the Example entitled “Expression analysis of 151P3D4 in normal tissues, and patient specimens,” where a 151P3D4 polynucleotide fragment is used as a probe to show the expression of 151P3D4 RNAs in cancer cells. In addition, variant polynucleotide sequences are typically used as primers and probes for the corresponding mRNAs in PCR and Northern analyses (see, e.g., Sawai et al., Fetal Diagn. Ther. 1996 November-December 11(6):407-13 and Current Protocols In Molecular Biology, Volume 2, Unit 2, Frederick M. Ausubel et al. eds., 1995)). Polynucleotide fragments and variants are useful in this context where they are capable of binding to a target polynucleotide sequence (e.g., a 151P3D4 polynucleotide shown in FIG. 2 or variant thereof) under conditions of high stringency.

Furthermore, PSA polypeptides which contain an epitope that can be recognized by an antibody or T cell that specifically binds to that epitope are used in methods of monitoring PSA. 151P3D4 polypeptide fragments and polypeptide analogs or variants can also be used in an analogous manner. This practice of using polypeptide fragments or polypeptide variants to generate antibodies (such as anti-PSA antibodies or T cells) is typical in the art with a wide variety of systems such as fusion proteins being used by practitioners (see, e.g., Current Protocols In Molecular Biology, Volume 2, Unit 16, Frederick M. Ausubel et al. eds., 1995). In this context, each epitope(s) functions to provide the architecture with which an antibody or T cell is reactive. Typically, skilled artisans create a variety of different polypeptide fragments that can be used in order to generate immune responses specific for different portions of a polypeptide of interest (see, e.g., U.S. Pat. No. 5,840,501 and U.S. Pat. No. 5,939,533). For example it may be preferable to utilize a polypeptide comprising one of the 151P3D4 biological motifs discussed herein or a motif-bearing subsequence which is readily identified by one of skill in the art based on motifs available in the art. Polypeptide fragments, variants or analogs are typically useful in this context as long as they comprise an epitope capable of generating an antibody or T cell specific for a target polypeptide sequence (e.g. a 151P3D4 polypeptide shown in FIG. 3).

As shown herein, the 151P3D4 polynucleotides and polypeptides (as well as the 151P3D4 polynucleotide probes and anti-151P3D4 antibodies or T cells used to identify the presence of these molecules) exhibit specific properties that make them useful in diagnosing cancers such as those listed in Table I. Diagnostic assays that measure the presence of 151P3D4 gene products, in order to evaluate the presence or onset of a disease condition described herein, such as prostate cancer, are used to identify patients for preventive measures or further monitoring, as has been done so successfully with PSA. Moreover, these materials satisfy a need in the art for molecules having similar or complementary characteristics to PSA in situations where, for example, a definite diagnosis of metastasis of prostatic origin cannot be made on the basis of a test for PSA alone (see, e.g., Alanen et al., Pathol. Res. Pract. 192(3): 233-237 (1996)), and consequently, materials such as 151P3D4 polynucleotides and polypeptides (as well as the 151P3D4 polynucleotide probes and anti-151P3D4 antibodies used to identify the presence of these molecules) need to be employed to confirm a metastases of prostatic origin.

Finally, in addition to their use in diagnostic assays, the 151P3D4 polynucleotides disclosed herein have a number of other utilities such as their use in the identification of oncogenetic associated chromosomal abnormalities in the chromosomal region to which the 151P3D4 gene maps (see the Example entitled “Chromosomal Mapping of 151P3D4” below). Moreover, in addition to their use in diagnostic assays, the 151P3D4-related proteins and polynucleotides disclosed herein have other utilities such as their use in the forensic analysis of tissues of unknown origin (see, e.g., Takahama K Forensic Sci Int 1996 Jun. 28; 80(1-2): 63-9).

Additionally, 151P3D4-related proteins or polynucleotides of the invention can be used to treat a pathologic condition characterized by the over-expression of 151P3D4. For example, the amino acid or nucleic acid sequence of FIG. 2 or FIG. 3, or fragments of either, can be used to generate an immune response to a 151P3D4 antigen. Antibodies or other molecules that react with 151P3D4 can be used to modulate the function of this molecule, and thereby provide a therapeutic benefit.

Inhibition of 151P3D4 Protein Function

The invention includes various methods and compositions for inhibiting the binding of 151P3D4 to its binding partner or its association with other protein(s) as well as methods for inhibiting 151P3D4 function.

Inhibition of 151P3D4 with Intracellular Antibodies

In one approach, a recombinant vector that encodes single chain antibodies that specifically bind to 151P3D4 are introduced into 151P3D4 expressing cells via gene transfer technologies. Accordingly, the encoded single chain anti-151P3D4 antibody is expressed intracellularly, binds to 151P3D4 protein, and thereby inhibits its function. Methods for engineering such intracellular single chain antibodies are well known. Such intracellular antibodies, also known as “intrabodies”, are specifically targeted to a particular compartment within the cell, providing control over where the inhibitory activity of the treatment is focused. This technology has been successfully applied in the art (for review, see Richardson and Marasco, 1995, TIBTECH vol. 13). Intrabodies have been shown to virtually eliminate the expression of otherwise abundant cell surface receptors (see, e.g., Richardson et al., 1995, Proc. Natl. Acad. Sci. USA 92: 3137-3141; Beerli et al., 1994, J. Biol. Chem. 289: 23931-23936; Deshane et al., 1994, Gene Ther. 1: 332-337).

Single chain antibodies comprise the variable domains of the heavy and light chain joined by a flexible linker polypeptide, and are expressed as a single polypeptide. Optionally, single chain antibodies are expressed as a single chain variable region fragment joined to the light chain constant region. Well-known intracellular trafficking signals are engineered into recombinant polynucleotide vectors encoding such single chain antibodies in order to precisely target the intrabody to the desired intracellular compartment. For example, intrabodies targeted to the endoplasmic reticulum (ER) are engineered to incorporate a leader peptide and, optionally, a C-terminal ER retention signal, such as the KDEL amino acid motif. Intrabodies intended to exert activity in the nucleus are engineered to include a nuclear localization signal. Lipid moieties are joined to intrabodies in order to tether the intrabody to the cytosolic side of the plasma membrane. Intrabodies can also be targeted to exert function in the cytosol. For example, cytosolic intrabodies are used to sequester factors within the cytosol, thereby preventing them from being transported to their natural cellular destination.

In one embodiment, intrabodies are used to capture 151P3D4 in the nucleus, thereby preventing its activity within the nucleus. Nuclear targeting signals are engineered into such 151P3D4 intrabodies in order to achieve the desired targeting. Such 151P3D4 intrabodies are designed to bind specifically to a particular 151P3D4 domain. In another embodiment, cytosolic intrabodies that specifically bind to a 151P3D4 protein are used to prevent 151P3D4 from gaining access to the nucleus, thereby preventing it from exerting any biological activity within the nucleus (e.g., preventing 151P3D4 from forming transcription complexes with other factors).

In order to specifically direct the expression of such intrabodies to particular cells, the transcription of the intrabody is placed under the regulatory control of an appropriate tumor-specific promoter and/or enhancer. In order to target intrabody expression specifically to prostate, for example, the PSA promoter and/or promoter/enhancer can be utilized (See, for example, U.S. Pat. No. 5,919,652 issued 6 Jul. 1999).

Inhibition of 151P3D4 with Recombinant Proteins

In another approach, recombinant molecules bind to 151P3D4 and thereby inhibit 151P3D4 function. For example, these recombinant molecules prevent or inhibit 151P3D4 from accessing/binding to its binding partner(s) or associating with other protein(s). Such recombinant molecules can, for example, contain the reactive part(s) of a 151P3D4 specific antibody molecule. In a particular embodiment, the 151P3D4 binding domain of a 151P3D4 binding partner is engineered into a dimeric fusion protein, whereby the fusion protein comprises two 151P3D4 ligand binding domains linked to the Fc portion of a human IgG, such as human IgG1. Such IgG portion can contain, for example, the C_H2 and C_H3 domains and the hinge region, but not the C_H1 domain. Such dimeric fusion proteins are administered in soluble form to patients suffering from a cancer associated with the expression of 151P3D4, whereby the dimeric fusion protein specifically binds to 151P3D4 and blocks 151P3D4 interaction with a binding partner. Such dimeric fusion proteins are further combined into multimeric proteins using known antibody linking technologies.

Inhibition of 151P3D4 Transcription or Translation

The present invention also comprises various methods and compositions for inhibiting the transcription of the 151P3D4 gene. Similarly, the invention also provides methods and compositions for inhibiting the translation of 151P3D4 mRNA into protein.

In one approach, a method of inhibiting the transcription of the 151P3D4 gene comprises contacting the 151P3D4 gene with a 151P3D4 antisense polynucleotide. In another approach, a method of inhibiting 151P3D4 mRNA translation comprises contacting a 151P3D4 mRNA with an antisense polynucleotide. In another approach, a 151P3D4 specific ribozyme is used to cleave a 151P3D4 message, thereby inhibiting translation. Such antisense and ribozyme based methods can also be directed to the regulatory regions of the 151P3D4 gene, such as 151P3D4 promoter and/or enhancer elements. Similarly, proteins capable of inhibiting a 151P3D4 gene transcription factor are used to inhibit 151P3D4 mRNA transcription. The various polynucleotides and compositions useful in the aforementioned methods have been described above. The use of antisense and ribozyme molecules to inhibit transcription and translation is well known in the art.

Other factors that inhibit the transcription of 151P3D4 by interfering with 151P3D4 transcriptional activation are also useful to treat cancers expressing 151P3D4. Similarly, factors that interfere with 151P3D4 processing are useful to treat cancers that express 151P3D4. Cancer treatment methods utilizing such factors are also within the scope of the invention.

General Considerations for Therapeutic Strategies

Gene transfer and gene therapy technologies can be used to deliver therapeutic polynucleotide molecules to tumor cells synthesizing 151P3D4 (i.e., antisense, ribozyme, polynucleotides encoding intrabodies and other 151P3D4 inhibitory molecules). A number of gene therapy approaches are known in the art. Recombinant vectors encoding 151P3D4 antisense polynucleotides, ribozymes, factors capable of interfering with 151P3D4 transcription, and so forth, can be delivered to target tumor cells using such gene therapy approaches.

The above therapeutic approaches can be combined with any one of a wide variety of surgical, chemotherapy or radiation therapy regimens. The therapeutic approaches of the invention can enable the use of reduced dosages of chemotherapy (or other therapies) and/or less frequent administration, an advantage for all patients and particularly for those that do not tolerate the toxicity of the chemotherapeutic agent well.

The anti-tumor activity of a particular composition (e.g., antisense, ribozyme, intrabody), or a combination of such compositions, can be evaluated using various in vitro and in vivo assay systems. In vitro assays that evaluate therapeutic activity include cell growth assays, soft agar assays and other assays indicative of tumor promoting activity, binding assays capable of determining the extent to which a therapeutic composition will inhibit the binding of 151P3D4 to a binding partner, etc.

In vivo, the effect of a 151P3D4 therapeutic composition can be evaluated in a suitable animal model. For example, xenogenic prostate cancer models can be used, wherein human prostate cancer explants or passaged xenograft tissues are introduced into immune compromised animals, such as nude or SCID mice (Klein et al., 1997, Nature Medicine 3: 402-408). For example, PCT Patent Application WO98/16628 and U.S. Pat. No. 6,107,540 describe various xenograft models of human prostate cancer capable of recapitulating the development of primary tumors, micrometastasis, and the formation of osteoblastic metastases characteristic of late stage disease. Efficacy can be predicted using assays that measure inhibition of tumor formation, tumor regression or metastasis, and the like.

In vivo assays that evaluate the promotion of apoptosis are useful in evaluating therapeutic compositions. In one embodiment, xenografts from tumor bearing mice treated with the therapeutic composition can be examined for the presence of apoptotic foci and compared to untreated control xenograft-bearing mice. The extent to which apoptotic foci are found in the tumors of the treated mice provides an indication of the therapeutic efficacy of the composition.

The therapeutic compositions used in the practice of the foregoing methods can be formulated into pharmaceutical compositions comprising a carrier suitable for the desired delivery method. Suitable carriers include any material that when combined with the therapeutic composition retains the anti-tumor function of the therapeutic composition and is generally non-reactive with the patient's immune system. Examples include, but are not limited to, any of a number of standard pharmaceutical carriers such as sterile phosphate buffered saline solutions, bacteriostatic water, and the like (see, generally, Remington's Pharmaceutical Sciences 16^th Edition, A. Osal., Ed., 1980).

Therapeutic formulations can be solubilized and administered via any route capable of delivering the therapeutic composition to the tumor site. Potentially effective routes of administration include, but are not limited to, intravenous, parenteral, intraperitoneal, intramuscular, intratumor, intradermal, intraorgan, orthotopic, and the like. A preferred formulation for intravenous injection comprises the therapeutic composition in a solution of preserved bacteriostatic water, sterile unpreserved water, and/or diluted in polyvinylchloride or polyethylene bags containing 0.9% sterile Sodium Chloride for Injection, USP. Therapeutic protein preparations can be lyophilized and stored as sterile powders, preferably under vacuum, and then reconstituted in bacteriostatic water (containing for example, benzyl alcohol preservative) or in sterile water prior to injection.

Dosages and administration protocols for the treatment of cancers using the foregoing methods will vary with the method and the target cancer, and will generally depend on a number of other factors appreciated in the art.

Kits

For use in the diagnostic and therapeutic applications described herein, kits are also within the scope of the invention. Such kits can comprise a carrier, package or container that is compartmentalized to receive one or more containers such as vials, tubes, and the like, each of the container(s) comprising one of the separate elements to be used in the method. For example, the container(s) can comprise a probe that is or can be detectably labeled. Such probe can be an antibody or polynucleotide specific for a 151P3D4-related protein or a 151P3D4 gene or message, respectively. Where the method utilizes nucleic acid hybridization to detect the target nucleic acid, the kit can also have containers containing nucleotide(s) for amplification of the target nucleic acid sequence and/or a container comprising a reporter-means, such as a biotin-binding protein, such as avidin or streptavidin, bound to a reporter molecule, such as an enzymatic, florescent, or radioisotope label. The kit can include all or part of the amino acid sequence of FIG. 2 or FIG. 3 or analogs thereof, or a nucleic acid molecules that encodes such amino acid sequences.

The kit of the invention will typically comprise the container described above and one or more other containers comprising materials desirable from a commercial and user standpoint, including buffers, diluents, filters, needles, syringes, and package inserts with instructions for use.

A label can be present on the container to indicate that the composition is used for a specific therapy or non-therapeutic application, and can also indicate directions for either in vivo or in vitro use, such as those described above. Directions and or other information can also be included on an insert which is included with the kit.

EXAMPLES

Various aspects of the invention are further described and illustrated by way of the several examples that follow, none of which are intended to limit the scope of the invention.

Example 1

SSH-Generated Isolation of a cDNA Fragment of the 151P3D4 Gene

To isolate genes that are over-expressed in bladder cancer we used the Suppression Subtractive Hybridization (SSH) procedure using cDNA derived from the LNCaP prostate cancer cell line.

The 151P3D4 SSH cDNA sequence was derived from a subtraction consisting of two different populations of LNCaP cells. The 151P3D4 SSH cDNA sequence of 417 by is listed in FIG. 1.

The full-length 151P3D4 v.1 clone 1-placenta was cloned from normal placenta cDNA, revealing an ORF of 354 amino acids (FIG. 2 and FIG. 3). Other variants of 151P3D4 were also identified and these are listed in FIGS. 2 and 3.

Materials and Methods

Human Tissues:

The patient cancer and normal tissues were purchased from different sources such as the NDRI (Philadelphia, Pa.). mRNA for some normal tissues were purchased from Clontech, Palo Alto, Calif.

RNA Isolation:

Tissues were homogenized in Trizol reagent (Life Technologies, Gibco BRL) using 10 ml/g tissue isolate total RNA. Poly A RNA was purified from total RNA using Qiagen's Oligotex mRNA Mini and Midi kits. Total and mRNA were quantified by spectrophotometric analysis (O.D. 260/280 nm) and analyzed by gel electrophoresis.

Oligonucleotides:

The following HPLC purified oligonucleotides were used.

DPNCDN (cDNA synthesis primer):
(SEQ ID NO: 48)
5′TTTTGATCAAGCTT303′
Adaptor 1:
(SEQ ID NO: 49)
5′CTAATACGACTCACTATAGGGCTCGAGCGGCCGCCCGGGCAG3′
(SEQ ID NO: 50)
3′GGCCCGTCCTAG5′
Adaptor 2:
(SEQ ID NO: 51)
5′GTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAG3′
(SEQ ID NO: 52)
3′CGGCTCCTAG5′
PCR primer 1:
(SEQ ID NO: 53)
5′CTAATACGACTCACTATAGGGC3′
Nested primer (NP)1:
(SEQ ID NO: 54)
5′TCGAGCGGCCGCCCGGGCAGGA3′
Nested primer (NP)2:
(SEQ ID NO: 55)
5′AGCGTGGTCGCGGCCGAGGA3′

Suppression Subtractive Hybridization:

Suppression Subtractive Hybridization (SSH) was used to identify cDNAs corresponding to genes that may be differentially expressed in prostate cancer. The SSH reaction utilized cDNA from two different clones of LNCaP cells.

The gene 151P3D4 was derived from one population of LNCaP cells minus another population of LNCaP cells cDNA subtraction. The 151P3D4 SSH DNA sequence (FIG. 1) was identified.

The cDNA derived from one population of LNCaP cells was used as the source of the “driver” cDNA, while the cDNA from another population of LNCaP cells was used as the source of the “tester” cDNA. Double stranded cDNAs corresponding to tester and driver cDNAs were synthesized from 2 μg of poly(A)⁺ RNA isolated from the relevant tissue, as described above, using CLONTECH's PCR-Select cDNA Subtraction Kit and 1 ng of oligonucleotide DPNCDN as primer. First- and second-strand synthesis were carried out as described in the Kit's user manual protocol (CLONTECH Protocol No. PT1117-1, Catalog No. K1804-1). The resulting cDNA was digested with Dpn II for 3 hrs at 37° C. Digested cDNA was extracted with phenol/chloroform (1:1) and ethanol precipitated.

Driver cDNA was generated by combining in a 1:1 ratio Dpn II digested cDNA from the relevant source (see above). Tester cDNA was generated by diluting 1 μl of Dpn II digested cDNA from the relevant source (see above) (400 ng) in 5 μl of water. The diluted cDNA (2 μl, 160 ng) was then ligated to 2 μl of Adaptor 1 and Adaptor 2 (10 μM), in separate ligation reactions, in a total volume of 10 μl at 16° C. overnight, using 400 u of T4 DNA ligase (CLONTECH). Ligation was terminated with 1 μl of 0.2 M EDTA and heating at 72° C. for 5 min.

The first hybridization was performed by adding 1.5 μl (600 ng) of driver cDNA to each of two tubes containing 1.5 μl (20 ng) Adaptor 1- and Adaptor 2-ligated tester cDNA. In a final volume of 4 the samples were overlaid with mineral oil, denatured in an MJ Research thermal cycler at 98° C. for 1.5 minutes, and then were allowed to hybridize for 8 hrs at 68° C. The two hybridizations were then mixed together with an additional 1 μl of fresh denatured driver cDNA and were allowed to hybridize overnight at 68° C. The second hybridization was then diluted in 200 μl of 20 mM Hepes, pH 8.3, 50 mM NaCl, 0.2 mM EDTA, heated at 70° C. for 7 min. and stored at −20° C.

PCR Amplification, Cloning and Sequencing of Gene Fragments Generated from SSH:

To amplify gene fragments resulting from SSH reactions, two PCR amplifications were performed. In the primary PCR reaction 1 μl of the diluted final hybridization mix was added to 1 μl of PCR primer 1 (10 μM), 0.5 μl dNTP mix (10 μM), 2.5 μl 10× reaction buffer (CLONTECH) and 0.5 μl 50× Advantage cDNA polymerase Mix (CLONTECH) in a final volume of 25 μl. PCR 1 was conducted using the following conditions: 75° C. for 5 min., 94° C. for 25 sec., then 27 cycles of 94° C. for 10 sec, 66° C. for 30 sec, 72° C. for 1.5 min. Five separate primary PCR reactions were performed for each experiment. The products were pooled and diluted 1:10 with water. For the secondary PCR reaction, 1 μl from the pooled and diluted primary PCR reaction was added to the same reaction mix as used for PCR 1, except that primers NP1 and NP2 (10 μM) were used instead of PCR primer 1. PCR 2 was performed using 10-12 cycles of 94° C. for 10 sec, 68° C. for 30 sec, and 72° C. for 1.5 minutes. The PCR products were analyzed using 2% agarose gel electrophoresis.

The PCR products were inserted into pCR2.1 using the T/A vector cloning kit (Invitrogen). Transformed E. coli were subjected to blue/white and ampicillin selection. White colonies were picked and arrayed into 96 well plates and were grown in liquid culture overnight. To identify inserts, PCR amplification was performed on 1 ml of bacterial culture using the conditions of PCR1 and NP1 and NP2 as primers. PCR products were analyzed using 2% agarose gel electrophoresis.

Bacterial clones were stored in 20% glycerol in a 96 well format. Plasmid DNA was prepared, sequenced, and subjected to nucleic acid homology searches of the GenBank, dBest, and NCI-CGAP databases.

RT-PCR Expression Analysis:

First strand cDNAs can be generated from 1 μg of mRNA with oligo (dT)12-18 priming using the Gibco-BRL Superscript Preamplification system. The manufacturer's protocol was used which included an incubation for 50 min at 42° C. with reverse transcriptase followed by RNAse H treatment at 37° C. for 20 min. After completing the reaction, the volume can be increased to 200 μl with water prior to normalization. First strand cDNAs from 16 different normal human tissues can be obtained from Clontech.

Normalization of the first strand cDNAs from multiple tissues was performed by using the primers 5′ atatcgccgcgctcgtcgtcgacaa3′ (SEQ ID NO: 56) and 5′ agccacacgcagctcattgtagaagg 3′ (SEQ ID NO: 57) to amplify β-actin. First strand cDNA (5 μl) were amplified in a total volume of 50 μl containing 0.4 μM primers, 0.2 μM each dNTPs, 1×PCR buffer (Clontech, 10 mM Tris-HCL, 1.5 mM MgCl₂, 50 mM KCl, pH8.3) and 1× Klentaq DNA polymerase (Clontech). Five μl of the PCR reaction can be removed at 18, 20, and 22 cycles and used for agarose gel electrophoresis. PCR was performed using an MJ Research thermal cycler under the following conditions: initial denaturation can be at 94° C. for 15 sec, followed by a 18, 20, and 22 cycles of 94° C. for 15, 65° C. for 2 min, 72° C. for 5 sec. A final extension at 72° C. was carried out for 2 min. After agarose gel electrophoresis, the band intensities of the 283 b.p. β-actin bands from multiple tissues were compared by visual inspection. Dilution factors for the first strand cDNAs were calculated to result in equal β-actin band intensities in all tissues after 22 cycles of PCR. Three rounds of normalization can be required to achieve equal band intensities in all tissues after 22 cycles of PCR.

To determine expression levels of the 151P3D4 gene, 5 μl of normalized first strand cDNA were analyzed by PCR using 26, and 30 cycles of amplification. Semi-quantitative expression analysis can be achieved by comparing the PCR products at cycle numbers that give light band intensities. The primers used for RT-PCR were designed using the 151P3D4 SSH sequence and are listed below:

151P3D4.1
5′-CCCACCAAACTGACCTATGATGAA-3′  (SEQ ID NO: 58)
151P3D4.2
5′-TGTATGCTCTGAAGCAGTAGACACC-3′ (SEQ ID NO: 59)

A typical RT-PCR expression study is shown in FIG. 14. First strand cDNA was prepared from vital pool 1 (liver, lung and kidney), vital pool 2 (pancreas, colon and stomach), bladder cancer pool, kidney cancer pool, colon cancer pool, lung cancer pool, ovary cancer pool, breast cancer pool, and cancer metastasis pool. Normalization was performed by PCR using primers to actin and GAPDH. Semi-quantitative PCR, using primers to 151P3D4, was performed at 26 and 30 cycles of amplification. Results show strong expression of 151P3D4 in ovary cancer pool. Expression of 151P3D4 was also detected in bladder cancer pool, kidney cancer pool, colon cancer pool, lung cancer pool, breast cancer pool, cancer metastasis pool, vital pool 2, but not in vital pool 1.

Example 2

Full Length Cloning of 151P3D4

To isolate genes that are expressed in prostate cancer, we used the Suppression Subtractive Hybridization (SSH) procedure using cDNA derived from two different populations of LNCaP cells.

The 151P3D4 SSH cDNA sequence was derived from a subtraction consisting of one population of LNCaP cells minus another population of LNCaP cells. The 151P3D4 SSH cDNA sequence of 417 bp is listed in FIG. 1.

The full-length 151P3D4 v.1 (151P3D4 clone 1-placenta) was cloned from normal placenta cDNA, revealing an ORF of 354 amino acids (FIG. 2 and FIG. 3). 151P3D4 v.1 showed 99% identity over 1492 nucleotides with the human mRNA for cartilage link protein (gi463246) (FIG. 4A). 151P3D4 v.1 protein showed 100% identity over 354 amino acids with the human cartilage link protein (FIG. 4B). Also, 151P3D4 v.1 was 96% identical over 355 amino acids with the mouse link protein (gi4218976) (FIG. 4C).

Other variants of 151P3D4 were also identified and these are listed in FIGS. 2 and 3. 151P3D4 v.2 codes for a novel protein that contains sequences not present in 151P3D4 v.1. These are from amino acids 1 to 400. Amino acids 401 to 721 of 151P3D4 v.2 align with 151P3D4 v.1 at positions 34 to 354 (FIG. 4D). A small portion of 151P3D4 v.2 demonstrates homology to the hypothetical protein XP_—094318 (FIG. 4E). The two proteins show 99% identity over 168 amino acids. The other variants 151P3D4 v.3 through v.11 each differ from 151P3D4 v.1 by one nucleotide (FIG. 10).

Example 3

Chromosomal Mapping of 151P3D4

Chromosomal localization can implicate genes in disease pathogenesis. Several chromosome mapping approaches are available including fluorescent in situ hybridization (FISH), human/hamster radiation hybrid (RH) panels (Walter et al., 1994; Nature Genetics 7:22; Research Genetics, Huntsville, Ala.), human-rodent somatic cell hybrid panels such as is available from the Coriell Institute (Camden, N.J.), and genomic viewers utilizing BLAST homologies to sequenced and mapped genomic clones (NCBI, Bethesda, Md.).

151P3D4 maps to chromosome 5q13-q14.1 using 151P3D4 sequence and the NCBI BLAST tool: located on the World Wide Web at (.ncbi.nlm.nih.gov/genome/seq/page.cgi?F=HsBlast.html&&ORG=Hs).

Example 4

Expression Analysis of 151P3D4 in Normal Tissues and Patient Specimens

Expression analysis by RT-PCR demonstrated that 151P3D4 is strongly expressed in cancer patient specimens (FIG. 14). First strand cDNA was prepared from vital pool 1 (liver, lung and kidney), vital pool 2 (pancreas, colon and stomach), bladder cancer pool, kidney cancer pool, colon cancer pool, lung cancer pool, ovary cancer pool, breast cancer pool, and cancer metastasis pool. Normalization was performed by PCR using primers to actin and GAPDH. Semi-quantitative PCR, using primers to 151P3D4, was performed at 26 and 30 cycles of amplification. Results show strong expression of 151P3D4 in ovary cancer pool. Expression of 151P3D4 was also detected in bladder cancer pool, kidney cancer pool, colon cancer pool, lung cancer pool, breast cancer pool, cancer metastasis pool, vital pool 2, but not in vital pool 1.

Extensive northern blot analysis of 151P3D4 in multiple human normal tissues is shown in FIG. 15. Two multiple tissue northern blots (Clontech) both with 2 ug of mRNA/lane were probed with the 151P3D4 SSH sequence. Size standards in kilobases (kb) are indicated on the side. Results show expression of 151P3D4 in small intestine and placenta. Lower level expression was also detected in heart and colon, but not in the other normal tissues tested.

Expression of 151P3D4 in patient bladder cancer specimens is shown in FIG. 16. RNA was extracted from normal bladder (NB), bladder cancer cell lines (CL; UM-UC-3, J82, SCaBER), bladder cancer patient tumors (T) and normal adjacent tissue (NAT). Northern blots with 10 ug of total RNA were probed with the 151P3D4 SSH sequence. Size standards in kilobases are indicated on the side. Results show expression of 151P3D4 in patient bladder cancer tissues, and in UM-UC-3 bladder cancer cell lines, but not in normal bladder nor in the other bladder cancer cell lines tested.

FIG. 17 shows that 151P3D4 was expressed in kidney cancer patient specimens. RNA was extracted from kidney cancer cell lines (CL: 769-P, A498, SW839), normal kidney (NK), kidney cancer patient tumors (T) and their normal adjacent tissues (NAT). Northern blots with 10 ug of total RNA were probed with the 151P3D4 SSH sequence. Size standards in kilobases are on the side. Results show expression of 151P3D4 in patient kidney tumor tissues, but not in normal kidney, nor in the cell lines tested.

Expression of 151P3D4 was also detected in ovary cancer patient specimen (FIG. 18). RNA was extracted from ovary and cervical cancer cell lines (CL), normal ovary (N), and ovary cancer patient tumor (T). Northern blots with 10 ug of total RNA were probed with the 151P3D4 SSH sequence. Size standards in kilobases are on the side. Results show strong expression of 151P3D4 in patient ovary cancer tissues, but not in normal ovary nor in the ovary and cervical cancer cell lines.

FIG. 19 shows that 151P3D4 was also expressed in stomach cancers and in uterus cancers. Expression of 151P3D4 was assayed in a panel of human stomach and uterus cancers (T) and their respective matched normal tissues (N) on RNA dot blots. 151P3D4 expression was seen in both stomach and uterus cancers.

The restricted expression of 151P3D4 in normal tissues and the expression detected in human cancers suggest that 151P3D4 is a potential therapeutic target and a diagnostic marker for human cancers.

Example 5

Transcript Variants of 151P3D4

Transcript variants are variants of matured mRNA from the same gene by alternative transcription or alternative splicing. Alternative transcripts are transcripts from the same gene but start transcription at different points. Splice variants are mRNA variants spliced differently from the same transcript. In eukaryotes, when a multi-exon gene is transcribed from genomic DNA, the initial RNA is spliced to produce functional mRNA, which has only exons and is used for translation into an amino acid sequence. Accordingly, a given gene can have zero to many alternative transcripts and each transcript can have zero to many splice variants. Each transcript variant has a unique exon makeup, and can have different coding and/or non-coding (5′ or 3′ end) portions, from the original transcript. Transcript variants can code for similar or different proteins with the same or a similar function or may encode proteins with different functions, and may be expressed in the same tissue at the same time, or at different tissue, or at different times, proteins encoded by transcript variants can have similar or different cellular or extracellular localizations, i.e., be secreted.

Transcript variants are identified by a variety of art-accepted methods. For example, alternative transcripts and splice variants are identified in a full-length cloning experiment, or by use of full-length transcript and EST sequences. First, all human ESTs were grouped into clusters which show direct or indirect identity with each other. Second, ESTs in the same cluster were further grouped into sub-clusters and assembled into a consensus sequence. The original gene sequence is compared to the consensus sequence(s) or other full-length sequences. Each consensus sequence is a potential splice variant for that gene (see, e.g., the website located on the World Wide Web at (.doubletwist.com/products/c11_agentsOverview.jhtml)). Even when a variant is identified that is not a full-length clone, that portion of the variant is very useful for antigen generation and for further cloning of the full-length splice variant, using techniques known in the art.

Moreover, computer programs are available in the art that identify transcript variants based on genomic sequences. Genomic-based transcript variant identification programs include FgenesH (A. Salamov and V. Solovyev, “Ab initio gene finding in Drosophila genomic DNA,” Genome Research. 2000 April; 10(4):516-22); Grail Internet website (compbio.ornl.gov/Grail-bin/EmptyGrailForm) and GenScan Internet website (genes.mit.edu/GENSCAN.html). For a general discussion of splice variant identification protocols see., e.g., Southan, C., A genomic perspective on human proteases, FEBS Lett. 2001 Jun. 8; 498(2-3):214-8; de Souza, S. J., et al., Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags, Proc. Natl. Acad Sci USA. 2000 Nov. 7; 97(23):12690-3.

To further confirm the parameters of a transcript variant, a variety of techniques are available in the art, such as full-length cloning, proteomic validation, PCR-based validation, and 5′ RACE validation, etc. (see e.g., Proteomic Validation: Brennan, S. O., et al., Albumin banks peninsula: a new termination variant characterized by electrospray mass spectrometry, Biochem Biophys Acta. 1999 Aug. 17; 1433(1-2):321-6; Ferranti P, et al., Differential splicing of pre-messenger RNA produces multiple forms of mature caprine alpha(s1)-casein, Eur J. Biochem. 1997 Oct. 1; 249(1):1-7. For PCR-based Validation: Wellmann S, et al., Specific reverse transcription-PCR quantification of vascular endothelial growth factor (VEGF) splice variants by LightCycler technology, Clin Chem. 2001 April; 47(4):654-60; Jia, H. P., et al., Discovery of new human beta-defensins using a genomics-based approach, Gene. 2001 Jan. 24; 263(1-2):211-8. For PCR-based and 5′ RACE Validation: Brigle, K. E., et al., Organization of the murine reduced folate carrier gene and identification of variant splice forms, Biochem Biophys Acta. 1997 Aug. 7; 1353(2): 191-8).

It is known in the art that genomic regions are modulated in cancers. When the genomic region to which a gene maps is modulated in a particular cancer, the alternative transcripts or splice variants of the gene are modulated as well. Disclosed herein is that 151P3D4 has a particular expression profile. Alternative transcripts and splice variants of 151P3D4 that are structurally and/or functionally similar to 151P3D4 share this expression pattern, thus serving as tumor associated markers/antigens.

The exon composition of the original transcript, designated as 151P3D4 v.1, is shown in Table LII (A). Using the full-length gene and EST sequences, one alternative transcript was identified, designated as 151P3D4 v.2. Compared with 151P3D4 v.1, transcript variant 151P3D4 v.2 has 10 exons, as shown in Table LII (B) and FIG. 12. Exons 8 and 9 are the same as exons 3 and 4 of 151P3D4 v.1, and exon 10 is the coding portion of exon 5 of 151P3D4 v.1. Each different combination of exons in spatial order, e.g. exons 2 and 3, is a potential splice variant. FIG. 12 shows the schematic alignment of exons of the two transcript variants.

Table LIII shows nucleotide sequence of the transcript variant, 151P3D4 v.2 (see also FIG. 2B). Table LIV shows the alignment of the transcript variant 151P3D4 v.2 with nucleic acid sequence of 151P3D4 v.1. FIG. 3B provides the amino acid translation of the transcript variant 151P3D4 v.2 for the identified reading frame orientation. Table LV displays alignments of the amino acid sequence encoded by the transcript variant 151P3D4 v.2 with that of 151P3D4 v.1.

Example 6

Single Nucleotide Polymorphisms of 151P3D4

Single Nucleotide Polymorphism (SNP) is a single base pair variation in nucleotide sequences. At a specific point of the genome, there are four possible nucleotide base pairs: A/T, C/G, G/C and T/A. Genotype refers to the base pair make-up of one or more spots in the genome of an individual, while haplotype refers to base pair make-up of more than one varied spots on the same DNA molecule (chromosome in higher organism). SNPs that occur on a cDNA are called cSNPs. These cSNPs may change amino acids of the protein encoded by the gene and thus change the functions of the protein. Some SNPs cause inherited diseases and some others contribute to quantitative variations in phenotype and reactions to environmental factors including diet and drugs among individuals. Therefore, SNPs and/or combinations of alleles (called haplotypes) have many applications including diagnosis of inherited diseases, determination of drug reactions and dosage, identification of genes responsible for diseases and discovery of genetic relationship between individuals (P. Nowotny, J. M. Kwon and A. M. Goate, “SNP analysis to dissect human traits,” Curr. Opin. Neurobiol. 2001 October; 11(5):637-641; M. Pirmohamed and B. K. Park, “Genetic susceptibility to adverse drug reactions,” Trends Pharmacol. Sci. 2001 June; 22(6):298-305; J. H. Riley, C. J. Allan, E. Lai and A. Roses, “The use of single nucleotide polymorphisms in the isolation of common disease genes,” Pharmacogenomics. 2000 February; 1(1):39-47; R. Judson, J. C. Stephens and A. Windemuth, “The predictive power of haplotypes in clinical response,” Pharmacogenomics. 2000 February; 1(1):15-26).

SNPs are identified by a variety of art-accepted methods (P. Bean, “The promising voyage of SNP target discovery,” Am. Clin. Lab. 2001 October-November; 20(9):18-20; K. M. Weiss, “In search of human variation,” Genome Res. 1998 July; 8(7):691-697; M. M. She, “Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies,” Clin. Chem. 2001 February; 47(2):164-172). For example, SNPs are identified by sequencing DNA fragments that show polymorphism by gel-based methods such as restriction fragment length polymorphism (RFLP) and denaturing gradient gel electrophoresis (DGGE). They can also be discovered by direct sequencing of DNA samples pooled from different individuals or by comparing sequences from different DNA samples. With the rapid accumulation of sequence data in public and private databases, one can discover SNPs by comparing sequences using computer programs (Z. Gu, L. Hillier and P. Y. Kwok, “Single nucleotide polymorphism hunting in cyberspace,” Hum. Mutat. 1998; 12(4):221-225). SNPs can be verified and genotype or haplotype of an individual can be determined by a variety of methods including direct sequencing and high throughput microarrays (P. Y. Kwok, “Methods for genotyping single nucleotide polymorphisms,” Annu. Rev. Genomics Hum. Genet. 2001; 2:235-258; M. Kokoris, K. Dix, K. Moynihan, J. Mathis, B. Erwin, P. Grass, B. Hines and A. Duesterhoeft, “High-throughput SNP genotyping with the Masscode system,” Mol. Diagn. 2000 December; 5(4):329-340).

Using the methods described above, nine SNPs were identified in the original transcript, 151P3D4 v.1, at positions 154 (A/G), 218 (C/G), 219 (G/C), 999 (C/G), 1326 (C/T), 1399 (T/C), 1400 (C/T), 1653 (T/C) and 1726 (A/G). The transcripts or proteins with alternative alleles were designated as variants 151P3D4 v.3, v.4, v.5, v.6, v.7, v.8, v.9, v.10 and v.11. FIGS. 10 and 12 show the schematic alignment of the nucleotide variants. FIG. 11 shows the schematic alignment of protein variants, corresponding to nucleotide variants. Nucleotide variants that code for the same amino acid sequence as variant 1 are not shown in FIG. 11. These alleles of the SNPs, though shown separately here, can occur in different combinations (haplotypes) and in any one of the transcript variants that contains the sequence context of the SNPs, e.g., 151P3D4 v.7.

Example 7

Production of Recombinant 151P3D4 in Prokaryotic Systems

To express recombinant 151P3D4 and 151P3D4 variants in prokaryotic cells, the full or partial length 151P3D4 and 151P3D4 variant cDNA sequences are cloned into any one of a variety of expression vectors known in the art. One or more of the following regions of 151P3D4 variants are expressed: the full length sequence presented in FIGS. 2 and 3, or any 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more contiguous amino acids from 151P3D4, variants, or analogs thereof.

A. In Vitro Transcription and Translation Constructs:

pCRII: To generate 151P3D4 sense and anti-sense RNA probes for RNA in situ investigations, pCRII constructs (Invitrogen, Carlsbad Calif.) are generated encoding either all or fragments of the 151P3D4 cDNA. The pCRII vector has Sp6 and T7 promoters flanking the insert to drive the transcription of 151P3D4 RNA for use as probes in RNA in situ hybridization experiments. These probes are used to analyze the cell and tissue expression of 151P3D4 at the RNA level. Transcribed 151P3D4 RNA representing the cDNA amino acid coding region of the 151P3D4 gene is used in in vitro translation systems such as the TnT™ Coupled Reticulolysate System (Promega, Corp., Madison, Wis.) to synthesize 151P3D4 protein.

B. Bacterial Constructs:

pGEX Constructs: To generate recombinant 151P3D4 proteins in bacteria that are fused to the Glutathione S-transferase (GST) protein, all or parts of the 151P3D4 cDNA protein coding sequence are cloned into the pGEX family of GST-fusion vectors (Amersham Pharmacia Biotech, Piscataway, N.J.). These constructs allow controlled expression of recombinant 151P3D4 protein sequences with GST fused at the amino-terminus and a six histidine epitope (6× His) at the carboxyl-terminus. The GST and 6× His tags permit purification of the recombinant fusion protein from induced bacteria with the appropriate affinity matrix and allow recognition of the fusion protein with anti-GST and anti-His antibodies. The 6× His tag is generated by adding 6 histidine codons to the cloning primer at the 3′ end, e.g., of the open reading frame (ORF). A proteolytic cleavage site, such as the PreScission™ recognition site in pGEX-6P-1, may be employed such that it permits cleavage of the GST tag from 151P3D4-related protein. The ampicillin resistance gene and pBR322 origin permits selection and maintenance of the pGEX plasmids in E. coli.

pMAL Constructs: To generate, in bacteria, recombinant 151P3D4 proteins that are fused to maltose-binding protein (MBP), all or parts of the 151P3D4 cDNA protein coding sequence are fused to the MBP gene by cloning into the pMAL-c2X and pMAL-p2X vectors (New England Biolabs, Beverly, Mass.). These constructs allow controlled expression of recombinant 151P3D4 protein sequences with MBP fused at the amino-terminus and a 6× His epitope tag at the carboxyl-terminus. The MBP and 6× His tags permit purification of the recombinant protein from induced bacteria with the appropriate affinity matrix and allow recognition of the fusion protein with anti-MBP and anti-His antibodies. The 6× His epitope tag is generated by adding 6 histidine codons to the 3′ cloning primer. A Factor Xa recognition site permits cleavage of the pMAL tag from 151P3D4. The pMAL-c2X and pMAL-p2X vectors are optimized to express the recombinant protein in the cytoplasm or periplasm respectively. Periplasm expression enhances folding of proteins with disulfide bonds.

pET Constructs: To express 151P3D4 in bacterial cells, all or parts of the 151P3D4 cDNA protein coding sequence are cloned into the pET family of vectors (Novagen, Madison, Wis.). These vectors allow tightly controlled expression of recombinant 151P3D4 protein in bacteria with and without fusion to proteins that enhance solubility, such as NusA and thioredoxin (Trx), and epitope tags, such as 6× His and S-Tag™ that aid purification and detection of the recombinant protein. For example, constructs are made utilizing pET NusA fusion system 43.1 such that regions of the 151P3D4 protein are expressed as amino-terminal fusions to NusA.

C. Yeast Constructs:

pESC Constructs: To express 151P3D4 in the yeast species Saccharomyces cerevisiae for generation of recombinant protein and functional studies, all or parts of the 151P3D4 cDNA protein coding sequence are cloned into the pESC family of vectors each of which contain 1 of 4 selectable markers, HIS3, TRP1, LEU2, and URA3 (Stratagene, La Jolla, Calif.). These vectors allow controlled expression from the same plasmid of up to 2 different genes or cloned sequences containing either Flag™ or Myc epitope tags in the same yeast cell. This system is useful to confirm protein-protein interactions of 151P3D4. In addition, expression in yeast yields similar post-translational modifications, such as glycosylations and phosphorylations, that are found when expressed in eukaryotic cells.

pESP Constructs: To express 151P3D4 in the yeast species Saccharomyces pombe, all or parts of the 151P3D4 cDNA protein coding sequence are cloned into the pESP family of vectors. These vectors allow controlled high level of expression of a 151P3D4 protein sequence that is fused at either the amino terminus or at the carboxyl terminus to GST which aids purification of the recombinant protein. A Flag™ epitope tag allows detection of the recombinant protein with anti-Flag™ antibody.

Example 8

Production of Recombinant 151P3D4 in Eukaryotic Systems

A. Mammalian Constructs:

To express recombinant 151P3D4 in eukaryotic cells, the full or partial length 151P3D4 cDNA sequences can be cloned into any one of a variety of expression vectors known in the art. One or more of the following regions of 151P3D4 are expressed in these constructs, amino acids 1 to 354 of 151P3D4 v.1, amino acids 1 to 721 of 151P3D4 v.2, or any 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or more contiguous amino acids from 151P3D4, variants, or analogs thereof. In certain embodiments a region of a specific variant of 151P3D4 is expressed that encodes an amino acid at a specific position which differs from the amino acid of any other variant found at that position. In other embodiments, a region of a variant of 151P3D4 is expressed that lies partly or entirely within a sequence that is unique to that variant.

The constructs can be transfected into any one of a wide variety of mammalian cells such as 293T cells. Transfected 293T cell lysates can be probed with the anti-151P3D4 polyclonal serum, described herein.

pcDNA4/HisMax Constructs: To express 151P3D4 in mammalian cells, a 151P3D4 ORF, or portions thereof, of 151P3D4 are cloned into pcDNA4/HisMax Version A (Invitrogen, Carlsbad, Calif.). Protein expression is driven from the cytomegalovirus (CMV) promoter and the SP16 translational enhancer. The recombinant protein has Xpress™ and six histidine (6× His) epitopes fused to the amino-terminus. The pcDNA4/HisMax vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Zeocin resistance gene allows for selection of mammalian cells expressing the protein and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in E. coli.

pcDNA3.1/MycHis Constructs: To express 151P3D4 in mammalian cells, a 151P3D4 ORF, or portions thereof, of 151P3D4 with a consensus Kozak translation initiation site was cloned into pcDNA3.1/MycHis Version A (Invitrogen, Carlsbad, Calif.). Protein expression is driven from the cytomegalovirus (CMV) promoter. The recombinant protein has the myc epitope and 6× His epitope fused to the carboxyl-terminus. The pcDNA3.1/MycHis vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability, along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Neomycin resistance gene was used, as it allows for selection of mammalian cells expressing the protein and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in E. coli. Results of expression from 151P3D4 .pcDNA3.1/MycHis construct are shown in FIG. 20.

pcDNA3.1/CT-GFP-TOPO Construct: To express 151P3D4 in mammalian cells and to allow detection of the recombinant proteins using fluorescence, a 151P3D4 ORF, or portions thereof, with a consensus Kozak translation initiation site are cloned into pcDNA3.1/CT-GFP-TOPO (Invitrogen, CA). Protein expression is driven from the cytomegalovirus (CMV) promoter. The recombinant proteins have the Green Fluorescent Protein (GFP) fused to the carboxyl-terminus facilitating non-invasive, in vivo detection and cell biology studies. The pcDNA3.1CT-GFP-TOPO vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Neomycin resistance gene allows for selection of mammalian cells that express the protein, and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in E. coli. Additional constructs with an amino-terminal GFP fusion are made in pcDNA3.1/NT-GFP-TOPO spanning the entire length of a 151P3D4 protein.

PAPtag: A 151P3D4 ORF, or portions thereof, is cloned into pAPtag-5 (GenHunter Corp. Nashville, Tenn.). This construct generates an alkaline phosphatase fusion at the carboxyl-terminus of a 151P3D4 protein while fusing the IgGK signal sequence to the amino-terminus. Constructs are also generated in which alkaline phosphatase with an amino-terminal IgGK signal sequence is fused to the amino-terminus of a 151P3D4 protein. The resulting recombinant 151P3D4 proteins are optimized for secretion into the media of transfected mammalian cells and can be used to identify proteins such as ligands or receptors that interact with 151P3D4 proteins. Protein expression is driven from the CMV promoter and the recombinant proteins also contain myc and 6× His epitopes fused at the carboxyl-terminus that facilitates detection and purification. The Zeocin resistance gene present in the vector allows for selection of mammalian cells expressing the recombinant protein and the ampicillin resistance gene permits selection of the plasmid in E. coli.

ptag5: A 151P3D4 ORF, or portions thereof, is cloned into pTag-5. This vector is similar to pAPtag but without the alkaline phosphatase fusion. This construct generates 151P3D4 protein with an amino-terminal IgGκ signal sequence and myc and 6× His epitope tags at the carboxyl-terminus that facilitate detection and affinity purification. The resulting recombinant 151P3D4 protein is optimized for secretion into the media of transfected mammalian cells, and is used as immunogen or ligand to identify proteins such as ligands or receptors that interact with the 151P3D4 proteins. Protein expression is driven from the CMV promoter. The Zeocin resistance gene present in the vector allows for selection of mammalian cells expressing the protein, and the ampicillin resistance gene permits selection of the plasmid in E. coli.

PsecFc: A 151P3D4 ORF, or portions thereof, is also cloned into psecFc. The psecFc vector was assembled by cloning the human immunoglobulin G1 (IgG) Fc (hinge, CH2, CH3 regions) into pSecTag2 (Invitrogen, California). This construct generates an IgG1 Fc fusion at the carboxyl-terminus of the 151P3D4 proteins, while fusing the IgGK signal sequence to N-terminus. 151P3D4 fusions utilizing the murine IgG1 Fc region are also used. The resulting recombinant 151P3D4 proteins are optimized for secretion into the media of transfected mammalian cells, and can be used as immunogens or to identify proteins such as ligands or receptors that interact with 151P3D4 protein. Protein expression is driven from the CMV promoter. The hygromycin resistance gene present in the vector allows for selection of mammalian cells that express the recombinant protein, and the ampicillin resistance gene permits selection of the plasmid in E. coli.

pSRα Constructs: To generate mammalian cell lines that express 151P3D4 constitutively, 151P3D4 ORF, or portions thereof, of 151P3D4 are cloned into pSRα constructs. Amphotropic and ecotropic retroviruses are generated by transfection of pSRα constructs into the 293T-10A1 packaging line or co-transfection of pSRα and a helper plasmid (containing deleted packaging sequences) into the 293 cells, respectively. The retrovirus is used to infect a variety of mammalian cell lines, resulting in the integration of the cloned gene, 151P3D4, into the host cell-lines. Protein expression is driven from a long terminal repeat (LTR). The Neomycin resistance gene present in the vector allows for selection of mammalian cells that express the protein, and the ampicillin resistance gene and ColE1 origin permit selection and maintenance of the plasmid in E. coli. The retroviral vectors can thereafter be used for infection and generation of various cell lines using, for example, PC3, NIH 3T3, TsuPr1, 293 or rat-1 cells.

Additional pSRα constructs are made that fuse an epitope tag such as the FLAG™ tag to the carboxyl-terminus of 151P3D4 sequences to allow detection using anti-Flag antibodies. For example, the FLAG™ sequence 5′ gat tac aag gat gac gac gat aag 3′ (SEQ ID NO: 60) is added to cloning primer at the 3′ end of the ORF. Additional pSRα constructs are made to produce both amino-terminal and carboxyl-terminal GFP and myc/6× His fusion proteins of the full-length 151P3D4 proteins.

Additional Viral Vectors: Additional constructs are made for viral-mediated delivery and expression of 151P3D4. High virus titer leading to high level expression of 151P3D4 is achieved in viral delivery systems such as adenoviral vectors and herpes amplicon vectors. A 151P3D4 coding sequences or fragments thereof are amplified by PCR and subcloned into the AdEasy shuttle vector (Stratagene). Recombination and virus packaging are performed according to the manufacturer's instructions to generate adenoviral vectors. Alternatively, 151P3D4 coding sequences or fragments thereof are cloned into the HSV-1 vector (Imgenex) to generate herpes viral vectors. The viral vectors are thereafter used for infection of various cell lines such as PC3, NIH 3T3, 293 or rat-1 cells.

Regulated Expression Systems: To control expression of 151P3D4 in mammalian cells, coding sequences of 151P3D4, or portions thereof, are cloned into regulated mammalian expression systems such as the T-Rex System (Invitrogen), the GeneSwitch System (Invitrogen) and the tightly-regulated Ecdysone System (Sratagene). These systems allow the study of the temporal and concentration dependent effects of recombinant 151P3D4. These vectors are thereafter used to control expression of 151P3D4 in various cell lines such as PC3, NIH 3T3, 293 or rat-1 cells.

B. Baculovirus Expression Systems

To generate recombinant 151P3D4 proteins in a baculovirus expression system, 151P3D4 ORF, or portions thereof, are cloned into the baculovirus transfer vector pBlueBac 4.5 (Invitrogen), which provides a His-tag at the N-terminus. Specifically, pBlueBac-151P3D4 is co-transfected with helper plasmid pBac-N-Blue (Invitrogen) into SF9 (Spodoptera frugiperda) insect cells to generate recombinant baculovirus (see Invitrogen instruction manual for details). Baculovirus is then collected from cell supernatant and purified by plaque assay.

Recombinant 151P3D4 protein is then generated by infection of HighFive insect cells (Invitrogen) with purified baculovirus. Recombinant 151P3D4 protein can be detected using anti-151P3D4 or anti-His-tag antibody. 151P3D4 protein can be purified and used in various cell-based assays or as immunogen to generate polyclonal and monoclonal antibodies specific for 151P3D4.

Example 9

Antigenicity Profiles and Secondary Structure

FIGS. 5(A & B), FIGS. 6(A & B), FIGS. 7(A & B), FIGS. 8(A & B), and FIGS. 9(A & B) depict graphically five amino acid profiles of 151P3D4 variants 1 and 2, each assessment available by accessing the ProtScale website located on the World Wide Web at (.expasy.ch/cgi-bin/protscale.pl) on the ExPasy molecular biology server.

These profiles: FIG. 5, Hydrophilicity, (Hopp T. P., Woods K. R., 1981. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828); FIG. 6, Hydropathicity, (Kyte J., Doolittle R. F., 1982. J. Mol. Biol. 157:105-132); FIG. 7, Percentage Accessible Residues (Janin J., 1979 Nature 277:491-492); FIG. 8, Average Flexibility, (Bhaskaran R., and Ponnuswamy P. K., 1988. Int. J. Pept. Protein Res. 32:242-255); FIG. 9, Beta-turn (Deleage, G., Roux B. 1987 Protein Engineering 1:289-294); and optionally others available in the art, such as on the ProtScale website, were used to identify antigenic regions of the 151P3D4 protein. Each of the above amino acid profiles of 151P3D4 were generated using the following ProtScale parameters for analysis: 1) A window size of 9; 2) 100% weight of the window edges compared to the window center; and, 3) amino acid profile values normalized to lie between 0 and 1.

Hydrophilicity (FIG. 5), Hydropathicity (FIG. 6) and Percentage Accessible Residues (FIG. 7) profiles were used to determine stretches of hydrophilic amino acids (i.e., values greater than 0.5 on the Hydrophilicity and Percentage Accessible Residues profile, and values less than 0.5 on the Hydropathicity profile). Such regions are likely to be exposed to the aqueous environment, be present on the surface of the protein, and thus available for immune recognition, such as by antibodies.

Average Flexibility (FIG. 8) and Beta-turn (FIG. 9) profiles determine stretches of amino acids (i.e., values greater than 0.5 on the Beta-turn profile and the Average Flexibility profile) that are not constrained in secondary structures such as beta sheets and alpha helices. Such regions are also more likely to be exposed on the protein and thus accessible to immune recognition, such as by antibodies.

Antigenic sequences of the 151P3D4 variant proteins indicated, e.g., by the profiles set forth in FIGS. 5(A & B), FIGS. 6(A & B), FIGS. 7(A & B), FIGS. 8(A & B), and/or FIGS. 9(A & B) are used to prepare immunogens, either peptides or nucleic acids that encode them, to generate therapeutic and diagnostic anti-151P3D4 antibodies. The immunogen can be any 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or more than 50 contiguous amino acids, or the corresponding nucleic acids that encode them, from the 151P3D4 protein variants 1 and 2 listed in FIGS. 2 and 3. In particular, peptide immunogens of the invention can comprise, a peptide region of at least 5 amino acids of FIGS. 2 and 3 in any whole number increment that includes an amino acid position having a value greater than 0.5 in the Hydrophilicity profiles of FIG. 5; a peptide region of at least 5 amino acids of FIGS. 2 and 3 in any whole number increment that includes an amino acid position having a value less than 0.5 in the Hydropathicity profile of FIG. 6; a peptide region of at least 5 amino acids of FIGS. 2 and 3 in any whole number increment that includes an amino acid position having a value greater than 0.5 in the Percent Accessible Residues profiles of FIG. 7; a peptide region of at least 5 amino acids of FIGS. 2 and 3 in any whole number increment that includes an amino acid position having a value greater than 0.5 in the Average Flexibility profiles on FIG. 8; and, a peptide region of at least 5 amino acids of FIGS. 2 and 3 in any whole number increment that includes an amino acid position having a value greater than 0.5 in the Beta-turn profile of FIG. 9. Peptide immunogens of the invention can also comprise nucleic acids that encode any of the forgoing.

All immunogens of the invention, peptide or nucleic acid, can be embodied in human unit dose form, or comprised by a composition that includes a pharmaceutical excipient compatible with human physiology.

The secondary structure of 151P3D4 protein variants 1 and 2, namely the predicted presence and location of alpha helices, extended strands, and random coils, is predicted from the primary amino acid sequence using the HNN—Hierarchical Neural Network method (Guermeur, 1997, Internet website pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_nn.html), accessed from the ExPasy molecular biology server located on the World Wide Web at (.expasy.ch/tools/). The analysis indicates that 151P3D4 variant 1 is composed of 25.71% alpha helix, 21.47% extended strand, and 52.82% random coil (FIG. 13A). Variant 2 is composed of 25.80% alpha helix, 16.64% extended strand, and 57.56% random coil (FIG. 13B).

Analysis for the potential presence of transmembrane domains in the 151P3D4 variant proteins was carried out using a variety of transmembrane prediction algorithms accessed from the ExPasy molecular biology server located on the World Wide Web at (.expasy.ch/tools/). The programs do not predict the presence of transmembrane domains in the 151P3D4 protein variants, suggesting that they are soluble proteins.

Example 10

Generation of 151P3D4 Polyclonal Antibodies Johnstone

Polyclonal antibodies can be raised in a mammal, for example, by one or more injections of an immunizing agent and, if desired, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections. In addition to immunizing with a full length 151P3D4 protein variant, computer algorithms are employed in design of immunogens that, based on amino acid sequence analysis contain characteristics of being antigenic and available for recognition by the immune system of the immunized host (see the Example entitled “Antigenicity Profiles”). Such regions would be predicted to be hydrophilic, flexible, in beta-turn conformations, and be exposed on the surface of the protein (see, e.g., FIGS. 5(A & B), FIGS. 6(A & B), FIGS. 7(A & B), FIGS. 8(A & B), or FIGS. 9(A & B) for amino acid profiles that indicate such regions of 151P3D4 protein variants).

For example, recombinant bacterial fusion proteins or peptides containing hydrophilic, flexible, beta-turn regions of 151P3D4 protein variants are used as antigens to generate polyclonal antibodies in New Zealand White rabbits. For example, in 151P3D4 variant 1, such regions include, but are not limited to, amino acids 99-151, amino acids 218-249, and amino acids 311-332. In sequence specific for variant 2, such regions include, but are not limited to, amino acids 16-38, amino acids 76-90, amino acids 182-230, and amino acids 383-400. It is useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include, but are not limited to, keyhole limpet hemocyanin (KLH), serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. In one embodiment, a peptide encoding amino acids 311-332 of 151P3D4 variant 1 is conjugated to KLH and used to immunize the rabbit. Alternatively the immunizing agent may include all or portions of the 151P3D4 variant proteins, analogs or fusion proteins thereof. For example, the 151P3D4 variant 1 amino acid sequence can be fused using recombinant DNA techniques to any one of a variety of fusion protein partners that are well known in the art, such as glutathione-S-transferase (GST) and HIS tagged fusion proteins. Such fusion proteins are purified from induced bacteria using the appropriate affinity matrix.

In one embodiment, a GST-fusion protein encoding the N-terminal region of 151P3D4 variant 1, amino acids 16-150, minus the first 15 amino acids that likely encodes a cleavable signal peptide, is produced and purified and used as immunogen. Other recombinant bacterial fusion proteins that may be employed include maltose binding protein, LacZ, thioredoxin, NusA, or an immunoglobulin constant region (see the section entitled “Production of 151P3D4 in Prokaryotic Systems” and Current Protocols In Molecular Biology, Volume 2, Unit 16, Frederick M. Ausubul et al. eds., 1995; Linsley, P. S., Brady, W., Urnes, M., Grosmaire, L., Damle, N., and Ledbetter, L. (1991) J. Exp. Med. 174, 561-566).

In addition to bacterial derived fusion proteins, mammalian expressed protein antigens are also used. These antigens are expressed from mammalian expression vectors such as the Tag5 and Fc-fusion vectors (see the section entitled “Production of Recombinant 151P3D4 in Eukaryotic Systems”), and retain post-translational modifications such as glycosylations found in native protein. In one embodiment, amino acids 16-354 of variant 1, minus the endogenous signal peptide, is cloned into the Tag5 mammalian secretion vector. The recombinant protein is purified by metal chelate chromatography from tissue culture supernatants of 293T cells stably expressing the recombinant vector. The purified Tag5 151P3D4 protein is then used as immunogen.

During the immunization protocol, it is useful to mix or emulsify the antigen in adjuvants that enhance the immune response of the host animal. Examples of adjuvants include, but are not limited to, complete Freund's adjuvant (CFA) and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate).

In a typical protocol, rabbits are initially immunized subcutaneously with up to 200 μg, typically 100-200 μg, of fusion protein or peptide conjugated to KLH mixed in complete Freund's adjuvant (CFA). Rabbits are then injected subcutaneously every two weeks with up to 200 μg, typically 100-200 μg, of the immunogen in incomplete Freund's adjuvant (IFA). Test bleeds are taken approximately 7-10 days following each immunization and used to monitor the titer of the antiserum by ELISA.

To test reactivity and specificity of immune serum, such as the rabbit serum derived from immunization with the Tag5-151P3D4 variant 1 protein, the full-length 151P3D4 variant 1 cDNA is cloned into pCDNA 3.1 myc-his expression vector (Invitrogen, see the Example entitled “Production of Recombinant 151P3D4 in Eukaryotic Systems”). After transfection of the constructs into 293T cells, cell lysates are probed with the anti-151P3D4 serum and with anti-His antibody (Santa Cruz Biotechnologies, Santa Cruz, Calif.) to determine specific reactivity to denatured 151P3D4 protein using the Western blot technique (FIG. 20) shows expression of Myc His epitope tagged 151P3D4 variant 1 protein in 293T cells as detected by an anti-His antibody. In addition, the immune serum is tested by fluorescence microscopy, flow cytometry and immunoprecipitation against 293T and other recombinant 151P3D4-expressing cells to determine specific recognition of native protein. Western blot, immunoprecipitation, fluorescent microscopy, and flow cytometric techniques using cells that endogenously express 151P3D4 are also carried out to test reactivity and specificity.

Anti-serum from rabbits immunized with 151P3D4 variant fusion proteins, such as GST and MBP fusion proteins, are purified by depletion of antibodies reactive to the fusion partner sequence by passage over an affinity column containing the fusion partner either alone or in the context of an irrelevant fusion protein. For example, antiserum derived from a GST-151P3D4 variant 1 fusion protein encoding amino acids 16-150 is first purified by passage over a column of GST protein covalently coupled to AffiGel matrix (BioRad, Hercules, Calif.). The antiserum is then affinity purified by passage over a column composed of a MBP-fusion protein also encoding amino acids 16-150 covalently coupled to Affigel matrix. The serum is then further purified by protein G affinity chromatography to isolate the IgG fraction. Sera from other His-tagged antigens and peptide immunized rabbits as well as fusion partner depleted sera are affinity purified by passage over a column matrix composed of the original protein immunogen or free peptide.

Example 11

Generation of 151P3D4 Monoclonal Antibodies (mAbs)

In one embodiment, therapeutic mAbs to 151P3D4 variants comprise those that react with epitopes specific for each variant protein or specific to sequences in common between the variants that would disrupt or modulate the biological function of the 151P3D4 variants, for example those that would disrupt the interaction with ligands and binding partners. Immunogens for generation of such mAbs include those designed to encode or contain the entire 151P3D4 protein variant sequence, regions of the 151P3D4 protein variants predicted to be antigenic from computer analysis of the amino acid sequence (see, e.g., FIGS. 5(A & B), FIGS. 6(A & B), FIGS. 7(A & B), FIGS. 8(A & B), or FIGS. 9(A & B), and the Example entitled “Antigenicity Profiles”). Immunogens include peptides, recombinant bacterial proteins, and mammalian expressed Tag 5 proteins and human and murine IgG FC fusion proteins. In addition, cells engineered to express high levels of a respective 151P3D4 variant, such as 293T-151P3D4 variant 1 or 300.19-151P3D4 variant 1 murine Pre-B cells, are used to immunize mice.

To generate mAbs to a 151P3D4 variant, mice are first immunized intraperitoneally (IP) with, typically, 10-50 μg of protein immunogen or 10⁷ 151P3D4-expressing cells mixed in complete Freund's adjuvant. Mice are then subsequently immunized IP every 2-4 weeks with, typically, 10-50 μg of protein immunogen or 10⁷ cells mixed in incomplete Freund's adjuvant. Alternatively, MPL-TDM adjuvant is used in immunizations. In addition to the above protein and cell-based immunization strategies, a DNA-based immunization protocol is employed in which a mammalian expression vector encoding a 151P3D4 variant sequence is used to immunize mice by direct injection of the plasmid DNA. For example, amino acids 16-354 is cloned into the Tag5 mammalian secretion vector and the recombinant vector is used as immunogen. In another example the same amino acids are cloned into an Fc-fusion secretion vector in which the 151P3D4 variant 1 sequence is fused at the amino-terminus to an IgK leader sequence and at the carboxyl-terminus to the coding sequence of the human or murine IgG Fc region. This recombinant vector is then used as immunogen. The plasmid immunization protocols are used in combination with purified proteins expressed from the same vector and with cells expressing the respective 151P3D4 variant.

During the immunization protocol, test bleeds are taken 7-10 days following an injection to monitor titer and specificity of the immune response. Once appropriate reactivity and specificity is obtained as determined by ELISA, Western blotting, immunoprecipitation, fluorescence microscopy, and flow cytometric analyses, fusion and hybridoma generation is then carried out with established procedures well known in the art (see, e.g., Harlow and Lane, 1988).

In one embodiment for generating 151P3D4 monoclonal antibodies, a Tag5-151P3D4 variant 1 antigen encoding amino acids 16-354, is expressed and purified from stably transfected 293T cells. Balb C mice are initially immunized intraperitoneally with 25 μg of the Tag5-151P3D4 variant 1 protein mixed in complete Freund's adjuvant. Mice are subsequently immunized every two weeks with 25 μg of the antigen mixed in incomplete Freund's adjuvant for a total of three immunizations. ELISA using the Tag5 antigen determines the titer of serum from immunized mice. Reactivity and specificity of serum to full length 151P3D4 variant 1 protein is monitored by Western blotting, immunoprecipitation and flow cytometry using 293T cells transfected with an expression vector encoding the 151P3D4 variant 1 cDNA (see e.g., the Example entitled “Production of Recombinant 151P3D4 in Eukaryotic Systems” and FIG. 20. Other recombinant 151P3D4 variant 1-expressing cells or cells endogenously expressing 151P3D4 variant 1 are also used. Mice showing the strongest reactivity are rested and given a final injection of Tag5 antigen in PBS and then sacrificed four days later. The spleens of the sacrificed mice are harvested and fused to SPO/2 myeloma cells using standard procedures (Harlow and Lane, 1988). Supernatants from HAT selected growth wells are screened by ELISA, Western blot, immunoprecipitation, fluorescent microscopy, and flow cytometry to identify 151P3D4 specific antibody-producing clones.

In another embodiment, a Tag5 antigen encoding amino acids 1-400 of variant 2 is produced, purified and used as immunogen to derive monoclonal antibodies specific to 151P3D4 variant 2. Hybridoma supernatants are then screened on both 151P3D4 variant 2- and 151P3D4 variant 1-expressing cells to identify specific anti-151P3D4 variant 2 monoclonal antibodies.

The binding affinity of a 151P3D4 monoclonal antibody is determined using standard technologies. Affinity measurements quantify the strength of antibody to epitope binding and are used to help define which 151P3D4 monoclonal antibodies preferred for diagnostic or therapeutic use, as appreciated by one of skill in the art. The BIAcore system (Uppsala, Sweden) is a preferred method for determining binding affinity. The BIAcore system uses surface plasmon resonance (SPR, Welford K. 1991, Opt. Quant. Elect. 23:1; Morton and Myszka, 1998, Methods in Enzymology 295: 268) to monitor biomolecular interactions in real time. BIAcore analysis conveniently generates association rate constants, dissociation rate constants, equilibrium dissociation constants, and affinity constants.

Example 12

HLA Class I and Class II Binding Assays

HLA class I and class II binding assays using purified HLA molecules are performed in accordance with disclosed protocols (e.g., PCT publications WO 94/20127 and WO 94/03205; Sidney et al., Current Protocols in Immunology 18.3.1 (1998); Sidney, et al., J. Immunol. 154:247 (1995); Sette, et al., Mol. Immunol. 31:813 (1994)). Briefly, purified MHC molecules (5 to 500 nM) are incubated with various unlabeled peptide inhibitors and 1-10 nM ¹²⁵I-radiolabeled probe peptides as described. Following incubation, MHC-peptide complexes are separated from free peptide by gel filtration and the fraction of peptide bound is determined. Typically, in preliminary experiments, each MHC preparation is titered in the presence of fixed amounts of radiolabeled peptides to determine the concentration of HLA molecules necessary to bind 10-20% of the total radioactivity. All subsequent inhibition and direct binding assays are performed using these HLA concentrations.

Since under these conditions [label]<[HLA] and IC₅₀≧[HLA], the measured IC₅₀ values are reasonable approximations of the true K_D values. Peptide inhibitors are typically tested at concentrations ranging from 120 μg/ml to 1.2 ng/ml, and are tested in two to four completely independent experiments. To allow comparison of the data obtained in different experiments, a relative binding figure is calculated for each peptide by dividing the IC₅₀ of a positive control for inhibition by the IC₅₀ for each tested peptide (typically unlabeled versions of the radiolabeled probe peptide). For database purposes, and inter-experiment comparisons, relative binding values are compiled. These values can subsequently be converted back into IC₅₀ nM values by dividing the IC₅₀ nM of the positive controls for inhibition by the relative binding of the peptide of interest. This method of data compilation is accurate and consistent for comparing peptides that have been tested on different days, or with different lots of purified MHC.

Binding assays as outlined above may be used to analyze HLA supermotif and/or HLA motif-bearing peptides (see Table IV).

Example 13

Identification of HLA Supermotif- and Motif-Bearing CTL Candidate Epitopes

HLA vaccine compositions of the invention can include multiple epitopes. The multiple epitopes can comprise multiple HLA supermotifs or motifs to achieve broad population coverage. This example illustrates the identification and confirmation of supermotif- and motif-bearing epitopes for the inclusion in such a vaccine composition. Calculation of population coverage is performed using the strategy described below.

Computer Searches and Algorithms for Identification of Supermotif and/or Motif-Bearing Epitopes

The searches performed to identify the motif-bearing peptide sequences in the Example entitled “Antigenicity Profiles” and Tables V-XVIII and XXII-LI employ the protein sequence data from the gene product of 151P3D4 set forth in FIGS. 2 and 3.

Computer searches for epitopes bearing HLA Class I or Class II supermotifs or motifs are performed as follows. All translated 151P3D4 protein sequences are analyzed using a text string search software program to identify potential peptide sequences containing appropriate HLA binding motifs; such programs are readily produced in accordance with information in the art in view of known motif/supermotif disclosures. Furthermore, such calculations can be made mentally.

Identified A2-, A3-, and DR-supermotif sequences are scored using polynomial algorithms to predict their capacity to bind to specific HLA-Class I or Class II molecules. These polynomial algorithms account for the impact of different amino acids at different positions, and are essentially based on the premise that the overall affinity (or ΔG) of peptide-HLA molecule interactions can be approximated as a linear polynomial function of the type:

“ΔG”=a_1i×a_2i×a_3i . . . ×a_ni

where a_ji is a coefficient which represents the effect of the presence of a given amino acid (j) at a given position (i) along the sequence of a peptide of n amino acids. The crucial assumption of this method is that the effects at each position are essentially independent of each other (i.e., independent binding of individual side-chains). When residue j occurs at position i in the peptide, it is assumed to contribute a constant amount j_i to the free energy of binding of the peptide irrespective of the sequence of the rest of the peptide.

The method of derivation of specific algorithm coefficients has been described in Gulukota et al., J. Mol. Biol. 267:1258-126, 1997; (see also Sidney et al., Human Immunol. 45:79-93, 1996; and Southwood et al., J. Immunol. 160:3363-3373, 1998). Briefly, for all i positions, anchor and non-anchor alike, the geometric mean of the average relative binding (ARB) of all peptides carrying j is calculated relative to the remainder of the group, and used as the estimate of j_i. For Class II peptides, if multiple alignments are possible, only the highest scoring alignment is utilized, following an iterative procedure. To calculate an algorithm score of a given peptide in a test set, the ARB values corresponding to the sequence of the peptide are multiplied. If this product exceeds a chosen threshold, the peptide is predicted to bind. Appropriate thresholds are chosen as a function of the degree of stringency of prediction desired.

Selection of HLA-A2 Supertype Cross-Reactive Peptides

Protein sequences from 151P3D4 are scanned utilizing motif identification software, to identify 8-, 9-10- and 11-mer sequences containing the HLA-A2-supermotif main anchor specificity. Typically, these sequences are then scored using the protocol described above and the peptides corresponding to the positive-scoring sequences are synthesized and tested for their capacity to bind purified HLA-A*0201 molecules in vitro (HLA-A*0201 is considered a prototype A2 supertype molecule).

These peptides are then tested for the capacity to bind to additional A2-supertype molecules (A*0202, A*0203, A*0206, and A*6802). Peptides that bind to at least three of the five A2-supertype alleles tested are typically deemed A2-supertype cross-reactive binders. Preferred peptides bind at an affinity equal to or less than 500 nM to three or more HLA-A2 supertype molecules.

Selection of HLA-A3 Supermotif-Bearing Epitopes

The 151P3D4 protein sequence(s) scanned above is also examined for the presence of peptides with the HLA-A3-supermotif primary anchors. Peptides corresponding to the HLA A3 supermotif-bearing sequences are then synthesized and tested for binding to HLA-A*0301 and HLA-A*1101 molecules, the molecules encoded by the two most prevalent A3-supertype alleles. The peptides that bind at least one of the two alleles with binding affinities of ≦500 nM, often ≦200 nM, are then tested for binding cross-reactivity to the other common A3-supertype alleles (e.g., A*3101, A*3301, and A*6801) to identify those that can bind at least three of the five HLA-A3-supertype molecules tested.

Selection of HLA-B7 Supermotif Bearing Epitopes

The 151P3D4 protein(s) scanned above is also analyzed for the presence of 8-, 9-10-, or 11-mer peptides with the HLA-B7-supermotif. Corresponding peptides are synthesized and tested for binding to HLA-B*0702, the molecule encoded by the most common B7-supertype allele (i.e., the prototype B7 supertype allele). Peptides binding B*0702 with IC₅₀ of ≦500 nM are identified using standard methods. These peptides are then tested for binding to other common B7-supertype molecules (e.g., B*3501, B*5101, B*5301, and B*5401). Peptides capable of binding to three or more of the five B7-supertype alleles tested are thereby identified.

Selection of A1 and A24 Motif-Bearing Epitopes

To further increase population coverage, HLA-A1 and -A24 epitopes can also be incorporated into vaccine compositions. An analysis of the 151P3D4 protein can also be performed to identify HLA-A1- and A24-motif-containing sequences.

High affinity and/or cross-reactive binding epitopes that bear other motif and/or supermotifs are identified using analogous methodology.

Example 14

Confirmation of Immunogenicity

Cross-reactive candidate CTL A2-supermotif-bearing peptides that are identified as described herein are selected to confirm in vitro immunogenicity. Confirmation is performed using the following methodology:

Target Cell Lines for Cellular Screening:

The 0.221A2.1 cell line, produced by transferring the HLA-A2.1 gene into the HLA-A, -B, -C null mutant human B-lymphoblastoid cell line 721.221, is used as the peptide-loaded target to measure activity of HLA-A2.1-restricted CTL. This cell line is grown in RPMI-1640 medium supplemented with antibiotics, sodium pyruvate, nonessential amino acids and 10% (v/v) heat inactivated FCS. Cells that express an antigen of interest, or transfectants comprising the gene encoding the antigen of interest, can be used as target cells to confirm the ability of peptide-specific CTLs to recognize endogenous antigen.

Primary CTL Induction Cultures:

Generation of Dendritic Cells (DC): PBMCs are thawed in RPMI with 30 μg/ml DNAse, washed twice and resuspended in complete medium (RPMI-1640 plus 5% AB human serum, non-essential amino acids, sodium pyruvate, L-glutamine and penicillin/streptomycin). The monocytes are purified by plating 10×10⁶ PBMC/well in a 6-well plate. After 2 hours at 37° C., the non-adherent cells are removed by gently shaking the plates and aspirating the supernatants. The wells are washed a total of three times with 3 ml RPMI to remove most of the non-adherent and loosely adherent cells. Three ml of complete medium containing 50 ng/ml of GM-CSF and 1,000 U/ml of IL-4 are then added to each well. TNFα is added to the DCs on day 6 at 75 ng/ml and the cells are used for CTL induction cultures on day 7.

Induction of CTL with DC and Peptide: CD8+ T-cells are isolated by positive selection with Dynal immunomagnetic beads (Dynabeads® M-450) and the Detacha-bead® reagent. Typically about 200-250×10⁶ PBMC are processed to obtain 24×10⁶ CD8⁺ T-cells (enough for a 48-well plate culture). Briefly, the PBMCs are thawed in RPMI with 30 μg/ml DNAse, washed once with PBS containing 1% human AB serum and resuspended in PBS/1% AB serum at a concentration of 20×10⁶ cells/ml. The magnetic beads are washed 3 times with PBS/AB serum, added to the cells (140 μl beads/20×10⁶ cells) and incubated for 1 hour at 4° C. with continuous mixing. The beads and cells are washed 4× with PBS/AB serum to remove the nonadherent cells and resuspended at 100×10⁶ cells/ml (based on the original cell number) in PBS/AB serum containing 100 μl/ml Detacha-bead® reagent and 30 μg/ml DNAse. The mixture is incubated for 1 hour at room temperature with continuous mixing. The beads are washed again with PBS/AB/DNAse to collect the CD8+T-cells. The DC are collected and centrifuged at 1300 rpm for 5-7 minutes, washed once with PBS with 1% BSA, counted and pulsed with 40 μg/ml of peptide at a cell concentration of 1-2×10⁶/ml in the presence of 3 μg/ml β₂-microglobulin for 4 hours at 20° C. The DC are then irradiated (4,200 rads), washed 1 time with medium and counted again.

Setting up induction cultures: 0.25 ml cytokine-generated DC (at 1×10⁵ cells/ml) are co-cultured with 0.25 ml of CD8+ T-cells (at 2×10⁶ cell/ml) in each well of a 48-well plate in the presence of 10 ng/ml of IL-7. Recombinant human IL-10 is added the next day at a final concentration of 10 ng/ml and rhuman IL-2 is added 48 hours later at 10 IU/ml.

Restimulation of the induction cultures with peptide-pulsed adherent cells: Seven and fourteen days after the primary induction, the cells are restimulated with peptide-pulsed adherent cells. The PBMCs are thawed and washed twice with RPMI and DNAse. The cells are resuspended at 5×10⁶ cells/ml and irradiated at ˜4200 rads. The PBMCs are plated at 2×10⁶ in 0.5 ml complete medium per well and incubated for 2 hours at 37° C. The plates are washed twice with RPMI by tapping the plate gently to remove the nonadherent cells and the adherent cells pulsed with 10 μg/ml of peptide in the presence of 3 μg/ml β₂ microglobulin in 0.25 ml RPMI/5% AB per well for 2 hours at 37° C. Peptide solution from each well is aspirated and the wells are washed once with RPMI. Most of the media is aspirated from the induction cultures (CD8+ cells) and brought to 0.5 ml with fresh media. The cells are then transferred to the wells containing the peptide-pulsed adherent cells. Twenty four hours later recombinant human IL-10 is added at a final concentration of 10 ng/ml and recombinant human IL2 is added the next day and again 2-3 days later at 50 IU/ml (Tsai et al., Critical Reviews in Immunology 18(1-2):65-75, 1998). Seven days later, the cultures are assayed for CTL activity in a ⁵¹Cr release assay. In some experiments the cultures are assayed for peptide-specific recognition in the in situ IFNγ ELISA at the time of the second restimulation followed by assay of endogenous recognition 7 days later. After expansion, activity is measured in both assays for a side-by-side comparison.

Measurement of CTL Lytic Activity by ⁵¹Cr Release.

Seven days after the second restimulation, cytotoxicity is determined in a standard (5 hr) ⁵¹Cr release assay by assaying individual wells at a single E:T. Peptide-pulsed targets are prepared by incubating the cells with 10 μg/ml peptide overnight at 37° C.

Adherent target cells are removed from culture flasks with trypsin-EDTA. Target cells are labeled with 200 μCi of ⁵¹Cr sodium chromate (Dupont, Wilmington, Del.) for 1 hour at 37° C. Labeled target cells are resuspended at 10⁶ per ml and diluted 1:10 with K562 cells at a concentration of 3.3×10⁶/ml (an NK-sensitive erythroblastoma cell line used to reduce non-specific lysis). Target cells (100 μl) and effectors (100 μl) are plated in 96 well round-bottom plates and incubated for 5 hours at 37° C. At that time, 100 μl of supernatant are collected from each well and percent lysis is determined according to the formula:

[(cpm of the test sample−cpm of the spontaneous ⁵¹Cr release sample)/(cpm of the maximal ⁵¹Cr release sample−cpm of the spontaneous ⁵¹Cr release sample)]×100.

Maximum and spontaneous release are determined by incubating the labeled targets with 1% Triton X-100 and media alone, respectively. A positive culture is defined as one in which the specific lysis (sample-background) is 10% or higher in the case of individual wells and is 15% or more at the two highest E:T ratios when expanded cultures are assayed.

In Situ Measurement of Human IFNγ Production as an Indicator of Peptide-Specific and Endogenous Recognition

Immulon 2 plates are coated with mouse anti-human IFNγ monoclonal antibody (4 μg/ml 0.1M NaHCO₃, pH8.2) overnight at 4° C. The plates are washed with Ca²⁺, Mg²⁺-free PBS/0.05% Tween 20 and blocked with PBS/10% FCS for two hours, after which the CTLs (100 μl/well) and targets (100 μl/well) are added to each well, leaving empty wells for the standards and blanks (which received media only). The target cells, either peptide-pulsed or endogenous targets, are used at a concentration of 1×10⁶ cells/ml. The plates are incubated for 48 hours at 37° C. with 5% CO₂.

Recombinant human IFN-gamma is added to the standard wells starting at 400 pg or 1200 pg/100 microliter/well and the plate incubated for two hours at 37° C. The plates are washed and 100 μl of biotinylated mouse anti-human IFN-gamma monoclonal antibody (2 microgram/ml in PBS/3% FCS/0.05% Tween 20) are added and incubated for 2 hours at room temperature. After washing again, 100 microliter HRP-streptavidin (1:4000) are added and the plates incubated for one hour at room temperature. The plates are then washed 6× with wash buffer, 100 microliter/well developing solution (TMB 1:1) are added, and the plates allowed to develop for 5-15 minutes. The reaction is stopped with 50 microliter/well 1M H₃PO₄ and read at OD450. A culture is considered positive if it measured at least 50 pg of IFN-gamma/well above background and is twice the background level of expression.

CTL Expansion.

Those cultures that demonstrate specific lytic activity against peptide-pulsed targets and/or tumor targets are expanded over a two week period with anti-CD3. Briefly, 5×10⁴ CD8+ cells are added to a T25 flask containing the following: 1×10⁶ irradiated (4,200 rad) PBMC (autologous or allogeneic) per ml, 2×10⁵ irradiated (8,000 rad) EBV-transformed cells per ml, and OKT3 (anti-CD3) at 30 ng per ml in RPMI-1640 containing 10% (v/v) human AB serum, non-essential amino acids, sodium pyruvate, 25 μM 2-mercaptoethanol, L-glutamine and penicillin/streptomycin. Recombinant human IL2 is added 24 hours later at a final concentration of 200 IU/ml and every three days thereafter with fresh media at 50 IU/ml. The cells are split if the cell concentration exceeds 1×10⁶/ml and the cultures are assayed between days 13 and 15 at E:T ratios of 30, 10, 3 and 1:1 in the ⁵¹Cr release assay or at 1×10⁶/ml in the in situ IFNγ assay using the same targets as before the expansion.

Cultures are expanded in the absence of anti-CD3⁺ as follows. Those cultures that demonstrate specific lytic activity against peptide and endogenous targets are selected and 5×10⁴ CD8⁺ cells are added to a T25 flask containing the following: 1×10⁶ autologous PBMC per ml which have been peptide-pulsed with 10 μg/ml peptide for two hours at 37° C. and irradiated (4,200 rad); 2×10⁵ irradiated (8,000 rad) EBV-transformed cells per ml RPMI-1640 containing 10% (v/v) human AB serum, non-essential AA, sodium pyruvate, 25 mM 2-ME, L-glutamine and gentamicin.

Immunogenicity of A2 Supermotif-Bearing Peptides

A2-supermotif cross-reactive binding peptides are tested in the cellular assay for the ability to induce peptide-specific CTL in normal individuals. In this analysis, a peptide is typically considered to be an epitope if it induces peptide-specific CTLs in at least individuals, and preferably, also recognizes the endogenously expressed peptide.

Immunogenicity can also be confirmed using PBMCs isolated from patients bearing a tumor that expresses 151P3D4. Briefly, PBMCs are isolated from patients, re-stimulated with peptide-pulsed monocytes and assayed for the ability to recognize peptide-pulsed target cells as well as transfected cells endogenously expressing the antigen.

Evaluation of A*03/A11 Immunogenicity

HLA-A3 supermotif-bearing cross-reactive binding peptides are also evaluated for immunogenicity using methodology analogous for that used to evaluate the immunogenicity of the HLA-A2 supermotif peptides.

Evaluation of B7 Immunogenicity

Immunogenicity screening of the B7-supertype cross-reactive binding peptides identified as set forth herein are confirmed in a manner analogous to the confirmation of A2- and A3-supermotif-bearing peptides.

Peptides bearing other supermotifs/motifs, e.g., HLA-A1, HLA-A24 etc. are also confirmed using similar methodology

Example 15

Implementation of the Extended Supermotif to Improve the Binding Capacity of Native Epitopes by Creating Analogs

HLA motifs and supermotifs (comprising primary and/or secondary residues) are useful in the identification and preparation of highly cross-reactive native peptides, as demonstrated herein. Moreover, the definition of HLA motifs and supermotifs also allows one to engineer highly cross-reactive epitopes by identifying residues within a native peptide sequence which can be analoged to confer upon the peptide certain characteristics, e.g. greater cross-reactivity within the group of HLA molecules that comprise a supertype, and/or greater binding affinity for some or all of those HLA molecules. Examples of analoging peptides to exhibit modulated binding affinity are set forth in this example.

Analoging at Primary Anchor Residues

Peptide engineering strategies are implemented to further increase the cross-reactivity of the epitopes. For example, the main anchors of A2-supermotif-bearing peptides are altered, for example, to introduce a preferred L, I, V, or M at position 2, and I or V at the C-terminus.

To analyze the cross-reactivity of the analog peptides, each engineered analog is initially tested for binding to the prototype A2 supertype allele A*0201, then, if A*0201 binding capacity is maintained, for A2-supertype cross-reactivity.

Alternatively, a peptide is confirmed as binding one or all supertype members and then analoged to modulate binding affinity to any one (or more) of the supertype members to add population coverage.

The selection of analogs for immunogenicity in a cellular screening analysis is typically further restricted by the capacity of the parent wild type (WT) peptide to bind at least weakly, i.e., bind at an IC₅₀ of 5000 nM or less, to three of more A2 supertype alleles. The rationale for this requirement is that the WT peptides must be present endogenously in sufficient quantity to be biologically relevant. Analoged peptides have been shown to have increased immunogenicity and cross-reactivity by T cells specific for the parent epitope (see, e.g., Parkhurst et al., J. Immunol. 157:2539, 1996; and Pogue et al., Proc. Natl. Acad. Sci. USA 92:8166, 1995).

In the cellular screening of these peptide analogs, it is important to confirm that analog-specific CTLs are also able to recognize the wild-type peptide and, when possible, target cells that endogenously express the epitope.

Analoging of HLA-A3 and B7-Supermotif-Bearing Peptides

Analogs of HLA-A3 supermotif-bearing epitopes are generated using strategies similar to those employed in analoging HLA-A2 supermotif-bearing peptides. For example, peptides binding to 3/5 of the A3-supertype molecules are engineered at primary anchor residues to possess a preferred residue (V, S, M, or A) at position 2.

The analog peptides are then tested for the ability to bind A*03 and A*11 (prototype A3 supertype alleles). Those peptides that demonstrate 500 nM binding capacity are then confirmed as having A3-supertype cross-reactivity.

Similarly to the A2- and A3-motif bearing peptides, peptides binding 3 or more B7-supertype alleles can be improved, where possible, to achieve increased cross-reactive binding or greater binding affinity or binding half life. B7 supermotif-bearing peptides are, for example, engineered to possess a preferred residue (V, I, L, or F) at the C-terminal primary anchor position, as demonstrated by Sidney et al. (J. Immunol. 157:3480-3490, 1996).

Analoging at primary anchor residues of other motif and/or supermotif-bearing epitopes is performed in a like manner.

The analog peptides are then be confirmed for immunogenicity, typically in a cellular screening assay. Again, it is generally important to demonstrate that analog-specific CTLs are also able to recognize the wild-type peptide and, when possible, targets that endogenously express the epitope.

Analoging at Secondary Anchor Residues

Moreover, HLA supermotifs are of value in engineering highly cross-reactive peptides and/or peptides that bind HLA molecules with increased affinity by identifying particular residues at secondary anchor positions that are associated with such properties. For example, the binding capacity of a B7 supermotif-bearing peptide with an F residue at position 1 is analyzed. The peptide is then analoged to, for example, substitute L for F at position 1. The analoged peptide is evaluated for increased binding affinity, binding half life and/or increased cross-reactivity. Such a procedure identifies analoged peptides with enhanced properties.

Engineered analogs with sufficiently improved binding capacity or cross-reactivity can also be tested for immunogenicity in HLA-B7-transgenic mice, following for example, IFA immunization or lipopeptide immunization. Analoged peptides are additionally tested for the ability to stimulate a recall response using PBMC from patients with 151P3D4-expressing tumors.

Other Analoging Strategies

Another form of peptide analoging, unrelated to anchor positions, involves the substitution of a cysteine with α-amino butyric acid. Due to its chemical nature, cysteine has the propensity to form disulfide bridges and sufficiently alter the peptide structurally so as to reduce binding capacity. Substitution of α-amino butyric acid for cysteine not only alleviates this problem, but has been shown to improve binding and crossbinding capabilities in some instances (see, e.g., the review by Sette et al., In: Persistent Viral Infections, Eds. R. Ahmed and I. Chen, John Wiley & Sons, England, 1999).

Thus, by the use of single amino acid substitutions, the binding properties and/or cross-reactivity of peptide ligands for HLA supertype molecules can be modulated.

Example 16

Identification and Confirmation of 151P3D4-Derived Sequences with HLA-DR Binding Motifs

Peptide epitopes bearing an HLA class II supermotif or motif are identified and confirmed as outlined below using methodology similar to that described for HLA Class I peptides.

Selection of HLA-DR-Supermotif-Bearing Epitopes.

To identify 151P3D4-derived, HLA class II HTL epitopes, a 151P3D4 antigen is analyzed for the presence of sequences bearing an HLA-DR-motif or supermotif. Specifically, 15-mer sequences are selected comprising a DR-supermotif, comprising a 9-mer core, and three-residue N- and C-terminal flanking regions (15 amino acids total).

Protocols for predicting peptide binding to DR molecules have been developed (Southwood et al., J. Immunol. 160:3363-3373, 1998). These protocols, specific for individual DR molecules, allow the scoring, and ranking, of 9-mer core regions. Each protocol not only scores peptide sequences for the presence of DR-supermotif primary anchors (i.e., at position 1 and position 6) within a 9-mer core, but additionally evaluates sequences for the presence of secondary anchors. Using allele-specific selection tables (see, e.g., Southwood et al., ibid.), it has been found that these protocols efficiently select peptide sequences with a high probability of binding a particular DR molecule. Additionally, it has been found that performing these protocols in tandem, specifically those for DR1, DR4w4, and DR7, can efficiently select DR cross-reactive peptides.

The 151P3D4-derived peptides identified above are tested for their binding capacity for various common HLA-DR molecules. All peptides are initially tested for binding to the DR molecules in the primary panel: DR1, DR4w4, and DR7. Peptides binding at least two of these three DR molecules are then tested for binding to DR2w2 β1, DR2w2 β2, DR6w19, and DR9 molecules in secondary assays. Finally, peptides binding at least two of the four secondary panel DR molecules, and thus cumulatively at least four of seven different DR molecules, are screened for binding to DR4w15, DR5w11, and DR8w2 molecules in tertiary assays. Peptides binding at least seven of the ten DR molecules comprising the primary, secondary, and tertiary screening assays are considered cross-reactive DR binders. 151P3D4-derived peptides found to bind common HLA-DR alleles are of particular interest.

Selection of DR3 Motif Peptides

Because HLA-DR3 is an allele that is prevalent in Caucasian, Black, and Hispanic populations, DR3 binding capacity is a relevant criterion in the selection of HTL epitopes. Thus, peptides shown to be candidates may also be assayed for their DR3 binding capacity. However, in view of the binding specificity of the DR3 motif, peptides binding only to DR3 can also be considered as candidates for inclusion in a vaccine formulation.

To efficiently identify peptides that bind DR3, target 151P3D4 antigens are analyzed for sequences carrying one of the two DR3-specific binding motifs reported by Geluk et al. (J. Immunol. 152:5742-5748, 1994). The corresponding peptides are then synthesized and confirmed as having the ability to bind DR3 with an affinity of 1 μM or better, i.e., less than 1 μM. Peptides are found that meet this binding criterion and qualify as HLA class II high affinity binders.

DR3 binding epitopes identified in this manner are included in vaccine compositions with DR supermotif-bearing peptide epitopes.

Similarly to the case of HLA class I motif-bearing peptides, the class II motif-bearing peptides are analoged to improve affinity or cross-reactivity. For example, aspartic acid at position 4 of the 9-mer core sequence is an optimal residue for DR3 binding, and substitution for that residue often improves DR 3 binding.

Example 17

Immunogenicity of 151P3D4-Derived HTL Epitopes

This example determines immunogenic DR supermotif- and DR3 motif-bearing epitopes among those identified using the methodology set forth herein.

Immunogenicity of HTL epitopes are confirmed in a manner analogous to the determination of immunogenicity of CTL epitopes, by assessing the ability to stimulate HTL responses and/or by using appropriate transgenic mouse models. Immunogenicity is determined by screening for: 1.) in vitro primary induction using normal PBMC or 2.) recall responses from patients who have 151P3D4-expressing tumors.

Example 18

Calculation of Phenotypic Frequencies of HLA-Supertypes in Various Ethnic Backgrounds to Determine Breadth of Population Coverage

This example illustrates the assessment of the breadth of population coverage of a vaccine composition comprised of multiple epitopes comprising multiple supermotifs and/or motifs.

In order to analyze population coverage, gene frequencies of HLA alleles are determined. Gene frequencies for each HLA allele are calculated from antigen or allele frequencies utilizing the binomial distribution formulae gf=1−(SQRT(1−af)) (see, e.g., Sidney et al., Human Immunol. 45:79-93, 1996). To obtain overall phenotypic frequencies, cumulative gene frequencies are calculated, and the cumulative antigen frequencies derived by the use of the inverse formula [af=1−(1−Cgf)²].

Where frequency data is not available at the level of DNA typing, correspondence to the serologically defined antigen frequencies is assumed. To obtain total potential supertype population coverage no linkage disequilibrium is assumed, and only alleles confirmed to belong to each of the supertypes are included (minimal estimates). Estimates of total potential coverage achieved by inter-loci combinations are made by adding to the A coverage the proportion of the non-A covered population that could be expected to be covered by the B alleles considered (e.g., total=A+B*(1−A)). Confirmed members of the A3-like supertype are A3, A11, A31, A*3301, and A*6801. Although the A3-like supertype may also include A34, A66, and A*7401, these alleles were not included in overall frequency calculations Likewise, confirmed members of the A2-like supertype family are A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207, A*6802, and A*6901. Finally, the B7-like supertype-confirmed alleles are: B7, B*3501-03, B51, B*5301, B*5401, B*5501-2, B*5601, B*6701, and B*7801 (potentially also B*1401, B*3504-06, B*4201, and B*5602).

Population coverage achieved by combining the A2-, A3- and B7-supertypes is approximately 86% in five major ethnic groups. Coverage may be extended by including peptides bearing the A1 and A24 motifs. On average, A1 is present in 12% and A24 in 29% of the population across five different major ethnic groups (Caucasian, North American Black, Chinese, Japanese, and Hispanic). Together, these alleles are represented with an average frequency of 39% in these same ethnic populations. The total coverage across the major ethnicities when A1 and A24 are combined with the coverage of the A2-, A3- and B7-supertype alleles is >95%. An analogous approach can be used to estimate population coverage achieved with combinations of class II motif-bearing epitopes.

Immunogenicity studies in humans (e.g., Bertoni et al., J. Clin. Invest. 100:503, 1997; Doolan et al., Immunity 7:97, 1997; and Threlkeld et al., J. Immunol. 159:1648, 1997) have shown that highly cross-reactive binding peptides are almost always recognized as epitopes. The use of highly cross-reactive binding peptides is an important selection criterion in identifying candidate epitopes for inclusion in a vaccine that is immunogenic in a diverse population.

With a sufficient number of epitopes (as disclosed herein and from the art), an average population coverage is predicted to be greater than 95% in each of five major ethnic populations. The game theory Monte Carlo simulation analysis, which is known in the art (see e.g., Osborne, M. J. and Rubinstein, A. “A course in game theory” MIT Press, 1994), can be used to estimate what percentage of the individuals in a population comprised of the Caucasian, North American Black, Japanese, Chinese, and Hispanic ethnic groups would recognize the vaccine epitopes described herein. A preferred percentage is 90%. A more preferred percentage is 95%.

Example 19

CTL Recognition of Endogenously Processed Antigens after Priming

This example confirms that CTL induced by native or analoged peptide epitopes identified and selected as described herein recognize endogenously synthesized, i.e., native antigens.

Effector cells isolated from transgenic mice that are immunized with peptide epitopes, for example HLA-A2 supermotif-bearing epitopes, are re-stimulated in vitro using peptide-coated stimulator cells. Six days later, effector cells are assayed for cytotoxicity and the cell lines that contain peptide-specific cytotoxic activity are further re-stimulated. An additional six days later, these cell lines are tested for cytotoxic activity on ⁵¹Cr labeled Jurkat-A2.1/K^b target cells in the absence or presence of peptide, and also tested on ⁵¹Cr labeled target cells bearing the endogenously synthesized antigen, i.e. cells that are stably transfected with 151P3D4 expression vectors.

The results demonstrate that CTL lines obtained from animals primed with peptide epitope recognize endogenously synthesized 151P3D4 antigen. The choice of transgenic mouse model to be used for such an analysis depends upon the epitope(s) that are being evaluated. In addition to HLA-A*0201/K^b transgenic mice, several other transgenic mouse models including mice with human A11, which may also be used to evaluate A3 epitopes, and B7 alleles have been characterized and others (e.g., transgenic mice for HLA-A1 and A24) are being developed. HLA-DR1 and HLA-DR3 mouse models have also been developed, which may be used to evaluate HTL epitopes.

Example 20

Activity of CTL-HTL Conjugated Epitopes in Transgenic Mice

This example illustrates the induction of CTLs and HTLs in transgenic mice, by use of a 151P3D4-derived CTL and HTL peptide vaccine compositions. The vaccine composition used herein comprise peptides to be administered to a patient with a 151P3D4-expressing tumor. The peptide composition can comprise multiple CTL and/or HTL epitopes. The epitopes are identified using methodology as described herein. This example also illustrates that enhanced immunogenicity can be achieved by inclusion of one or more HTL epitopes in a CTL vaccine composition; such a peptide composition can comprise an HTL epitope conjugated to a CTL epitope. The CTL epitope can be one that binds to multiple HLA family members at an affinity of 500 nM or less, or analogs of that epitope. The peptides may be lipidated, if desired.

Immunization procedures: Immunization of transgenic mice is performed as described (Alexander et al., J. Immunol. 159:4753-4761, 1997). For example, A2/K^b mice, which are transgenic for the human HLA A2.1 allele and are used to confirm the immunogenicity of HLA-A*0201 motif- or HLA-A2 supermotif-bearing epitopes, and are primed subcutaneously (base of the tail) with a 0.1 ml of peptide in Incomplete Freund's Adjuvant, or if the peptide composition is a lipidated CTL/HTL conjugate, in DMSO/saline, or if the peptide composition is a polypeptide, in PBS or Incomplete Freund's Adjuvant. Seven days after priming, splenocytes obtained from these animals are restimulated with syngenic irradiated LPS-activated lymphoblasts coated with peptide.

Cell lines: Target cells for peptide-specific cytotoxicity assays are Jurkat cells transfected with the HLA-A2.1/K^b chimeric gene (e.g., Vitiello et al., J. Exp. Med. 173:1007, 1991)

In vitro CTL activation: One week after priming, spleen cells (30×10⁶ cells/flask) are co-cultured at 37° C. with syngeneic, irradiated (3000 rads), peptide coated lymphoblasts (10×10⁶ cells/flask) in 10 ml of culture medium/T25 flask. After six days, effector cells are harvested and assayed for cytotoxic activity.

Assay for cytotoxic activity: Target cells (1.0 to 1.5×10⁶) are incubated at 37° C. in the presence of 200 μl of ⁵¹Cr. After 60 minutes, cells are washed three times and resuspended in R10 medium. Peptide is added where required at a concentration of 1 μg/ml. For the assay, 10^{4 51}Cr-labeled target cells are added to different concentrations of effector cells (final volume of 200 μl) in U-bottom 96-well plates. After a six hour incubation period at 37° C., a 0.1 ml aliquot of supernatant is removed from each well and radioactivity is determined in a Micromedic automatic gamma counter. The percent specific lysis is determined by the formula: percent specific release=100×(experimental release−spontaneous release)/(maximum release−spontaneous release). To facilitate comparison between separate CTL assays run under the same conditions, % ⁵¹Cr release data is expressed as lytic units/10⁶ cells. One lytic unit is arbitrarily defined as the number of effector cells required to achieve 30% lysis of 10,000 target cells in a six hour ⁵¹Cr release assay. To obtain specific lytic units/10⁶, the lytic units/10⁶ obtained in the absence of peptide is subtracted from the lytic units/10⁶ obtained in the presence of peptide. For example, if 30% ⁵¹Cr release is obtained at the effector (E): target (T) ratio of 50:1 (i.e., 5×10⁵ effector cells for 10,000 targets) in the absence of peptide and 5:1 (i.e., 5×10⁴ effector cells for 10,000 targets) in the presence of peptide, the specific lytic units would be: [(1/50,000)−(1/500,000)]×10⁶=18 LU.

The results are analyzed to assess the magnitude of the CTL responses of animals injected with the immunogenic CTL/HTL conjugate vaccine preparation and are compared to the magnitude of the CTL response achieved using, for example, CTL epitopes as outlined above in the Example entitled “Confirmation of Immunogenicity.” Analyses similar to this may be performed to confirm the immunogenicity of peptide conjugates containing multiple CTL epitopes and/or multiple HTL epitopes. In accordance with these procedures, it is found that a CTL response is induced, and concomitantly that an HTL response is induced upon administration of such compositions.

Example 21

Selection of CTL and HTL Epitopes for Inclusion in a 151P3D4-Specific Vaccine

This example illustrates a procedure for selecting peptide epitopes for vaccine compositions of the invention. The peptides in the composition can be in the form of a nucleic acid sequence, either single or one or more sequences (i.e., minigene) that encodes peptide(s), or can be single and/or polyepitopic peptides.

The following principles are utilized when selecting a plurality of epitopes for inclusion in a vaccine composition. Each of the following principles is balanced in order to make the selection.

Epitopes are selected which, upon administration, mimic immune responses that are correlated with 151P3D4 clearance. The number of epitopes used depends on observations of patients who spontaneously clear 151P3D4. For example, if it has been observed that patients who spontaneously clear 151P3D4-expressing cells generate an immune response to at least three (3) epitopes from 151P3D4 antigen, then at least three epitopes should be included for HLA class I. A similar rationale is used to determine HLA class II epitopes.

Epitopes are often selected that have a binding affinity of an IC₅₀ of 500 nM or less for an HLA class I molecule, or for class II, an IC₅₀ of 1000 nM or less; or HLA Class I peptides with high binding scores from the BIMAS web site, at URL bimas.dcrt.nih.gov/.

In order to achieve broad coverage of the vaccine through out a diverse population, sufficient supermotif bearing peptides, or a sufficient array of allele-specific motif bearing peptides, are selected to give broad population coverage. In one embodiment, epitopes are selected to provide at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art, can be employed to assess breadth, or redundancy, of population coverage.

When creating polyepitopic compositions, or a minigene that encodes same, it is typically desirable to generate the smallest peptide possible that encompasses the epitopes of interest. The principles employed are similar, if not the same, as those employed when selecting a peptide comprising nested epitopes. For example, a protein sequence for the vaccine composition is selected because it has maximal number of epitopes contained within the sequence, i.e., it has a high concentration of epitopes. Epitopes may be nested or overlapping (i.e., frame shifted relative to one another). For example, with overlapping epitopes, two 9-mer epitopes and one 10-mer epitope can be present in a 10 amino acid peptide. Each epitope can be exposed and bound by an HLA molecule upon administration of such a peptide. A multi-epitopic, peptide can be generated synthetically, recombinantly, or via cleavage from the native source. Alternatively, an analog can be made of this native sequence, whereby one or more of the epitopes comprise substitutions that alter the cross-reactivity and/or binding affinity properties of the polyepitopic peptide. Such a vaccine composition is administered for therapeutic or prophylactic purposes. This embodiment provides for the possibility that an as yet undiscovered aspect of immune system processing will apply to the native nested sequence and thereby facilitate the production of therapeutic or prophylactic immune response-inducing vaccine compositions. Additionally such an embodiment provides for the possibility of motif-bearing epitopes for an HLA makeup that is presently unknown. Furthermore, this embodiment (absent the creating of any analogs) directs the immune response to multiple peptide sequences that are actually present in 151P3D4, thus avoiding the need to evaluate any junctional epitopes. Lastly, the embodiment provides an economy of scale when producing nucleic acid vaccine compositions. Related to this embodiment, computer programs can be derived in accordance with principles in the art, which identify in a target sequence, the greatest number of epitopes per sequence length.

A vaccine composition comprised of selected peptides, when administered, is safe, efficacious, and elicits an immune response similar in magnitude to an immune response that controls or clears cells that bear or overexpress 151P3D4.

Example 22

Construction of “Minigene” Multi-Epitope DNA Plasmids

This example discusses the construction of a minigene expression plasmid. Minigene plasmids may, of course, contain various configurations of B cell, CTL and/or HTL epitopes or epitope analogs as described herein.

A minigene expression plasmid typically includes multiple CTL and HTL peptide epitopes. In the present example, HLA-A2, -A3, -B7 supermotif-bearing peptide epitopes and HLA-A1 and -A24 motif-bearing peptide epitopes are used in conjunction with DR supermotif-bearing epitopes and/or DR3 epitopes. HLA class I supermotif or motif-bearing peptide epitopes derived 151P3D4, are selected such that multiple supermotifs/motifs are represented to ensure broad population coverage. Similarly, HLA class II epitopes are selected from 151P3D4 to provide broad population coverage, i.e. both HLA DR-1-4-7 supermotif-bearing epitopes and HLA DR-3 motif-bearing epitopes are selected for inclusion in the minigene construct. The selected CTL and HTL epitopes are then incorporated into a minigene for expression in an expression vector.

Such a construct may additionally include sequences that direct the HTL epitopes to the endoplasmic reticulum. For example, the Ii protein may be fused to one or more HTL epitopes as described in the art, wherein the CLIP sequence of the Ii protein is removed and replaced with an HLA class II epitope sequence so that HLA class II epitope is directed to the endoplasmic reticulum, where the epitope binds to an HLA class II molecules.

This example illustrates the methods to be used for construction of a minigene-bearing expression plasmid. Other expression vectors that may be used for minigene compositions are available and known to those of skill in the art.

The minigene DNA plasmid of this example contains a consensus Kozak sequence and a consensus murine kappa Ig-light chain signal sequence followed by CTL and/or HTL epitopes selected in accordance with principles disclosed herein. The sequence encodes an open reading frame fused to the Myc and His antibody epitope tag coded for by the pcDNA 3.1 Myc-His vector.

Overlapping oligonucleotides that can, for example, average about 70 nucleotides in length with 15 nucleotide overlaps, are synthesized and HPLC-purified. The oligonucleotides encode the selected peptide epitopes as well as appropriate linker nucleotides, Kozak sequence, and signal sequence. The final multiepitope minigene is assembled by extending the overlapping oligonucleotides in three sets of reactions using PCR. A Perkin/Elmer 9600 PCR machine is used and a total of 30 cycles are performed using the following conditions: 95° C. for 15 sec, annealing temperature (5° below the lowest calculated Tm of each primer pair) for 30 sec, and 72° C. for 1 min.

For example, a minigene is prepared as follows. For a first PCR reaction, 5 μg of each of two oligonucleotides are annealed and extended: In an example using eight oligonucleotides, i.e., four pairs of primers, oligonucleotides 1+2, 3+4, 5+6, and 7+8 are combined in 100 μl reactions containing Pfu polymerase buffer (1×=10 mM KCL, 10 mM (NH4)₂SO₄, 20 mM Tris-chloride, pH 8.75, 2 mM MgSO₄, 0.1% Triton X-100, 100 μg/ml BSA), 0.25 mM each dNTP, and 2.5 U of Pfu polymerase. The full-length dimer products are gel-purified, and two reactions containing the product of 1+2 and 3+4, and the product of 5+6 and 7+8 are mixed, annealed, and extended for 10 cycles. Half of the two reactions are then mixed, and 5 cycles of annealing and extension carried out before flanking primers are added to amplify the full length product. The full-length product is gel-purified and cloned into pCR-blunt (Invitrogen) and individual clones are screened by sequencing.

Example 23

The Plasmid Construct and the Degree to which it Induces Immunogenicity

The degree to which a plasmid construct, for example a plasmid constructed in accordance with the previous Example, is able to induce immunogenicity is confirmed in vitro by determining epitope presentation by APC following transduction or transfection of the APC with an epitope-expressing nucleic acid construct. Such a study determines “antigenicity” and allows the use of human APC. The assay determines the ability of the epitope to be presented by the APC in a context that is recognized by a T cell by quantifying the density of epitope-HLA class I complexes on the cell surface. Quantitation can be performed by directly measuring the amount of peptide eluted from the APC (see, e.g., Sijts et al., J. Immunol. 156:683-692, 1996; Demotz et al., Nature 342:682-684, 1989); or the number of peptide-HLA class I complexes can be estimated by measuring the amount of lysis or lymphokine release induced by diseased or transfected target cells, and then determining the concentration of peptide necessary to obtain equivalent levels of lysis or lymphokine release (see, e.g., Kageyama et al., J. Immunol. 154:567-576, 1995).

Alternatively, immunogenicity is confirmed through in vivo injections into mice and subsequent in vitro assessment of CTL and HTL activity, which are analyzed using cytotoxicity and proliferation assays, respectively, as detailed e.g., in Alexander et al., Immunity 1:751-761, 1994.

For example, to confirm the capacity of a DNA minigene construct containing at least one HLA-A2 supermotif peptide to induce CTLs in vivo, HLA-A2.1/K^b transgenic mice, for example, are immunized intramuscularly with 100 μg of naked cDNA. As a means of comparing the level of CTLs induced by cDNA immunization, a control group of animals is also immunized with an actual peptide composition that comprises multiple epitopes synthesized as a single polypeptide as they would be encoded by the minigene.

Splenocytes from immunized animals are stimulated twice with each of the respective compositions (peptide epitopes encoded in the minigene or the polyepitopic peptide), then assayed for peptide-specific cytotoxic activity in a ⁵¹Cr release assay. The results indicate the magnitude of the CTL response directed against the A2-restricted epitope, thus indicating the in vivo immunogenicity of the minigene vaccine and polyepitopic vaccine.

It is, therefore, found that the minigene elicits immune responses directed toward the HLA-A2 supermotif peptide epitopes as does the polyepitopic peptide vaccine. A similar analysis is also performed using other HLA-A3 and HLA-B7 transgenic mouse models to assess CTL induction by HLA-A3 and HLA-B7 motif or supermotif epitopes, whereby it is also found that the minigene elicits appropriate immune responses directed toward the provided epitopes.

To confirm the capacity of a class II epitope-encoding minigene to induce HTLs in vivo, DR transgenic mice, or for those epitopes that cross react with the appropriate mouse MHC molecule, I-A^b-restricted mice, for example, are immunized intramuscularly with 100 μg of plasmid DNA. As a means of comparing the level of HTLs induced by DNA immunization, a group of control animals is also immunized with an actual peptide composition emulsified in complete Freund's adjuvant. CD4+ T cells, i.e. HTLs, are purified from splenocytes of immunized animals and stimulated with each of the respective compositions (peptides encoded in the minigene). The HTL response is measured using a ³H-thymidine incorporation proliferation assay, (see, e.g., Alexander et al. Immunity 1:751-761, 1994). The results indicate the magnitude of the HTL response, thus demonstrating the in vivo immunogenicity of the minigene.

DNA minigenes, constructed as described in the previous Example, can also be confirmed as a vaccine in combination with a boosting agent using a prime boost protocol. The boosting agent can consist of recombinant protein (e.g., Barnett et al., Aids Res. and Human Retroviruses 14, Supplement 3:S299-S309, 1998) or recombinant vaccinia, for example, expressing a minigene or DNA encoding the complete protein of interest (see, e.g., Hanke et al., Vaccine 16:439-445, 1998; Sedegah et al., Proc. Natl. Acad. Sci. USA 95:7648-53, 1998; Hanke and McMichael, Immunol. Letters 66:177-181, 1999; and Robinson et al., Nature Med. 5:526-34, 1999).

For example, the efficacy of the DNA minigene used in a prime boost protocol is initially evaluated in transgenic mice. In this example, A2.1/K^b transgenic mice are immunized IM with 100 μg of a DNA minigene encoding the immunogenic peptides including at least one HLA-A2 supermotif-bearing peptide. After an incubation period (ranging from 3-9 weeks), the mice are boosted IP with 10⁷ pfu/mouse of a recombinant vaccinia virus expressing the same sequence encoded by the DNA minigene. Control mice are immunized with 100 μg of DNA or recombinant vaccinia without the minigene sequence, or with DNA encoding the minigene, but without the vaccinia boost. After an additional incubation period of two weeks, splenocytes from the mice are immediately assayed for peptide-specific activity in an ELISPOT assay. Additionally, splenocytes are stimulated in vitro with the A2-restricted peptide epitopes encoded in the minigene and recombinant vaccinia, then assayed for peptide-specific activity in an alpha, beta and/or gamma IFN ELISA.

It is found that the minigene utilized in a prime-boost protocol elicits greater immune responses toward the HLA-A2 supermotif peptides than with DNA alone. Such an analysis can also be performed using HLA-A11 or HLA-B7 transgenic mouse models to assess CTL induction by HLA-A3 or HLA-B7 motif or supermotif epitopes. The use of prime boost protocols in humans is described below in the Example entitled “Induction of CTL Responses Using a Prime Boost Protocol.”

Example 24

Peptide Compositions for Prophylactic Uses

Vaccine compositions of the present invention can be used to prevent 151P3D4 expression in persons who are at risk for tumors that bear this antigen. For example, a polyepitopic peptide epitope composition (or a nucleic acid comprising the same) containing multiple CTL and HTL epitopes such as those selected in the above Examples, which are also selected to target greater than 80% of the population, is administered to individuals at risk for a 151P3D4-associated tumor.

For example, a peptide-based composition is provided as a single polypeptide that encompasses multiple epitopes. The vaccine is typically administered in a physiological solution that comprises an adjuvant, such as Incomplete Freunds Adjuvant. The dose of peptide for the initial immunization is from about 1 to about 50,000 μg, generally 100-5,000 μg, for a 70 kg patient. The initial administration of vaccine is followed by booster dosages at 4 weeks followed by evaluation of the magnitude of the immune response in the patient, by techniques that determine the presence of epitope-specific CTL populations in a PBMC sample. Additional booster doses are administered as required. The composition is found to be both safe and efficacious as a prophylaxis against 151P3D4-associated disease.

Alternatively, a composition typically comprising transfecting agents is used for the administration of a nucleic acid-based vaccine in accordance with methodologies known in the art and disclosed herein.

Example 25

Polyepitopic Vaccine Compositions Derived from Native 151P3D4 Sequences

A native 151P3D4 polyprotein sequence is analyzed, preferably using computer algorithms defined for each class I and/or class II supermotif or motif, to identify “relatively short” regions of the polyprotein that comprise multiple epitopes. The “relatively short” regions are preferably less in length than an entire native antigen. This relatively short sequence that contains multiple distinct or overlapping, “nested” epitopes can be used to generate a minigene construct. The construct is engineered to express the peptide, which corresponds to the native protein sequence. The “relatively short” peptide is generally less than 250 amino acids in length, often less than 100 amino acids in length, preferably less than 75 amino acids in length, and more preferably less than 50 amino acids in length. The protein sequence of the vaccine composition is selected because it has maximal number of epitopes contained within the sequence, i.e., it has a high concentration of epitopes. As noted herein, epitope motifs may be nested or overlapping (i.e., frame shifted relative to one another). For example, with overlapping epitopes, two 9-mer epitopes and one 10-mer epitope can be present in a 10 amino acid peptide. Such a vaccine composition is administered for therapeutic or prophylactic purposes.

The vaccine composition will include, for example, multiple CTL epitopes from 151P3D4 antigen and at least one HTL epitope. This polyepitopic native sequence is administered either as a peptide or as a nucleic acid sequence which encodes the peptide. Alternatively, an analog can be made of this native sequence, whereby one or more of the epitopes comprise substitutions that alter the cross-reactivity and/or binding affinity properties of the polyepitopic peptide.

The embodiment of this example provides for the possibility that an as yet undiscovered aspect of immune system processing will apply to the native nested sequence and thereby facilitate the production of therapeutic or prophylactic immune response-inducing vaccine compositions. Additionally, such an embodiment provides for the possibility of motif-bearing epitopes for an HLA makeup(s) that is presently unknown. Furthermore, this embodiment (excluding an analoged embodiment) directs the immune response to multiple peptide sequences that are actually present in native 151P3D4, thus avoiding the need to evaluate any junctional epitopes. Lastly, the embodiment provides an economy of scale when producing peptide or nucleic acid vaccine compositions.

Related to this embodiment, computer programs are available in the art which can be used to identify in a target sequence, the greatest number of epitopes per sequence length.

Example 26

Polyepitopic Vaccine Compositions from Multiple Antigens

The 151P3D4 peptide epitopes of the present invention are used in conjunction with epitopes from other target tumor-associated antigens, to create a vaccine composition that is useful for the prevention or treatment of cancer that expresses 151P3D4 and such other antigens. For example, a vaccine composition can be provided as a single polypeptide that incorporates multiple epitopes from 151P3D4 as well as tumor-associated antigens that are often expressed with a target cancer associated with 151P3D4 expression, or can be administered as a composition comprising a cocktail of one or more discrete epitopes. Alternatively, the vaccine can be administered as a minigene construct or as dendritic cells which have been loaded with the peptide epitopes in vitro.

Example 27

Use of Peptides to Evaluate an Immune Response

Peptides of the invention may be used to analyze an immune response for the presence of specific antibodies, CTL or HTL directed to 151P3D4. Such an analysis can be performed in a manner described by Ogg et al., Science 279:2103-2106, 1998. In this Example, peptides in accordance with the invention are used as a reagent for diagnostic or prognostic purposes, not as an immunogen.

In this example highly sensitive human leukocyte antigen tetrameric complexes (“tetramers”) are used for a cross-sectional analysis of, for example, 151P3D4 HLA-A*0201-specific CTL frequencies from HLA A*0201-positive individuals at different stages of disease or following immunization comprising a 151P3D4 peptide containing an A*0201 motif. Tetrameric complexes are synthesized as described (Musey et al., N. Engl. J. Med. 337:1267, 1997). Briefly, purified HLA heavy chain (A*0201 in this example) and β2-microglobulin are synthesized by means of a prokaryotic expression system. The heavy chain is modified by deletion of the transmembrane-cytosolic tail and COOH-terminal addition of a sequence containing a BirA enzymatic biotinylation site. The heavy chain, β2-microglobulin, and peptide are refolded by dilution. The 45-kD refolded product is isolated by fast protein liquid chromatography and then biotinylated by BirA in the presence of biotin (Sigma, St. Louis, Mo.), adenosine 5′ triphosphate and magnesium. Streptavidin-phycoerythrin conjugate is added in a 1:4 molar ratio, and the tetrameric product is concentrated to 1 mg/ml. The resulting product is referred to as tetramer-phycoerythrin.

For the analysis of patient blood samples, approximately one million PBMCs are centrifuged at 300 g for 5 minutes and resuspended in 50 μl of cold phosphate-buffered saline. Tri-color analysis is performed with the tetramer-phycoerythrin, along with anti-CD8-Tricolor, and anti-CD38. The PBMCs are incubated with tetramer and antibodies on ice for 30 to 60 min and then washed twice before formaldehyde fixation. Gates are applied to contain >99.98% of control samples. Controls for the tetramers include both A*0201-negative individuals and A*0201-positive non-diseased donors. The percentage of cells stained with the tetramer is then determined by flow cytometry. The results indicate the number of cells in the PBMC sample that contain epitope-restricted CTLs, thereby readily indicating the extent of immune response to the 151P3D4 epitope, and thus the status of exposure to 151P3D4, or exposure to a vaccine that elicits a protective or therapeutic response.

Example 28

Use of Peptide Epitopes to Evaluate Recall Responses

The peptide epitopes of the invention are used as reagents to evaluate T cell responses, such as acute or recall responses, in patients. Such an analysis may be performed on patients who have recovered from 151P3D4-associated disease or who have been vaccinated with a 151P3D4 vaccine.

For example, the class I restricted CTL response of persons who have been vaccinated may be analyzed. The vaccine may be any 151P3D4 vaccine. PBMC are collected from vaccinated individuals and HLA typed. Appropriate peptide epitopes of the invention that, optimally, bear supermotifs to provide cross-reactivity with multiple HLA supertype family members, are then used for analysis of samples derived from individuals who bear that HLA type.

PBMC from vaccinated individuals are separated on Ficoll-Histopaque density gradients (Sigma Chemical Co., St. Louis, Mo.), washed three times in HBSS (GIBCO Laboratories), resuspended in RPMI-1640 (GIBCO Laboratories) supplemented with L-glutamine (2 mM), penicillin (50 U/ml), streptomycin (50 μg/ml), and Hepes (10 mM) containing 10% heat-inactivated human AB serum (complete RPMI) and plated using microculture formats. A synthetic peptide comprising an epitope of the invention is added at 10 μg/ml to each well and HBV core 128-140 epitope is added at 1 μg/ml to each well as a source of T cell help during the first week of stimulation.

In the microculture format, 4×10⁵ PBMC are stimulated with peptide in 8 replicate cultures in 96-well round bottom plate in 100 μl/well of complete RPMI. On days 3 and 10, 100 μl of complete RPMI and 20 U/ml final concentration of rIL-2 are added to each well. On day 7 the cultures are transferred into a 96-well flat-bottom plate and restimulated with peptide, rIL-2 and 10⁵ irradiated (3,000 rad) autologous feeder cells. The cultures are tested for cytotoxic activity on day 14. A positive CTL response requires two or more of the eight replicate cultures to display greater than 10% specific ⁵¹Cr release, based on comparison with non-diseased control subjects as previously described (Rehermann, et al., Nature Med. 2:1104,1108, 1996; Rehermann et al., J. Clin. Invest. 97:1655-1665, 1996; and Rehermann et al. J. Clin. Invest. 98:1432-1440, 1996).

Target cell lines are autologous and allogeneic EBV-transformed B-LCL that are either purchased from the American Society for Histocompatibility and Immunogenetics (ASHI, Boston, Mass.) or established from the pool of patients as described (Guilhot, et al. J. Virol. 66:2670-2678, 1992).

Cytotoxicity assays are performed in the following manner. Target cells consist of either allogeneic HLA-matched or autologous EBV-transformed B lymphoblastoid cell line that are incubated overnight with the synthetic peptide epitope of the invention at 10 μM, and labeled with 100 μCi of ⁵¹Cr (Amersham Corp., Arlington Heights, Ill.) for 1 hour after which they are washed four times with HBSS.

Cytolytic activity is determined in a standard 4-h, split well ⁵¹Cr release assay using U-bottomed 96 well plates containing 3,000 targets/well. Stimulated PBMC are tested at effector/target (E/T) ratios of 20-50:1 on day 14. Percent cytotoxicity is determined from the formula: 100×[(experimental release−spontaneous release)/maximum release−spontaneous release)]. Maximum release is determined by lysis of targets by detergent (2% Triton X-100; Sigma Chemical Co., St. Louis, Mo.). Spontaneous release is <25% of maximum release for all experiments.

The results of such an analysis indicate the extent to which HLA-restricted CTL populations have been stimulated by previous exposure to 151P3D4 or a 151P3D4 vaccine.

Similarly, Class II restricted HTL responses may also be analyzed. Purified PBMC are cultured in a 96-well flat bottom plate at a density of 1.5×10⁵ cells/well and are stimulated with 10 μg/ml synthetic peptide of the invention, whole 151P3D4 antigen, or PHA. Cells are routinely plated in replicates of 4-6 wells for each condition. After seven days of culture, the medium is removed and replaced with fresh medium containing 10 U/ml IL-2. Two days later, 1 μCi ³H-thymidine is added to each well and incubation is continued for an additional 18 hours. Cellular DNA is then harvested on glass fiber mats and analyzed for ³H-thymidine incorporation. Antigen-specific T cell proliferation is calculated as the ratio of ³H-thymidine incorporation in the presence of antigen divided by the ³H-thymidine incorporation in the absence of antigen.

Example 29

Induction of Specific CTL Response in Humans

A human clinical trial for an immunogenic composition comprising CTL and HTL epitopes of the invention is set up as an IND Phase I, dose escalation study and carried out as a randomized, double-blind, placebo-controlled trial. Such a trial is designed, for example, as follows:

A total of about 27 individuals are enrolled and divided into 3 groups:

Group I: 3 subjects are injected with placebo and 6 subjects are injected with 5 μg of peptide composition;

Group II: 3 subjects are injected with placebo and 6 subjects are injected with 50 μg peptide composition;

Group III: 3 subjects are injected with placebo and 6 subjects are injected with 500 μg of peptide composition.

After 4 weeks following the first injection, all subjects receive a booster inoculation at the same dosage.

The endpoints measured in this study relate to the safety and tolerability of the peptide composition as well as its immunogenicity. Cellular immune responses to the peptide composition are an index of the intrinsic activity of this the peptide composition, and can therefore be viewed as a measure of biological efficacy. The following summarize the clinical and laboratory data that relate to safety and efficacy endpoints.

Safety: The incidence of adverse events is monitored in the placebo and drug treatment group and assessed in terms of degree and reversibility.

Evaluation of Vaccine Efficacy: For evaluation of vaccine efficacy, subjects are bled before and after injection. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.

The vaccine is found to be both safe and efficacious.

Example 30

Phase II Trials in Patients Expressing 151P3D4

Phase II trials are performed to study the effect of administering the CTL-HTL peptide compositions to patients having cancer that expresses 151P3D4. The main objectives of the trial are to determine an effective dose and regimen for inducing CTLs in cancer patients that express 151P3D4, to establish the safety of inducing a CTL and HTL response in these patients, and to see to what extent activation of CTLs improves the clinical picture of these patients, as manifested, e.g., by the reduction and/or shrinking of lesions. Such a study is designed, for example, as follows:

The studies are performed in multiple centers. The trial design is an open-label, uncontrolled, dose escalation protocol wherein the peptide composition is administered as a single dose followed six weeks later by a single booster shot of the same dose. The dosages are 50, 500 and 5,000 micrograms per injection. Drug-associated adverse effects (severity and reversibility) are recorded.

There are three patient groupings. The first group is injected with 50 micrograms of the peptide composition and the second and third groups with 500 and 5,000 micrograms of peptide composition, respectively. The patients within each group range in age from 21-65 and represent diverse ethnic backgrounds. All of them have a tumor that expresses 151P3D4.

Clinical manifestations or antigen-specific T-cell responses are monitored to assess the effects of administering the peptide compositions. The vaccine composition is found to be both safe and efficacious in the treatment of 151P3D4-associated disease.

Example 31

Induction of CTL Responses Using a Prime Boost Protocol

A prime boost protocol similar in its underlying principle to that used to confirm the efficacy of a DNA vaccine in transgenic mice, such as described above in the Example entitled “The Plasmid Construct and the Degree to Which It Induces Immunogenicity,” can also be used for the administration of the vaccine to humans. Such a vaccine regimen can include an initial administration of, for example, naked DNA followed by a boost using recombinant virus encoding the vaccine, or recombinant protein/polypeptide or a peptide mixture administered in an adjuvant.

For example, the initial immunization may be performed using an expression vector, such as that constructed in the Example entitled “Construction of “Minigene” Multi-Epitope DNA Plasmids” in the form of naked nucleic acid administered IM (or SC or ID) in the amounts of 0.5-5 mg at multiple sites. The nucleic acid (0.1 to 1000 μg) can also be administered using a gene gun. Following an incubation period of 3-4 weeks, a booster dose is then administered. The booster can be recombinant fowlpox virus administered at a dose of 5-10⁷ to 5×10⁹ pfu. An alternative recombinant virus, such as an MVA, canarypox, adenovirus, or adeno-associated virus, can also be used for the booster, or the polyepitopic protein or a mixture of the peptides can be administered. For evaluation of vaccine efficacy, patient blood samples are obtained before immunization as well as at intervals following administration of the initial vaccine and booster doses of the vaccine. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.

Analysis of the results indicates that a magnitude of response sufficient to achieve a therapeutic or protective immunity against 151P3D4 is generated.

Example 32

Administration of Vaccine Compositions Using Dendritic Cells (DC)

Vaccines comprising peptide epitopes of the invention can be administered using APCs, or “professional” APCs such as DC. In this example, peptide-pulsed DC are administered to a patient to stimulate a CTL response in vivo. In this method, dendritic cells are isolated, expanded, and pulsed with a vaccine comprising peptide CTL and HTL epitopes of the invention. The dendritic cells are infused back into the patient to elicit CTL and HTL responses in vivo. The induced CTL and HTL then destroy or facilitate destruction, respectively, of the target cells that bear the 151P3D4 protein from which the epitopes in the vaccine are derived.

For example, a cocktail of epitope-comprising peptides is administered ex vivo to PBMC, or isolated DC therefrom. A pharmaceutical to facilitate harvesting of DC can be used, such as Progenipoietin™ (Monsanto, St. Louis, Mo.) or GM-CSF/IL-4. After pulsing the DC with peptides, and prior to reinfusion into patients, the DC are washed to remove unbound peptides.

As appreciated clinically, and readily determined by one of skill based on clinical outcomes, the number of DC reinfused into the patient can vary (see, e.g., Nature Med. 4:328, 1998; Nature Med. 2:52, 1996 and Prostate 32:272, 1997). Although 2-50×10⁶ DC per patient are typically administered, larger number of DC, such as 10⁷ or 10⁸ can also be provided. Such cell populations typically contain between 50-90% DC.

In some embodiments, peptide-loaded PBMC are injected into patients without purification of the DC. For example, PBMC generated after treatment with an agent such as Progenipoietin™ are injected into patients without purification of the DC. The total number of PBMC that are administered often ranges from 10⁸ to 10¹⁰. Generally, the cell doses injected into patients is based on the percentage of DC in the blood of each patient, as determined, for example, by immunofluorescence analysis with specific anti-DC antibodies. Thus, for example, if Progenipoietin™ mobilizes 2% DC in the peripheral blood of a given patient, and that patient is to receive 5×10⁶ DC, then the patient will be injected with a total of 2.5×10⁸ peptide-loaded PBMC. The percent DC mobilized by an agent such as Progenipoietin™ is typically estimated to be between 2-10%, but can vary as appreciated by one of skill in the art.

Ex Vivo Activation of CTL/HTL Responses

Alternatively, ex vivo CTL or HTL responses to 151P3D4 antigens can be induced by incubating, in tissue culture, the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of APC, such as DC, and immunogenic peptides. After an appropriate incubation time (typically about 7-28 days), in which the precursor cells are activated and expanded into effector cells, the cells are infused into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cells, i.e., tumor cells.

Example 33

An Alternative Method of Identifying and Confirming Motif-Bearing Peptides

Another method of identifying and confirming motif-bearing peptides is to elute them from cells bearing defined MHC molecules. For example, EBV transformed B cell lines used for tissue typing have been extensively characterized to determine which HLA molecules they express. In certain cases these cells express only a single type of HLA molecule. These cells can be transfected with nucleic acids that express the antigen of interest, e.g. 151P3D4. Peptides produced by endogenous antigen processing of peptides produced as a result of transfection will then bind to HLA molecules within the cell and be transported and displayed on the cell's surface. Peptides are then eluted from the HLA molecules by exposure to mild acid conditions and their amino acid sequence determined, e.g., by mass spectral analysis (e.g., Kubo et al., J. Immunol. 152:3913, 1994). Because the majority of peptides that bind a particular HLA molecule are motif-bearing, this is an alternative modality for obtaining the motif-bearing peptides correlated with the particular HLA molecule expressed on the cell.

Alternatively, cell lines that do not express endogenous HLA molecules can be transfected with an expression construct encoding a single HLA allele. These cells can then be used as described, i.e., they can then be transfected with nucleic acids that encode 151P3D4 to isolate peptides corresponding to 151P3D4 that have been presented on the cell surface. Peptides obtained from such an analysis will bear motif(s) that correspond to binding to the single HLA allele that is expressed in the cell.

As appreciated by one in the art, one can perform a similar analysis on a cell bearing more than one HLA allele and subsequently determine peptides specific for each HLA allele expressed. Moreover, one of skill would also recognize that means other than transfection, such as loading with a protein antigen, can be used to provide a source of antigen to the cell.

Example 34

Complementary Polynucleotides

Sequences complementary to the 151P3D4-encoding sequences, or any parts thereof, are used to detect, decrease, or inhibit expression of naturally occurring 151P3D4. Although use of oligonucleotides comprising from about 15 to 30 base pairs is described, essentially the same procedure is used with smaller or with larger sequence fragments. Appropriate oligonucleotides are designed using, e.g., OLIGO 4.06 software (National Biosciences) and the coding sequence of 151P3D4. To inhibit transcription, a complementary oligonucleotide is designed from the most unique 5′ sequence and used to prevent promoter binding to the coding sequence. To inhibit translation, a complementary oligonucleotide is designed to prevent ribosomal binding to a 151P3D4-encoding transcript.

Example 35

Purification of Naturally-Occurring or Recombinant 151P3D4 Using 151P3D4-Specific Antibodies

Naturally occurring or recombinant 151P3D4 is substantially purified by immunoaffinity chromatography using antibodies specific for 151P3D4. An immunoaffinity column is constructed by covalently coupling anti-151P3D4 antibody to an activated chromatographic resin, such as CNBr-activated SEPHAROSE (Amersham Pharmacia Biotech). After the coupling, the resin is blocked and washed according to the manufacturer's instructions.

Media containing 151P3D4 are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of 151P3D4 (e.g., high ionic strength buffers in the presence of detergent). The column is eluted under conditions that disrupt antibody/151P3D4 binding (e.g., a buffer of pH 2 to pH 3, or a high concentration of a chaotrope, such as urea or thiocyanate ion), and GCR.P is collected.

Example 36

Identification of Molecules which Interact with 151P3D4

151P3D4, or biologically active fragments thereof, are labeled with 121 1 Bolton-Hunter reagent. (See, e.g., Bolton et al. (1973) Biochem. J. 133:529.) Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled 151P3D4, washed, and any wells with labeled 151P3D4 complex are assayed. Data obtained using different concentrations of 151P3D4 are used to calculate values for the number, affinity, and association of 151P3D4 with the candidate molecules.

Example 37

In Vivo Assay for 151P3D4 Tumor Growth Promotion

The effect of the 151P3D4 protein on tumor cell growth is evaluated in vivo by evaluating tumor development and growth of cells expressing or lacking 151P3D4. For example, SCID mice are injected subcutaneously on each flank with 1×10⁶ of either 3T3, bladder, kidney or ovary cancer cell lines (e.g. SCABER, J82, PA-1, CaOv3, A498 or 769P cells) containing tkNeo empty vector or 151P3D4. At least two strategies may be used: (1) Constitutive 151P3D4 expression under regulation of a promoter such as a constitutive promoter obtained from the genomes of viruses such as polyoma virus, fowlpox virus (UK 2,211,504 published 5 Jul. 1989), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), or from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, provided such promoters are compatible with the host cell systems, and (2) Regulated expression under control of an inducible vector system, such as ecdysone, tetracycline, etc., provided such promoters are compatible with the host cell systems. Tumor volume is then monitored by caliper measurement at the appearance of palpable tumors and followed over time to determine if 151P3D4-expressing cells grow at a faster rate and whether tumors produced by 151P3D4-expressing cells demonstrate characteristics of altered aggressiveness (e.g. enhanced metastasis, vascularization, reduced responsiveness to chemotherapeutic drugs).

Additionally, mice can be implanted with 1×10⁵ of the same cells orthotopically to determine if 151P3D4 has an effect on local growth in the bladder, kidney or ovary, and whether 151P3D4 affects the ability of the cells to metastasize, specifically to lymph nodes, adrenal, liver and bone (Miki T et al, Oncol Res. 2001; 12:209; Fu X et al, Int J. Cancer. 1991, 49:938; Kiguchi K et al, Clin Exp Metastasis. 1998, 16:751).

The assay is also useful to determine the 151P3D4 inhibitory effect of candidate therapeutic compositions, such as for example, 151P3D4 intrabodies, 151P3D4 antisense molecules and ribozymes.

Example 38

151P3D4 Monoclonal Antibody-Mediated Inhibition of Bladder, Kidney and Ovarian Tumors In Vivo

The significant expression of 151P3D4 in cancer tissues, together with its restrictive expression in normal tissues makes 151P3D4 a good target for antibody therapy. Similarly, 151P3D4 is a target for T cell-based immunotherapy. Thus, the therapeutic efficacy of anti-151P3D4 mAbs in human bladder cancer xenograft mouse models is evaluated by using recombinant cell lines such as SCABER-151P3D4, J82-151P3D4, and 3T3-151P3D4 (see, e.g., Kaighn, M. E., et al., Invest Urol, 1979. 17(1): p. 16-23). Similarly, anti-151P3D4 mAbs are evaluated in human kidney and ovarian cancer xenograft models using recombinant cell lines such as A498-151P3D4 and PA1-151P3D4.

Antibody efficacy on tumor growth and metastasis formation is studied, e.g., in a mouse orthotopic bladder cancer xenograft model, a mouse kidney cancer xenograft model and a mouse ovarian cancer xenograft model. The antibodies can be unconjugated, as discussed in this Example, or can be conjugated to a therapeutic modality, as appreciated in the art. Anti-151P3D4 mAbs inhibit formation of kidney, ovarian and bladder xenografts. Anti-151P3D4 mAbs also retard the growth of established orthotopic tumors and prolonged survival of tumor-bearing mice. These results indicate the utility of anti-151P3D4 mAbs in the treatment of local and advanced stages of ovarian, kidney and bladder cancer. (See, e.g., Saffran, D., et al., PNAS 10:1073-1078 or the website located on the World Wide Web at .pnas.org/cgi/doi/10.1073/pnas.051624698).

Administration of the anti-151P3D4 mAbs led to retardation of established orthotopic tumor growth and inhibition of metastasis to distant sites, resulting in a significant prolongation in the survival of tumor-bearing mice. These studies indicate that 151P3D4 as an attractive target for immunotherapy and demonstrate the therapeutic potential of anti-151P3D4 mAbs for the treatment of local and metastatic cancer. This example demonstrates that unconjugated 151P3D4 monoclonal antibodies are effective to inhibit the growth of human bladder, kidney and ovarian tumor xenografts grown in SCID mice; accordingly a combination of such efficacious monoclonal antibodies is also effective.

Tumor Inhibition Using Multiple Unconjugated 151P3D4 mABs

Materials and Methods

151P3D4 Monoclonal Antibodies:

Monoclonal antibodies are raised against 151P3D4 as described in the Example entitled “Generation of 151P3D4 Monoclonal Antibodies (mAbs).” The antibodies are characterized by ELISA, Western blot, FACS, and immunoprecipitation for their capacity to bind 151P3D4. Epitope mapping data for the anti-151P3D4 mAbs, as determined by ELISA and Western analysis, recognize epitopes on the 151P3D4 protein. Immunohistochemical analysis of prostate cancer tissues and cells with these antibodies is performed.

The monoclonal antibodies are purified from ascites or hybridoma tissue culture supernatants by Protein-G Sepharose chromatography, dialyzed against PBS, filter sterilized, and stored at −20° C. Protein determinations are performed by a Bradford assay (Bio-Rad, Hercules, Calif.). A therapeutic monoclonal antibody or a cocktail comprising a mixture of individual monoclonal antibodies is prepared and used for the treatment of mice receiving subcutaneous or orthotopic injections of SCABER, J82, A498, 769P, CaOv1 or PA1 tumor xenografts.

Cell Lines

The bladder, kidney and ovary carcinoma cell lines, SCABER, J82, A498, 769P, CaOv1 and PA1 as well as the fibroblast line NIH 3T3 (American Type Culture Collection) are maintained in DMEM supplemented with L-glutamine and 10% FBS.

A SCABER-151P3D4, J82-151P3D4, A498-151P3D4, 769P-151P3D4, CaOv1-151P3D4, PA1-151P3D4 and 3T3-151P3D4 cell populations are generated by retroviral gene transfer as described in Hubert, R. S., et al., Proc Natl Acad Sci USA, 1999. 96(25): 14523.

Xenograft Mouse Models.

Subcutaneous (s.c.) tumors are generated by injection of 1×10⁶ cancer cells mixed at a 1:1 dilution with Matrigel (Collaborative Research) in the right flank of male SCID mice. To test antibody efficacy on tumor formation, i.p. antibody injections are started on the same day as tumor-cell injections. As a control, mice are injected with either purified mouse IgG (ICN) or PBS; or a purified monoclonal antibody that recognizes an irrelevant antigen not expressed in human cells. Tumor sizes are determined by caliper measurements, and the tumor volume is calculated as: Length×Width×Height. Mice with s.c. tumors greater than 1.5 cm in diameter are sacrificed.

Orthotopic injections are performed under anesthesia by using ketamine/xylazine. For bladder orthotopic studies, an incision is made through the abdomen to expose the bladder, and tumor cells (5×10⁵) mixed with Matrigel are injected into the bladder wall in a 10-μl volume. To monitor tumor growth, mice are palpated and blood is collected on a weekly basis to measure BTA levels. For kidney and ovary orthopotic models, an incision is made through the abdominal muscles to expose the kidney or the ovary. Tumor cells mixed with Matrigel are injected under the kidney capsule or into the ovary in a 10-μl volume (Yoshida Y et al, Anticancer Res. 1998, 18:327; Ahn et al, Tumour Biol. 2001, 22:146). To monitor tumor growth, blood is collected on a weekly basis measuring G250 and SM047 levels. The mice are segregated into groups for the appropriate treatments, with anti-151P3D4 or control mAbs being injected i.p.

Anti-151P3D4 mABs Inhibit Growth of 151P3D4-Expressing Xenograft-Cancer Tumors

The effect of anti-151P3D4 mAbs on tumor formation is tested on the growth and progression of bladder, kidney and ovarian cancer xenografts using UC3-151P3D4, J82-151P3D4, A498-151P3D4, 769P-151P3D4, CaOv1-151P3D4 and PA1-151P3D4 orthotopic models. As compared with the s.c. tumor model, the orthotopic model, which requires injection of tumor cells directly in the mouse bladder, kidney and ovary, respectively, results in a local tumor growth, development of metastasis in distal sites, deterioration of mouse health, and subsequent death (Saffran, D., et al., PNAS supra; Fu, X., et al., Int J Cancer, 1992. 52(6): p. 987-90; Kubota, T., J Cell Biochem, 1994. 56(1): p. 4-8). The features make the orthotopic model more representative of human disease progression and allowed us to follow the therapeutic effect of mAbs on clinically relevant end points.

Accordingly, tumor cells are injected into the mouse bladder, kidney or ovary, and 2 days later, the mice are segregated into two groups and treated with either: a) 200-500 μg, of anti-151P3D4 Ab, or b) PBS three times per week for two to five weeks.

A major advantage of the orthotopic cancer models is the ability to study the development of metastases. Formation of metastasis in mice bearing established orthotopic tumors is studies by IHC analysis on lung sections using an antibody against a tumor-specific cell-surface protein such as anti-CK20 for bladder cancer, anti-G250 for kidney cancer and SM047 antibody for ovarian cancer models (Lin S et al, Cancer Detect Prey. 2001; 25:202; McCluggage W et al, Histopathol 2001, 38:542).

Mice bearing established orthotopic tumors are administered 1000 μg injections of either anti-151P3D4 mAb or PBS over a 4-week period. Mice in both groups are allowed to establish a high tumor burden, to ensure a high frequency of metastasis formation in mouse lungs. Mice then are killed and their bladders, livers, bone and lungs are analyzed for the presence of tumor cells by IHC analysis.

These studies demonstrate a broad anti-tumor efficacy of anti-151P3D4 antibodies on initiation and progression of prostate and kidney cancer in xenograft mouse models. Anti-151P3D4 antibodies inhibit tumor formation of tumors as well as retarding the growth of already established tumors and prolong the survival of treated mice. Moreover, anti-151P3D4 mAbs demonstrate a dramatic inhibitory effect on the spread of local bladder, kidney and ovarian tumor to distal sites, even in the presence of a large tumor burden. Thus, anti-151P3D4 mAbs are efficacious on major clinically relevant end points (tumor growth), prolongation of survival, and health.

Example 39

Therapeutic and Diagnostic Use of Anti-151P3D4 Antibodies in Humans

Anti-151P3D4 monoclonal antibodies are safely and effectively used for diagnostic, prophylactic, prognostic and/or therapeutic purposes in humans. Western blot and immunohistochemical analysis of cancer tissues and cancer xenografts with anti-151P3D4 mAb show strong extensive staining in carcinoma but significantly lower or undetectable levels in normal tissues. Detection of 151P3D4 in carcinoma and in metastatic disease demonstrates the usefulness of the mAb as a diagnostic and/or prognostic indicator. Anti-151P3D4 antibodies are therefore used in diagnostic applications such as immunohistochemistry of kidney biopsy specimens to detect cancer from suspect patients.

As determined by flow cytometry, anti-151P3D4 mAb specifically binds to carcinoma cells. Thus, anti-151P3D4 antibodies are used in diagnostic whole body imaging applications, such as radioimmunoscintigraphy and radioimmunotherapy, (see, e.g., Potamianos S., et. al. Anticancer Res 20(2A):925-948 (2000)) for the detection of localized and metastatic cancers that exhibit expression of 151P3D4. Shedding or release of an extracellular domain of 151P3D4 into the extracellular milieu, such as that seen for alkaline phosphodiesterase B10 (Meerson, N. R., Hepatology 27:563-568 (1998)), allows diagnostic detection of 151P3D4 by anti-151P3D4 antibodies in serum and/or urine samples from suspect patients.

Anti-151P3D4 antibodies that specifically bind 151P3D4 are used in therapeutic applications for the treatment of cancers that express 151P3D4. Anti-151P3D4 antibodies are used as an unconjugated modality and as conjugated form in which the antibodies are attached to one of various therapeutic or imaging modalities well known in the art, such as a prodrugs, enzymes or radioisotopes. In preclinical studies, unconjugated and conjugated anti-151P3D4 antibodies are tested for efficacy of tumor prevention and growth inhibition in the SCID mouse cancer xenograft models, e.g., kidney cancer models AGS-K3 and AGS-K6, (see, e.g., the Example entitled “151P3D4 Monoclonal Antibody-mediated Inhibition of Bladder and Lung Tumors In Vivo”). Conjugated and unconjugated anti-151P3D4 antibodies are used as a therapeutic modality in human clinical trials either alone or in combination with other treatments as described in following Examples.

Example 40

Human Clinical Trials for the Treatment and Diagnosis of Human Carcinomas Through Use of Human Anti-151P3D4 Antibodies In Vivo

Antibodies are used in accordance with the present invention which recognize an epitope on 151P3D4, and are used in the treatment of certain tumors such as those listed in Table I. Based upon a number of factors, including 151P3D4 expression levels, tumors such as those listed in Table I are presently preferred indications. In connection with each of these indications, three clinical approaches are successfully pursued.

I.) Adjunctive therapy: In adjunctive therapy, patients are treated with anti-151P3D4 antibodies in combination with a chemotherapeutic or antineoplastic agent and/or radiation therapy. Primary cancer targets, such as those listed in Table I, are treated under standard protocols by the addition anti-151P3D4 antibodies to standard first and second line therapy. Protocol designs address effectiveness as assessed by reduction in tumor mass as well as the ability to reduce usual doses of standard chemotherapy. These dosage reductions allow additional and/or prolonged therapy by reducing dose-related toxicity of the chemotherapeutic agent. Anti-151P3D4 antibodies are utilized in several adjunctive clinical trials in combination with the chemotherapeutic or antineoplastic agents adriamycin (advanced prostrate carcinoma), cisplatin (advanced head and neck and lung carcinomas), taxol (breast cancer), and doxorubicin (preclinical).

II.) Monotherapy: In connection with the use of the anti-151P3D4 antibodies in monotherapy of tumors, the antibodies are administered to patients without a chemotherapeutic or antineoplastic agent. In one embodiment, monotherapy is conducted clinically in end stage cancer patients with extensive metastatic disease. Patients show some disease stabilization. Trials demonstrate an effect in refractory patients with cancerous tumors.

III.) Imaging Agent: Through binding a radionuclide (e.g., iodine or yttrium (I¹³¹, Y⁹⁰) to anti-151P3D4 antibodies, the radiolabeled antibodies are utilized as a diagnostic and/or imaging agent. In such a role, the labeled antibodies localize to both solid tumors, as well as, metastatic lesions of cells expressing 151P3D4. In connection with the use of the anti-151P3D4 antibodies as imaging agents, the antibodies are used as an adjunct to surgical treatment of solid tumors, as both a pre-surgical screen as well as a post-operative follow-up to determine what tumor remains and/or returns. In one embodiment, a (¹¹¹In) 151P3D4 antibody is used as an imaging agent in a Phase I human clinical trial in patients having a carcinoma that expresses 151P3D4 (by analogy see, e.g., Divgi et al. J. Natl. Cancer Inst. 83:97-104 (1991)). Patients are followed with standard anterior and posterior gamma camera. The results indicate that primary lesions and metastatic lesions are identified

Dose and Route of Administration

As appreciated by those of ordinary skill in the art, dosing considerations can be determined through comparison with the analogous products that are in the clinic. Thus, anti-151P3D4 antibodies can be administered with doses in the range of 5 to 400 mg/m², with the lower doses used, e.g., in connection with safety studies. The affinity of anti-151P3D4 antibodies relative to the affinity of a known antibody for its target is one parameter used by those of skill in the art for determining analogous dose regimens. Further, anti-151P3D4 antibodies that are fully human antibodies, as compared to the chimeric antibody, have slower clearance; accordingly, dosing in patients with such fully human anti-151P3D4 antibodies can be lower, perhaps in the range of 50 to 300 mg/m², and still remain efficacious. Dosing in mg/m², as opposed to the conventional measurement of dose in mg/kg, is a measurement based on surface area and is a convenient dosing measurement that is designed to include patients of all sizes from infants to adults.

Three distinct delivery approaches are useful for delivery of anti-151P3D4 antibodies. Conventional intravenous delivery is one standard delivery technique for many tumors. However, in connection with tumors in the peritoneal cavity, such as tumors of the ovaries, biliary duct, other ducts, and the like, intraperitoneal administration may prove favorable for obtaining high dose of antibody at the tumor and to also minimize antibody clearance. In a similar manner, certain solid tumors possess vasculature that is appropriate for regional perfusion. Regional perfusion allows for a high dose of antibody at the site of a tumor and minimizes short term clearance of the antibody.

Clinical Development Plan (CDP)

Overview: The CDP follows and develops treatments of anti-151P3D4 antibodies in connection with adjunctive therapy, monotherapy, and as an imaging agent. Trials initially demonstrate safety and thereafter confirm efficacy in repeat doses. Trails are open label comparing standard chemotherapy with standard therapy plus anti-151P3D4 antibodies. As will be appreciated, one criteria that can be utilized in connection with enrollment of patients is 151P3D4 expression levels in their tumors as determined by biopsy.

As with any protein or antibody infusion-based therapeutic, safety concerns are related primarily to (i) cytokine release syndrome, i.e., hypotension, fever, shaking, chills; (ii) the development of an immunogenic response to the material (i.e., development of human antibodies by the patient to the antibody therapeutic, or HAHA response); and, (iii) toxicity to normal cells that express 151P3D4. Standard tests and follow-up are utilized to monitor each of these safety concerns. Anti-151P3D4 antibodies are found to be safe upon human administration.

Example 41

Human Clinical Trial Adjunctive Therapy with Human Anti-151P3D4 Antibody and Chemotherapeutic Agent

A phase I human clinical trial is initiated to assess the safety of six intravenous doses of a human anti-151P3D4 antibody in connection with the treatment of a solid tumor, e.g., a cancer of a tissue listed in Table I. In the study, the safety of single doses of anti-151P3D4 antibodies when utilized as an adjunctive therapy to an antineoplastic or chemotherapeutic agent, such as cisplatin, topotecan, doxorubicin, adriamycin, taxol, or the like, is assessed. The trial design includes delivery of six single doses of an anti-151P3D4 antibody with dosage of antibody escalating from approximately about 25 mg/m² to about 275 mg/m² over the course of the treatment in accordance with the following schedule:

	Day 0	Day 7	Day 14	Day 21	Day 28	Day 35
mAb Dose	25 mg/m2	75 mg/m2	125 mg/m2	175 mg/m2	225 mg/m2	275 mg/m2
Chemotherapy	+	+	+	+	+	+
(standard dose)

Patients are closely followed for one-week following each administration of antibody and chemotherapy. In particular, patients are assessed for the safety concerns mentioned above: (i) cytokine release syndrome, i.e., hypotension, fever, shaking, chills; (ii) the development of an immunogenic response to the material (i.e., development of human antibodies by the patient to the human antibody therapeutic, or HAHA response); and, (iii) toxicity to normal cells that express 151P3D4. Standard tests and follow-up are utilized to monitor each of these safety concerns. Patients are also assessed for clinical outcome, and particularly reduction in tumor mass as evidenced by MRI or other imaging.

The anti-151P3D4 antibodies are demonstrated to be safe and efficacious, Phase II trials confirm the efficacy and refine optimum dosing.

Example 42

Human Clinical Trial: Monotherapy with Human Anti-151P3D4 Antibody

Anti-151P3D4 antibodies are safe in connection with the above-discussed adjunctive trial, a Phase II human clinical trial confirms the efficacy and optimum dosing for monotherapy. Such trial is accomplished, and entails the same safety and outcome analyses, to the above-described adjunctive trial with the exception being that patients do not receive chemotherapy concurrently with the receipt of doses of anti-151P3D4 antibodies.

Example 43

Human Clinical Trial: Diagnostic Imaging with Anti-151P3D4 Antibody

Once again, as the adjunctive therapy discussed above is safe within the safety criteria discussed above, a human clinical trial is conducted concerning the use of anti-151P3D4 antibodies as a diagnostic imaging agent. The protocol is designed in a substantially similar manner to those described in the art, such as in Divgi et al. J. Natl. Cancer Inst. 83:97-104 (1991). The antibodies are found to be both safe and efficacious when used as a diagnostic modality.

Example 44

Homology Comparison of 151P3D4 to Known Sequences

Two variants of 151P3D4 have been identified, 151P3D4 v.1 and v 2. The 151P3D4 v.1 gene exhibits strong homology to a previously cloned gene, namely the human cartilage linking protein 1 (gi 4503053), and shows 100% identity to that gene over the entire length of the protein (FIG. 4B). In addition, the 151P3D4 v.1 protein shows homology to the bovine and rat homologs of the human cartilage linking protein (gi 1709660 and gi 9506519) (FIGS. 4F and 4G). 151P3D4 v.1 is a 354 aa protein which localizes primarily to the extracellular compartment (see Table XXI). The second variant, 151P3D4 v.2, is a 721 aa protein, that shares identity with 151P3D4 v.1 over 200 amino acids (Table LV and FIG. 4D). The 151P3D4 v.2 gene also exhibits homology to the human cartilage link protein-1 (gi 4503053), showing 99% identity and 99% homology to that protein (FIG. 4H). However, this homology between variant 2 and cartilage link protein does not extend over the entire length of variant 2, but is limited to the last 400 aa of that protein. The first 400 aa of 151P3D4 v.2 show homology to human ribosomal protein L13a of the 60S subunit (gi. 18574549) (see Table XXI). Besides the addition of 400 aa at its N-terminus, 151P3D4 v.2 also differs from variant 1 in its localization profile. 151P3D4 v.2 localizes to the cytosol, with potential localization to the nucleus (see Table XXI). Motif analysis revealed the presence of link motif as well as immunoglobulin domain in both 151P3D4 variants (see Table XXI).

Cartilage link protein-1, a protein with a known link motif, has been shown to regulate tissue remodeling, bone resorption and protein interaction (Chen Q et al. Dev Biol. 1995, 172:293). The importance of cartilage link protein 1 is illustrated in engineered mice lacking cartilage link protein (Watanabe H, Yamada Y. Nat. Genet. 1999, 21:225). These mutant mice demonstrate defects in cartilage and bone development. The cartilage link protein, via its link motif, mediates cell adhesion of fibroblasts and other cells to extracellular matrix (Yang B et al, Matrix Biol. 1998, 16:541). The link motif is a binding domain for hyaluronic acid (Kohda D et al, Cell. 1996, 86:767), with a structure very similar to type C-lectin. It plays a role in the assembly of extracellular matrix, cell adhesion, and migration (Kohda D et al, Cell. 1996, 86:767). The immunoglobulin domain is a 100 aa long motif which includes a conserved intra-domain disulfide bond. Immunoglobulin-like domains participate in protein interactions (Wang J, Springer T A. Immunol Rev. 1998, 163:197).

The presence of an immunoglobulin motif and a link motif indicate that 151P3D4 regulates protein interactions and participates in the process of cell adhesion, cell migration, tumor formation and progression. By way of its protein interaction domain, 151P3D4 functions in regulating signal transduction in mammalian cells, thereby regulating gene expression and cellular outcomes, including cell proliferation, survival, invasion, motility, etc, all of which have a direct effect on tumor growth and progression.

Accordingly, when 151P3D4 functions as a regulator of protein interactions, cell adhesion, tumor formation, invasion or cell signaling, 151P3D4 is used for therapeutic, diagnostic, prognostic and/or preventative purposes. In addition, when a variant of 151P3D4 is expressed in cancerous tissues, such as those listed in Table I, they are used for therapeutic, diagnostic, prognostic and/or preventative purposes.

Example 45

Regulation of Transcription

The localization of 151P3D4 coupled to the presence of protein interaction domains within its sequence, indicate that 151P3D4 modulates the transcriptional regulation of eukaryotic genes. Regulation of gene expression is confirmed, e.g., by studying gene expression in cells expressing or lacking 151P3D4. For this purpose, two types of experiments are performed.

In the first set of experiments, RNA from parental and 151P3D4-expressing cells are extracted and hybridized to commercially available gene arrays (Clontech) (Smid-Koopman E et al. Br J Cancer. 2000. 83:246). Resting cells as well as cells treated with FBS, androgen or growth factors are compared. Differentially expressed genes are identified in accordance with procedures known in the art. The differentially expressed genes are then mapped to biological pathways (Chen K et al. Thyroid. 2001. 11:41.).

In the second set of experiments, specific transcriptional pathway activation is evaluated using commercially available (Stratagene) luciferase reporter constructs including: NFkB-luc, SRE-luc, ELK1-luc, ARE-luc, p53-luc, and CRE-luc. These transcriptional reporters contain consensus binding sites for known transcription factors that lie downstream of well-characterized signal transduction pathways, and represent a good tool to ascertain pathway activation and screen for positive and negative modulators of pathway activation.

Thus, 151P3D4 plays a role in gene regulation, and it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.

Example 46

Identification and Confirmation of Potential Signal Transduction Pathways

Many mammalian proteins have been reported to interact with signaling molecules and to participate in regulating signaling pathways. (J Neurochem. 2001; 76:217-223). In particular, protein interaction motifs have been instrumental in inducing kinase activation, recruitment of proteins and complex formation (Samelson L. Annu Rev Immunol. 2002; 20:371). Based on the presence of a protein interaction motif, 151P3D4 regulates signaling pathways important for cell growth and invasion. In addition, the 151P3D4 protein contains several phosphorylation sites (see Table XX) indicating an association with specific signaling cascades. Using immunoprecipitation and Western blotting techniques, proteins are identified that associate with 151P3D4 and mediate signaling events. Several pathways known to play a role in cancer biology can be regulated by 151P3D4, including phospholipid pathways such as PI3K, AKT, etc, adhesion and migration pathways, including FAK, Rho, Rac-1, β-catenin, etc, as well as mitogenic/survival cascades such as ERK, p38, etc (Cell Growth Differ. 2000, 11:279; J Biol. Chem. 1999, 274:801; Oncogene. 2000, 19:3003, J. Cell Biol. 1997, 138:913.).

To confirm that 151P3D4 directly or indirectly activates known signal transduction pathways in cells, luciferase (luc) based transcriptional reporter assays are carried out in cells expressing individual genes. These transcriptional reporters contain consensus-binding sites for known transcription factors that lie downstream of well-characterized signal transduction pathways. The reporters and examples of these associated transcription factors, signal transduction pathways, and activation stimuli are listed below.

1. NFkB-luc, NFkB/Rel; Ik-kinase/SAPK; growth/apoptosis/stress

2. SRE-luc, SRF/TCF/ELK1; MAPK/SAPK; growth/differentiation

3. AP-1-luc, FOS/JUN; MAPK/SAPK/PKC; growth/apoptosis/stress

4. ARE-luc, androgen receptor; steroids/MAPK; growth/differentiation/apoptosis

5. p53-luc, p53; SAPK; growth/differentiation/apoptosis

6. CRE-luc, CREB/ATF2; PKA/p38; growth/apoptosis/stress

7. TCF-luc, TCF/Lef; β-catenin, Adhesion/invasion

Gene-mediated effects can be assayed in cells showing mRNA expression. Luciferase reporter plasmids can be introduced by lipid-mediated transfection (TFX-50, Promega). Luciferase activity, an indicator of relative transcriptional activity, is measured by incubation of cell extracts with luciferin substrate and luminescence of the reaction is monitored in a luminometer.

Signaling pathways activated by 151P3D4 are mapped and used for the identification and validation of therapeutic targets. When 151P3D4 is involved in cell signaling, it is used as target for diagnostic, prognostic, preventative and/or therapeutic purposes.

Example 47

Involvement in Tumor Progression

Based on the role of link motif in cell adhesion, cell migration and tumor formation, the 151P3D4 gene can contribute to tumor initiation and progression. The role of 151P3D4 in tumor growth is confirmed in a variety of primary and transfected cell lines including bladder, kidney and ovary cell lines, as well as NIH 3T3 cells engineered to stably express 151P3D4. Parental cells lacking 151P3D4 and cells expressing 151P3D4 are evaluated for cell growth using a well-documented proliferation assay (Fraser S P, Grimes J A, Djamgoz M B. Prostate. 2000; 44:61, Johnson D E, Ochieng J, Evans S L. Anticancer Drugs. 1996, 7:288).

To confirm the role of 151P3D4 in the transformation process, its effect in colony forming assays is investigated. Parental NIH-3T3 cells lacking 151P3D4 are compared to NIH-3T3 cells expressing 151P3D4, using a soft agar assay under stringent and more permissive conditions (Song Z. et al. Cancer Res. 2000; 60:6730).

To confirm the role of 151P3D4 in invasion and metastasis of cancer cells, a well-established assay is used, e.g., a Transwell Insert System assay (Becton Dickinson) (Cancer Res. 1999; 59:6010). Control cells, including bladder, ovary and kidney cell lines lacking 151P3D4 are compared to cells expressing 151P3D4. Cells are loaded with the fluorescent dye, calcein, and plated in the top well of the Transwell insert coated with a basement membrane analog. Invasion is determined by fluorescence of cells in the lower chamber relative to the fluorescence of the entire cell population.

151P3D4 can also play a role in cell cycle and apoptosis. Parental cells and cells expressing 151P3D4 are compared for differences in cell cycle regulation using a well-established BrdU assay (Abdel-Malek Z A. J Cell Physiol. 1988, 136:247). In short, cells are grown under both optimal (full serum) and limiting (low serum) conditions are labeled with BrdU and stained with anti-BrdU Ab and propidium iodide. Cells are analyzed for entry into the G1, S, and G2M phases of the cell cycle. Alternatively, the effect of stress on apoptosis is evaluated in control parental cells and cells expressing 151P3D4, including normal and tumor bladder, kidney and ovary cells. Engineered and parental cells are treated with various chemotherapeutic agents, such as etoposide, taxol, etc, and protein synthesis inhibitors, such as cycloheximide. Cells are stained with annexin V-FITC and cell death is measured by FACS analysis. The modulation of cell death by 151P3D4 can play a critical role in regulating tumor progression and tumor load.

When 151P3D4 plays a role in cell growth, transformation, invasion or apoptosis, it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.

Example 48

Involvement in Angiogenesis

Angiogenesis or new capillary blood vessel formation is necessary for tumor growth (Hanahan D, Folkman J. Cell. 1996, 86:353; Folkman J. Endocrinology. 1998 139:441). Based on the effect of phosphodiesterase inhibitors on endothelial cells, 151P3D4 plays a role in angiogenesis (DeFouw L et al, Microvasc Res 2001, 62:263). Several assays have been developed to measure angiogenesis in vitro and in vivo, such as the tissue culture assays endothelial cell tube formation and endothelial cell proliferation. Using these assays as well as in vitro neo-vascularization, the role of 151P3D4 in angiogenesis, enhancement or inhibition, is confirmed.

For example, endothelial cells engineered to express 151P3D4 are evaluated using tube formation and proliferation assays. The effect of 151P3D4 is also confirmed in animal models in vivo. For example, cells either expressing or lacking 151P3D4 are implanted subcutaneously in immunocompromised mice. Endothelial cell migration and angiogenesis are evaluated 5-15 days later using immunohistochemistry techniques. 151P3D4 affects angiogenesis, and it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes

Example 49

Involvement in Protein-Protein Interactions

Link as well as immunoglobulin motifs have been shown to mediate interaction with other proteins, resulting in the formation of a multi-protein complex ( ). Using immunoprecipitation techniques as well as two yeast hybrid systems, proteins are identified that associate with 151P3D4. Immunoprecipitates from cells expressing 151P3D4 and cells lacking 151P3D4 are compared for specific protein-protein associations.

Studies are performed to confirm the extent of association of 151P3D4 with effector molecules, such as nuclear proteins, transcription factors, kinases, phosphates etc. Studies comparing 151P3D4 positive and 151P3D4 negative cells as well as studies comparing unstimulated/resting cells and cells treated with epithelial cell activators, such as cytokines, growth factors and anti-integrin Ab reveal unique interactions.

In addition, protein-protein interactions are confirmed using two yeast hybrid methodology (Curr Opin Chem. Biol. 1999, 3:64). A vector carrying a library of proteins fused to the activation domain of a transcription factor is introduced into yeast expressing a 151P3D4-DNA-binding domain fusion protein and a reporter construct. Protein-protein interaction is detected by colorimetric reporter activity. Specific association with effector molecules and transcription factors directs one of skill to the mode of action of 151P3D4, and thus identifies therapeutic, prognostic, preventative and/or diagnostic targets for cancer. This and similar assays are also used to identify and screen for small molecules that interact with 151P3D4.

Thus it is found that 151P3D4 associates with proteins and small molecules. Accordingly, 151P3D4 and these proteins and small molecules are used for diagnostic, prognostic, preventative and/or therapeutic purposes.

Example 50

Involvement in Adhesion

Cell adhesion plays a critical role in tissue colonization and metastasis. The presence of link motif in 151P3D4 is indicative of its role in cell adhesion. To confirm that 151P3D4 plays a role in cell adhesion, control cells lacking 151P3D4 are compared to cells expressing 151P3D4, using techniques previously described (see, e.g., Haier et al, Br. J. Cancer. 1999, 80:1867; Lehr and Pienta, J. Natl. Cancer Inst. 1998, 90:118). Briefly, in one embodiment, cells labeled with a fluorescent indicator, such as calcein, are incubated on tissue culture wells coated with media alone or with matrix proteins. Adherent cells are detected by fluorimetric analysis and percent adhesion is calculated. This experimental system can be used to identify proteins, antibodies and/or small molecules that modulate cell adhesion to extracellular matrix and cell-cell interaction. Since cell adhesion plays a critical role in tumor growth, progression, and, colonization, the gene involved in this process can serves as a diagnostic, preventative and therapeutic modality.

Throughout this application, publications, patent applications and patents are referenced. The disclosures of each of these references are hereby incorporated by reference herein in their entireties.

The present invention is not to be limited in scope by the embodiments disclosed herein, which are intended as single illustrations of individual aspects of the invention, and any that are functionally equivalent are within the scope of the invention. Various modifications to the models and methods of the invention, in addition to those described herein, will become apparent to those skilled in the art from the foregoing description and teachings, and are similarly intended to fall within the scope of the invention. Such modifications or other embodiments can be practiced without departing from the true scope and spirit of the invention.

TABLE I
Tissues that Express 151P3D4 When Malignant
Bladder
Kidney
Colon
Lung
Ovary
Breast
Stomach
Uterus

TABLE II
Amino Acid Abbreviations
	SINGLE	THREE
	LETTER	LETTER	FULL NAME
	F	Phe	phenylalanine
	L	Leu	leucine
	S	Ser	serine
	Y	Tyr	tyrosine
	C	Cys	cysteine
	W	Trp	tryptophan
	P	Pro	proline
	H	His	histidine
	Q	Gln	glutamine
	R	Arg	arginine
	I	Ile	isoleucine
	M	Met	methionine
	T	Thr	threonine
	N	Asn	asparagine
	K	Lys	lysine
	V	Val	valine
	A	Ala	alanine
	D	Asp	aspartic acid
	E	Glu	glutamic acid
	G	Gly	glycine

TABLE III

Amino Acid Substitution Matrix

Adapted from the GCG Software 9.0 BLOSUM62 amino acid

substitution matrix (block substitution matrix). The higher

the value, the more likely a substitution is found in

related, natural proteins. (See URL located on the World

Wide Web at (.ikp.unibe.ch/manual/blosum62.html))

A

C

D

E

F

G

H

I

K

L

M

N

P

Q

R

S

T

V

W

Y

.

4

0

−2

−1

−2

0

−2

−1

−1

−1

−1

−2

−1

−1

−1

1

0

0

−3

−2

A

9

−3

−4

−2

−3

−3

−1

−3

−1

−1

−3

−3

−3

−3

−1

−1

−1

−2

−2

C

6

2

−3

−1

−1

−3

−1

−4

−3

1

−1

0

−2

0

−1

−3

−4

−3

D

5

−3

−2

0

−3

1

−3

−2

0

−1

2

0

0

−1

−2

−3

−2

E

6

−3

−1

0

−3

0

0

−3

−4

−3

−3

−2

−2

−1

1

3

F

6

−2

−4

−2

−4

−3

0

−2

−2

−2

0

−2

−3

−2

−3

G

8

−3

−1

−3

−2

1

−2

0

0

−1

−2

−3

−2

2

H

4

−3

2

1

−3

−3

−3

−3

−2

−1

3

−3

−1

I

5

−2

−1

0

−1

1

2

0

−1

−2

−3

−2

K

4

2

−3

−3

−2

−2

−2

−1

1

−2

−1

L

5

−2

−2

0

−1

−1

−1

1

−1

−1

M

6

−2

0

0

1

0

−3

−4

−2

N

7

−1

−2

−1

−1

−2

−4

−3

P

5

1

0

−1

−2

−2

−1

Q

5

−1

−1

−3

−3

−2

R

4

1

−2

−3

−2

S

5

0

−2

−2

T

4

−3

−1

V

11

2

W

7

Y

Table IV: HLA Class I/II Motifs/Supermotifs

TABLE IV (A)
HLA Class I Supermotifs/Motifs
			POSITION
	POSITION	POSITION	C Terminus
	2 (Primary	3 (Primary	(Primary
	Anchor)	Anchor)	Anchor)
SUPERMOTIFS
A1	TILVMS		FWY
A2	LIVMATQ		IVMATL
A3	VSMATLI		RK
A24	YFWIVLMT		FIYWLM
B7	P		VILFMWYA
B27	RHK		FYLWMIVA
B44	ED		FWYLIMVA
B58	ATS		FWYLIVMA
B62	QLIVMP		FWYMIVLA
MOTIFS
A1	TSM		Y
A1		DEAS	Y
A2.1	LMVQIAT		VLIMAT
A3	LMVISATFCGD		KYRHFA
A11	VTMLISAGNCDF		KRYH
A24	YFWM		FLIW
A*3101	MVTALIS		RK
A*3301	MVALFIST		RK
A*6801	AVTMSLI		RK
B*0702	P		LMFWYAIV
B*3501	P		LMFWYIVA
B51	P		LIVFWYAM
B*5301	P		IMFWYALV
B*5401	P		ATIVLMFWY
Bolded residues are preferred, italicized residues are less preferred: A peptide is considered motif-bearing if it has primary anchors at each primary anchor position for a motif or supermotif as specified in the above table.

TABLE IV (B)
HLA Class II Supermotif
1	6	9
W, F, Y, V, I, L	A, V, I, L, P, C, S, T	A, V, I, L, C, S, T, M, Y

TABLE IV (C)
HLA Class II Motifs
MOTIFS		1° anchor 1	2	3	4	5	1° anchor 6	7	8	9
DR4	preferred	FMYLIVW	M	T		I	VSTCPALIM	MH		MH
	deleterious				W			R		WDE
DR1	preferred	MFLIVWY			PAMQ		VMATSPLIC	M		AVM
	deleterious		C	CH	FD	CWD		GDE	D
DR7	preferred	MFLIVWY	M	W	A		IVMSACTPL	M		IV
	deleterious		C		G			GRD	N	G
DR3	MOTIFS	1° anchor 1	2	3	1° anchor 4	5	1° anchor 6
motif a		LIVMFY			D
preferred
motif b		LIVMFAY			DNQEST		KRH
preferred
DR		MFLIVWY					VMSTACPLI
Supermotif
Italicized residues indicate less preferred or “tolerated” residues

TABLE IV (D)
HLA Class I Supermotifs
SUPER-	POSITION:
MOTIFS	1	2	3	4	5	6	7	8	C-terminus
A1			1° Anchor							1° Anchor
			TILVMS							FWY
A2			1° Anchor							1° Anchor
			LIVMATQ							LIVMAT
A3	preferred		1° Anchor	YFW			YFW	YFW	P	1° Anchor
			VSMATLI	(4/5)			(3/5)	(4/5)	(4/5)	RK
	deleterious	DE (3/5);		DE
		P (5/5)		(4/5)
A24			1° Anchor							1° Anchor
			YFWIVLMT							FIYWLM
B7	preferred	FWY (5/5)	1° Anchor	FWY					FWY	1°Anchor
		LIVM (3/5)	P	(4/5)					(3/5)	VILFMWYA
	deleterious	DE (3/5);				DE	G	QN	DE
		P (5/5);				(3/5)	(4/5)	(4/5)	(4/5)
		G (4/5);
		A (3/5);
		QN (3/5)
B27			1° Anchor							1°Anchor
			RHK							FYLWMIVA
B44			1° Anchor							1° Anchor
			ED							FWYLIMVA
B58			1° Anchor							1° Anchor
			ATS							FWYLIVMA
B62			1° Anchor							1° Anchor
			QLIVMP							FWYMIVLA
Italicized residues indicate less preferred or “tolerated” residues

TABLE IV (E)
HLA Class I Motifs
	POSITION:
										9 or
										C-ter-	C-ter-
		1	2	3	4	5	6	7	8	minus	minus
A1	pre-	GFYW	1° Anchor	DEA	YFW		P	DEQN	YFW	1°
9-	ferred		STM							Anchor
mer	deleter-	DE		RHKLIVMP	A	G	A			Y
	ious
A1	pre-	GRHK	ASTCLIVM	1° Anchor	GSTC		ASTC	LIVM	DE	1°
9-	ferred			DEAS						Anchor
mer	deleter-	A	RHKDEPY		DE	PQN	RHK	PG	GP	Y
	ious		FW
A1	pre-	YFW	1° Anchor	DEAQN	A	YFWQN		PASTC	GDE	P	1°
10-	ferred		STM								Anchor
mer	deleter-	GP		RHKGLIVM	DE	RHK	QNA	RHKYFW	RHK	A	Y
	ious
A1	pre-	YFW	STCLIVM	1° Anchor	A	YFW		PG	G	YFW	1°
10-	ferred			DEAS							Anchor
mer	deleter-	RHK	RHKDEPY			P	G		PRHK	QN	Y
	ious		FW
A2.1	pre-	YFW	1° Anchor	YFW	STC	YFW		A	P	1°
9-	ferred		LMIVQAT							Anchor
mer	deleter-	DEP		DERKH			RKH	DERKH		VLIMAT
	ious
	POSITION:
											C-Ter-
		1	2	3	4	5	6	7	8	9	minus
A2.1	pre-	AYFW	1° Anchor	LVIM	G		G		FYWL		1°
10-	ferred		LMIVQAT						VIM		Anchor
mer	deleter-	DEP		DE	RKHA	P		RKH	DERKH	RKH	VLIMAT
	ious
A3	pre-	RHK	1° Anchor	YFW	PRHK	A	YFW		P	1°
	ferred		LMVISA		YFW					Anchor
			TFCGD							KYRHFA
	deleter-	DEP		DE
	ious
A11	pre-	A	1° Anchor	YFW	YFW	A	YFW	YFW	P	1°
	ferred		VTLMIS							Anchor
			AGNCDF							KRYH
	deleter-	DEP						A	G
	ious
A24	pre-	YFWRHK	1° Anchor		STC			YFW	YFW	1°
9-	ferred		YFWM							Anchor
mer	deleter-	DEG		DE	G	QNP	DERHK	G	AQN	FLIW
	ious
A24	pre-		1° Anchor		P	YFWP		P			1°
10-	ferred		YFWM								Anchor
mer	deleter-			GDE	QN	RHK	DE	A	QN	DEA	FLIW
	ious
A	pre-	RHK	1° Anchor	YFW	P		YFW	YFW	AP	1°
3110	ferred		MVTALIS							Anchor
	deleter-	DEP		DE		ADE	DE	DE	DE	RK
	ious
A	pre-		1° Anchor	YFW				AYFW		1°
3301	ferred		MVALFIST							Anchor
	deleter-	GP		DE						RK
	ious
A	pre-	YFWSTC	1° Anchor			YFWL		YFW	P	1°
6801	ferred		AVTMSLI			IVM				Anchor
	deleter-	GP		DEG		RHK			A	RK
	ious
B	pre-	RHKFWY	1° Anchor	RHK		RHK	RHK	RHK	PA	1°
0702	ferred		P							Anchor
	deleter-	DEQNP		DEP	DE	DE	GDE	QN	DE	LMFWY
	ious									AIV
B	pre-	FWYLIVM	1° Anchor	FWY				FWY		1°
3501	ferred		P							Anchor
	deleter-	AGP				G	G			LMFWY
	ious									IVA
B51	pre-	LIVMFWY	1° Anchor	FWY	STC	FWY		G	FWY	1°
	ferred		P							Anchor
	deleter-	AGPDE				DE	G	DEQN	GDE	LIVFW
	ious	RHKSTC								YAM
B	pre-	LIVMFWY	1° Anchor	FWY	STC	FWY		LIVMF	FWY	1°
5301	ferred		P					WY		Anchor
	deleter-	AGPQN					G	RHKQN	DE	IMFWY
	ious									ALV
B	pre-	FWY	1° Anchor	FWY		LIVM		ALIVM	FWYAP	1°
5401	ferred		P	LIVM						Anchor
	deleter-	GPQNDE		GDES		RHKDE	DE	QNDGE	DE	ATIVLM
	ious			TC						FWY
Italicized residues indicate less preferred or “tolerated” residues.
The information in this Table is specific for 9-mers unless otherwise specified.

TABLE V
v.1-A1-9mers: 151P3D4
Pos	1	2	3	4	5	6	7	8	9	Score	SeqID
126	I	T	D	L	T	L	E	D	Y	62.500	Portion of
264	L	I	H	P	T	K	L	T	Y	25.000	SEQ ID
14	W	A	D	H	L	S	D	N	Y	25.000	NO: 3;
130	T	L	E	D	Y	G	R	Y	K	18.000	each start
57	V	T	L	P	C	K	F	Y	R	12.500	position is
280	L	N	D	G	A	Q	I	A	K	12.500	specified,
230	N	T	V	P	G	V	R	N	Y	12.500	the length
153	A	L	D	L	Q	G	V	V	F	10.000	of peptide
18	L	S	D	N	Y	T	L	D	H	3.750	is 9 amino
293	F	A	A	W	K	I	L	G	Y	2.500	acids, the
155	D	L	Q	G	V	V	F	P	Y	2.500	end
144	G	L	E	D	D	T	V	V	V	1.800	position
43	E	A	E	Q	A	K	V	F	S	1.800	for each
41	L	V	E	A	E	Q	A	K	V	1.800	peptide is
213	G	S	V	Q	Y	P	I	T	K	1.500	the start
183	D	Q	D	A	V	I	A	S	F	1.500	position
119	D	S	D	A	S	L	V	I	T	1.500	plus eight.
64	Y	R	D	P	T	A	F	G	S	1.250
129	L	T	L	E	D	Y	G	R	Y	1.250
201	G	L	D	W	C	N	A	G	W	1.000
181	C	L	D	Q	D	A	V	I	A	1.000
23	T	L	D	H	D	R	A	I	H	1.000
209	W	L	S	D	G	S	V	Q	Y	1.000
308	W	L	A	D	G	S	V	R	Y	1.000
68	T	A	F	G	S	G	I	H	K	1.000
33	Q	A	E	N	G	P	H	L	L	0.900
141	V	I	E	G	L	E	D	D	T	0.900
254	T	S	N	F	N	G	R	F	Y	0.750
117	G	S	D	S	D	A	S	L	V	0.750
255	S	N	F	N	G	R	F	Y	Y	0.625
337	F	P	D	K	K	H	K	L	Y	0.625
56	N	V	T	L	P	C	K	F	Y	0.500
335	V	G	F	P	D	K	K	H	K	0.500
187	V	I	A	S	F	D	Q	L	Y	0.500
158	G	V	V	F	P	Y	F	P	R	0.500
91	E	V	D	V	F	V	S	M	G	0.500
325	C	S	P	T	E	A	A	V	R	0.300
253	F	T	S	N	F	N	G	R	F	0.250
103	K	T	Y	G	G	Y	Q	G	R	0.250
303	R	C	D	A	G	W	L	A	D	0.250
97	S	M	G	Y	H	K	K	T	Y	0.250
327	P	T	E	A	A	V	R	F	V	0.225
89	L	K	E	V	D	V	F	V	S	0.225
159	V	V	F	P	Y	F	P	R	L	0.200
95	F	V	S	M	G	Y	H	K	K	0.200
128	D	L	T	L	E	D	Y	G	R	0.200
324	R	C	S	P	T	E	A	A	V	0.200
40	L	L	V	E	A	E	Q	A	K	0.200
329	E	A	A	V	R	F	V	G	F	0.200
215	V	Q	Y	P	I	T	K	P	R	0.150
240	F	W	D	K	D	K	S	R	Y	0.125
92	V	D	V	F	V	S	M	G	Y	0.125
161	F	P	Y	F	P	R	L	G	R	0.125
247	R	Y	D	V	F	C	F	T	S	0.125
148	D	T	V	V	V	A	L	D	L	0.125
345	Y	G	V	Y	C	F	R	A	Y	0.125
343	K	L	Y	G	V	Y	C	F	R	0.100
54	G	G	N	V	T	L	P	C	K	0.100
249	D	V	F	C	F	T	S	N	F	0.100
289	V	G	Q	I	F	A	A	W	K	0.100
272	Y	D	E	A	V	Q	A	C	L	0.090
174	F	H	E	A	Q	Q	A	C	L	0.090
138	K	C	E	V	I	E	G	L	E	0.090
312	G	S	V	R	Y	P	I	S	R	0.075
245	K	S	R	Y	D	V	F	C	F	0.075
210	L	S	D	G	S	V	Q	Y	P	0.075
71	G	S	G	I	H	K	I	R	I	0.075
85	T	S	D	Y	L	K	E	V	D	0.075
314	V	R	Y	P	I	S	R	P	R	0.050
219	I	T	K	P	R	E	P	C	G	0.050
4	L	L	L	L	V	L	I	S	I	0.050
309	L	A	D	G	S	V	R	Y	P	0.050
185	D	A	V	I	A	S	F	D	Q	0.050
176	E	A	Q	Q	A	C	L	D	Q	0.050
146	E	D	D	T	V	V	V	A	L	0.050
270	L	T	Y	D	E	A	V	Q	A	0.050
166	R	L	G	R	Y	N	L	N	F	0.050
150	V	V	V	A	L	D	L	Q	G	0.050
107	G	Y	Q	G	R	V	F	L	K	0.050
6	L	L	V	L	I	S	I	C	W	0.050
3	S	L	L	L	L	V	L	I	S	0.050
326	S	P	T	E	A	A	V	R	F	0.050
72	S	G	I	H	K	I	R	I	K	0.050
123	S	L	V	I	T	D	L	T	L	0.050
145	L	E	D	D	T	V	V	V	A	0.050
251	F	C	F	T	S	N	F	N	G	0.050
232	V	P	G	V	R	N	Y	G	F	0.050
131	L	E	D	Y	G	R	Y	K	C	0.050
222	P	R	E	P	C	G	G	Q	N	0.045
156	L	Q	G	V	V	F	P	Y	F	0.030
189	A	S	F	D	Q	L	Y	D	A	0.030
2	K	S	L	L	L	L	V	L	I	0.030
162	P	Y	F	P	R	L	G	R	Y	0.025
316	Y	P	I	S	R	P	R	R	R	0.025
55	G	N	V	T	L	P	C	K	F	0.025
190	S	F	D	Q	L	Y	D	A	W	0.025
105	Y	G	G	Y	Q	G	R	V	F	0.025
70	F	G	S	G	I	H	K	I	R	0.025
271	T	Y	D	E	A	V	Q	A	C	0.025
194	L	Y	D	A	W	R	G	G	L	0.025
v.2-A1-9mers: 151P3D4
Pos	1	2	3	4	5	6	7	8	9	Score	SeqID
34	K	V	D	L	L	V	P	T	K	20.000	Portion of
385	S	L	E	E	G	L	G	G	K	18.000	SEQ ID
183	T	L	E	E	K	R	K	E	K	18.000	NO: 5; each
123	N	T	N	P	S	R	R	P	Y	12.500	start
1	M	L	E	H	T	T	K	T	F	9.000	position is
97	S	C	E	G	I	N	I	S	G	4.500	specified,
59	F	V	G	S	Y	K	L	A	Y	2.500	the length
367	P	A	D	L	A	G	S	G	Y	2.500	of peptide
220	Y	T	E	S	P	G	G	G	S	2.250	is 9 amino
238	T	I	A	P	L	A	A	T	R	2.000	acids, the
208	Q	A	E	K	N	M	K	K	K	1.800	end
157	A	S	E	A	Y	K	K	V	C	1.350	position for
354	K	S	E	N	N	S	W	Y	V	1.350	each
226	G	G	S	P	R	G	L	G	F	1.250	peptide is
302	S	T	Y	D	S	L	S	P	Y	1.250	the start
188	R	K	E	K	A	E	I	H	Y	1.125	position
400	K	A	E	N	G	P	H	L	L	0.900	plus eight.
191	K	A	E	I	H	Y	R	K	N	0.900
17	V	V	E	S	I	R	D	H	S	0.900
382	A	I	E	S	L	E	E	G	L	0.900
51	A	K	D	F	G	H	V	Q	F	0.500
7	K	T	F	P	L	R	A	L	H	0.500
134	Q	V	P	S	R	I	F	W	R	0.500
296	S	C	P	T	S	S	S	T	Y	0.500
70	D	G	E	H	W	T	V	Y	Q	0.450
105	G	S	F	C	R	N	K	L	K	0.300
103	I	S	G	S	F	C	R	N	K	0.300
373	S	G	Y	C	G	A	L	W	K	0.250
180	V	T	A	T	L	E	E	K	R	0.250
37	L	L	V	P	T	K	V	T	G	0.200
389	G	L	G	G	K	Q	K	D	K	0.200
168	G	A	P	H	E	V	G	W	K	0.200
181	T	A	T	L	E	E	K	R	K	0.200
179	A	V	T	A	T	L	E	E	K	0.200
56	H	V	Q	F	V	G	S	Y	K	0.200
306	S	L	S	P	Y	G	P	R	N	0.200
361	Y	V	E	N	G	R	P	A	D	0.180
323	P	S	G	G	G	G	L	K	K	0.150
207	K	Q	A	E	K	N	M	K	K	0.150
222	E	S	P	G	G	G	S	P	R	0.150
295	S	S	C	P	T	S	S	S	T	0.150
305	D	S	L	S	P	Y	G	P	R	0.150
83	R	K	D	K	V	L	L	G	R	0.125
68	S	N	D	G	E	H	W	T	V	0.125
101	I	N	I	S	G	S	F	C	R	0.125
169	A	P	H	E	V	G	W	K	Y	0.125
46	I	I	T	Q	G	A	K	D	F	0.100
150	S	C	C	P	Q	G	H	A	S	0.100
154	Q	G	H	A	S	E	A	Y	K	0.100
75	T	V	Y	Q	D	E	K	Q	R	0.100
78	Q	D	E	K	Q	R	K	D	K	0.090
384	E	S	L	E	E	G	L	G	G	0.075
133	F	Q	V	P	S	R	I	F	W	0.075
279	A	S	P	A	A	W	L	P	L	0.075
4	H	T	T	K	T	F	P	L	R	0.050
145	K	A	D	G	G	S	C	C	P	0.050
95	V	V	S	C	E	G	I	N	I	0.050
280	S	P	A	A	W	L	P	L	R	0.050
346	R	G	K	P	Q	R	K	P	K	0.050
265	H	R	P	P	A	L	S	A	R	0.050
377	G	A	L	W	K	A	I	E	S	0.050
44	T	G	I	I	T	Q	G	A	K	0.050
326	G	G	G	L	K	K	P	A	R	0.050
288	R	T	P	W	T	R	P	S	S	0.050
322	S	P	S	G	G	G	G	L	K	0.050
237	K	T	I	A	P	L	A	A	T	0.050
167	S	G	A	P	H	E	V	G	W	0.050
112	L	K	Y	L	A	F	L	H	K	0.050
121	R	M	N	T	N	P	S	R	R	0.050
303	T	Y	D	S	L	S	P	Y	G	0.050
199	N	K	Q	L	M	R	L	Q	K	0.050
386	L	E	E	G	L	G	G	K	Q	0.045
372	G	S	G	Y	C	G	A	L	W	0.030
261	G	S	S	A	H	R	P	P	A	0.030
262	S	S	A	H	R	P	P	A	L	0.030
69	N	D	G	E	H	W	T	V	Y	0.025
74	W	T	V	Y	Q	D	E	K	Q	0.025
21	I	R	D	H	S	G	Q	K	M	0.025
314	N	P	L	P	N	P	R	H	S	0.025
291	W	T	R	P	S	S	C	P	T	0.025
99	E	G	I	N	I	S	G	S	F	0.025
43	V	T	G	I	I	T	Q	G	A	0.025
316	L	P	N	P	R	H	S	P	S	0.025
47	I	T	Q	G	A	K	D	F	G	0.025
55	G	H	V	Q	F	V	G	S	Y	0.025
274	A	P	V	P	A	A	S	P	A	0.025
211	K	N	M	K	K	K	I	D	K	0.025
284	W	L	P	L	R	T	P	W	T	0.020
241	P	L	A	A	T	R	A	T	R	0.020
190	E	K	A	E	I	H	Y	R	K	0.020
344	L	A	R	G	K	P	Q	R	K	0.020
20	S	I	R	D	H	S	G	Q	K	0.020
163	K	V	C	L	S	G	A	P	H	0.020
155	G	H	A	S	E	A	Y	K	K	0.020
369	D	L	A	G	S	G	Y	C	G	0.020
87	V	L	L	G	R	K	A	V	V	0.020
343	V	L	A	R	G	K	P	Q	R	0.020
12	R	A	L	H	I	V	V	E	S	0.020
203	M	R	L	Q	K	Q	A	E	K	0.020
358	N	S	W	Y	V	E	N	G	R	0.015

TABLE VI

v.1-A1-10mers: 151P3D4

Pos

1

2

3

4

5

6

7

8

9

0

Score

SeqID

91

E

V

D

V

F

V

S

M

G

Y

125.000

Portion of

41

L

V

E

A

E

Q

A

K

V

F

9.000

SEQ ID

33

Q

A

E

N

G

P

H

L

L

V

4.500

NO: 3;

43

E

A

E

Q

A

K

V

F

S

H

4.500

each start

254

T

S

N

F

N

G

R

F

Y

Y

3.750

position is

117

G

S

D

S

D

A

S

L

V

I

3.750

specified,

181

C

L

D

Q

D

A

V

I

A

S

2.500

the length

23

T

L

D

H

D

R

A

I

H

I

2.500

of peptide

263

Y

L

I

H

P

T

K

L

T

Y

2.500

is 10

324

R

C

S

P

T

E

A

A

V

R

2.000

amino

130

T

L

E

D

Y

G

R

Y

K

C

1.800

acids, the

144

G

L

E

D

D

T

V

V

V

A

1.800

end

85

T

S

D

Y

L

K

E

V

D

V

1.500

position

210

L

S

D

G

S

V

Q

Y

P

I

1.500

for each

126

I

T

D

L

T

L

E

D

Y

G

1.250

peptide is

253

F

T

S

N

F

N

G

R

F

Y

1.250

the start

327

P

T

E

A

A

V

R

F

V

G

1.125

position

303

R

C

D

A

G

W

L

A

D

G

1.000

plus nine.

279

C

L

N

D

G

A

Q

I

A

K

1.000

309

L

A

D

G

S

V

R

Y

P

I

1.000

141

V

I

E

G

L

E

D

D

T

V

0.900

96

V

S

M

G

Y

H

K

K

T

Y

0.750

190

S

F

D

Q

L

Y

D

A

W

R

0.500

125

V

I

T

D

L

T

L

E

D

Y

0.500

201

G

L

D

W

C

N

A

G

W

L

0.500

56

N

V

T

L

P

C

K

F

Y

R

0.500

128

D

L

T

L

E

D

Y

G

R

Y

0.500

14

W

A

D

H

L

S

D

N

Y

T

0.500

129

L

T

L

E

D

Y

G

R

Y

K

0.500

186

A

V

I

A

S

F

D

Q

L

Y

0.500

138

K

C

E

V

I

E

G

L

E

D

0.450

93

D

V

F

V

S

M

G

Y

H

K

0.400

288

K

V

G

Q

I

F

A

A

W

K

0.400

119

D

S

D

A

S

L

V

I

T

D

0.375

71

G

S

G

I

H

K

I

R

I

K

0.300

325

C

S

P

T

E

A

A

V

R

F

0.300

106

G

G

Y

Q

G

R

V

F

L

K

0.250

64

Y

R

D

P

T

A

F

G

S

G

0.250

67

P

T

A

F

G

S

G

I

H

K

0.250

280

L

N

D

G

A

Q

I

A

K

V

0.250

230

N

T

V

P

G

V

R

N

Y

G

0.250

212

D

G

S

V

Q

Y

P

I

T

K

0.250

39

H

L

L

V

E

A

E

Q

A

K

0.200

155

D

L

Q

G

V

V

F

P

Y

F

0.200

334

F

V

G

F

P

D

K

K

H

K

0.200

231

T

V

P

G

V

R

N

Y

G

F

0.200

152

V

A

L

D

L

Q

G

V

V

F

0.200

154

L

D

L

Q

G

V

V

F

P

Y

0.125

292

I

F

A

A

W

K

I

L

G

Y

0.125

161

F

P

Y

F

P

R

L

G

R

Y

0.125

55

G

N

V

T

L

P

C

K

F

Y

0.125

157

Q

G

V

V

F

P

Y

F

P

R

0.125

229

Q

N

T

V

P

G

V

R

N

Y

0.125

311

D

G

S

V

R

Y

P

I

S

R

0.125

81

W

T

K

L

T

S

D

Y

L

K

0.100

53

R

G

G

N

V

T

L

P

C

K

0.100

314

V

R

Y

P

I

S

R

P

R

R

0.100

214

S

V

Q

Y

P

I

T

K

P

R

0.100

251

F

C

F

T

S

N

F

N

G

R

0.100

159

V

V

F

P

Y

F

P

R

L

G

0.100

153

A

L

D

L

Q

G

V

V

F

P

0.100

89

L

K

E

V

D

V

F

V

S

M

0.090

18

L

S

D

N

Y

T

L

D

H

D

0.075

2

K

S

L

L

L

L

V

L

I

S

0.075

122

A

S

L

V

I

T

D

L

T

L

0.075

337

F

P

D

K

K

H

K

L

Y

G

0.062

291

Q

I

F

A

A

W

K

I

L

G

0.050

22

Y

T

L

D

H

D

R

A

I

H

0.050

236

R

N

Y

G

F

W

D

K

D

K

0.050

145

L

E

D

D

T

V

V

V

A

L

0.050

149

T

V

V

V

A

L

D

L

Q

G

0.050

35

E

N

G

P

H

L

L

V

E

A

0.050

57

V

T

L

P

C

K

F

Y

R

D

0.050

343

K

L

Y

G

V

Y

C

F

R

A

0.050

208

G

W

L

S

D

G

S

V

Q

Y

0.050

3

S

L

L

L

L

V

L

I

S

I

0.050

17

H

L

S

D

N

Y

T

L

D

H

0.050

271

T

Y

D

E

A

V

Q

A

C

L

0.050

307

G

W

L

A

D

G

S

V

R

Y

0.050

5

L

L

L

V

L

I

S

I

C

W

0.050

222

P

R

E

P

C

G

G

Q

N

T

0.045

272

Y

D

E

A

V

Q

A

C

L

N

0.045

331

A

V

R

F

V

G

F

P

D

K

0.040

247

R

Y

D

V

F

C

F

T

S

N

0.025

13

C

W

A

D

H

L

S

D

N

Y

0.025

242

D

K

D

K

S

R

Y

D

V

F

0.025

219

I

T

K

P

R

E

P

C

G

G

0.025

160

V

F

P

Y

F

P

R

L

G

R

0.025

238

Y

G

F

W

D

K

D

K

S

R

0.025

103

K

T

Y

G

G

Y

Q

G

R

V

0.025

344

L

Y

G

V

Y

C

F

R

A

Y

0.025

335

V

G

F

P

D

K

K

H

K

L

0.025

270

L

T

Y

D

E

A

V

Q

A

C

0.025

54

G

G

N

V

T

L

P

C

K

F

0.025

148

D

T

V

V

V

A

L

D

L

Q

0.025

336

G

F

P

D

K

K

H

K

L

Y

0.025

227

G

G

Q

N

T

V

P

G

V

R

0.025

31

H

I

Q

A

E

N

G

P

H

L

0.020

40

L

L

V

E

A

E

Q

A

K

V

0.020

269

K

L

T

Y

D

E

A

V

Q

A

0.020

v.2-A1-10mers: 151P3D4

Pos

1

2

3

4

5

6

7

8

9

0

Score

SeqID

191

K

A

E

I

H

Y

R

K

N

K

18.000

Portion of

295

S

S

C

P

T

S

S

S

T

Y

7.500

SEQ ID NO:

68

S

N

D

G

E

H

W

T

V

Y

6.250

5; each start

400

K

A

E

N

G

P

H

L

L

V

4.500

position is

105

G

S

F

C

R

N

K

L

K

Y

3.750

specified, the

157

A

S

E

A

Y

K

K

V

C

L

2.700

length of

361

Y

V

E

N

G

R

P

A

D

L

1.800

peptide is 10

77

Y

Q

D

E

K

Q

R

K

D

K

1.500

amino acids,

372

G

S

G

Y

C

G

A

L

W

K

1.500

the end

7

K

T

F

P

L

R

A

L

H

I

1.250

position for

382

A

I

E

S

L

E

E

G

L

G

0.900

each peptide

385

S

L

E

E

G

L

G

G

K

Q

0.900

is the start

386

L

E

E

G

L

G

G

K

Q

K

0.900

position plus

183

T

L

E

E

K

R

K

E

K

A

0.900

nine.

17

V

V

E

S

I

R

D

H

S

G

0.900

97

S

C

E

G

I

N

I

S

G

S

0.900

133

F

Q

V

P

S

R

I

F

W

R

0.750

301

S

S

T

Y

D

S

L

S

P

Y

0.750

145

K

A

D

G

G

S

C

C

P

Q

0.500

123

N

T

N

P

S

R

R

P

Y

H

0.500

182

A

T

L

E

E

K

R

K

E

K

0.500

43

V

T

G

I

I

T

Q

G

A

K

0.500

168

G

A

P

H

E

V

G

W

K

Y

0.500

34

K

V

D

L

L

V

P

T

K

V

0.500

278

A

A

S

P

A

A

W

L

P

L

0.500

100

G

I

N

I

S

G

S

F

C

R

0.500

237

K

T

I

A

P

L

A

A

T

R

0.500

167

S

G

A

P

H

E

V

G

W

K

0.500

21

I

R

D

H

S

G

Q

K

M

K

0.500

180

V

T

A

T

L

E

E

K

R

K

0.500

24

H

S

G

Q

K

M

K

Q

D

K

0.300

321

H

S

P

S

G

G

G

G

L

K

0.300

384

E

S

L

E

E

G

L

G

G

K

0.300

279

A

S

P

A

A

W

L

P

L

R

0.300

354

K

S

E

N

N

S

W

Y

V

E

0.270

74

W

T

V

Y

Q

D

E

K

Q

R

0.250

322

S

P

S

G

G

G

G

L

K

K

0.250

250

I

G

H

P

G

G

R

T

P

R

0.250

220

Y

T

E

S

P

G

G

G

S

P

0.225

102

N

I

S

G

S

F

C

R

N

K

0.200

75

T

V

Y

Q

D

E

K

Q

R

K

0.200

342

N

V

L

A

R

G

K

P

Q

R

0.200

178

Q

A

V

T

A

T

L

E

E

K

0.200

47

I

T

Q

G

A

K

D

F

G

H

0.125

152

C

P

Q

G

H

A

S

E

A

Y

0.125

122

M

N

T

N

P

S

R

R

P

Y

0.125

58

Q

F

V

G

S

Y

K

L

A

Y

0.125

366

R

P

A

D

L

A

G

S

G

Y

0.125

225

G

G

G

S

P

R

G

L

G

F

0.125

54

F

G

H

V

Q

F

V

G

S

Y

0.125

238

T

I

A

P

L

A

A

T

R

A

0.100

154

Q

G

H

A

S

E

A

Y

K

K

0.100

284

W

L

P

L

R

T

P

W

T

R

0.100

45

G

I

I

T

Q

G

A

K

D

F

0.100

13

A

L

H

I

V

V

E

S

I

R

0.100

179

A

V

T

A

T

L

E

E

K

R

0.100

37

L

L

V

P

T

K

V

T

G

I

0.100

111

K

L

K

Y

L

A

F

L

H

K

0.100

1

M

L

E

H

T

T

K

T

F

P

0.090

208

Q

A

E

K

N

M

K

K

K

I

0.090

227

G

S

P

R

G

L

G

F

I

F

0.075

96

V

S

C

E

G

I

N

I

S

G

0.075

240

A

P

L

A

A

T

R

A

T

R

0.050

115

L

A

F

L

H

K

R

M

N

T

0.050

104

S

G

S

F

C

R

N

K

L

K

0.050

367

P

A

D

L

A

G

S

G

Y

C

0.050

206

Q

K

Q

A

E

K

N

M

K

K

0.050

302

S

T

Y

D

S

L

S

P

Y

G

0.050

221

T

E

S

P

G

G

G

S

P

R

0.050

129

R

P

Y

H

F

Q

V

P

S

R

0.050

94

V

V

V

S

C

E

G

I

N

I

0.050

291

W

T

R

P

S

S

C

P

T

S

0.050

83

R

K

D

K

V

L

L

G

R

K

0.050

274

A

P

V

P

A

A

S

P

A

A

0.050

216

K

I

D

K

Y

T

E

S

P

G

0.050

388

E

G

L

G

G

K

Q

K

D

K

0.050

325

G

G

G

G

L

K

K

P

A

R

0.050

124

T

N

P

S

R

R

P

Y

H

F

0.050

316

L

P

N

P

R

H

S

P

S

G

0.050

210

E

K

N

M

K

K

K

I

D

K

0.050

70

D

G

E

H

W

T

V

Y

Q

D

0.045

188

R

K

E

K

A

E

I

H

Y

R

0.045

30

K

Q

D

K

K

V

D

L

L

V

0.037

19

E

S

I

R

D

H

S

G

Q

K

0.030

305

D

S

L

S

P

Y

G

P

R

N

0.030

261

G

S

S

A

H

R

P

P

A

L

0.030

262

S

S

A

H

R

P

P

A

L

S

0.030

222

E

S

P

G

G

G

S

P

R

G

0.030

207

K

Q

A

E

K

N

M

K

K

K

0.030

166

L

S

G

A

P

H

E

V

G

W

0.030

288

R

T

P

W

T

R

P

S

S

C

0.025

198

K

N

K

Q

L

M

R

L

Q

K

0.025

228

S

P

R

G

L

G

F

I

F

K

0.025

357

N

N

S

W

Y

V

E

N

G

R

0.025

226

G

G

S

P

R

G

L

G

F

I

0.025

51

A

K

D

F

G

H

V

Q

F

V

0.025

247

A

T

R

I

G

H

P

G

G

R

0.025

202

L

M

R

L

Q

K

Q

A

E

K

0.020

59

F

V

G

S

Y

K

L

A

Y

S

0.020

33

K

K

V

D

L

L

V

P

T

K

0.020

TABLE VII
v.1-A2-9mers: 151P3D4
Pos	1	2	3	4	5	6	7	8	9	Score	SeqID
88	Y	L	K	E	V	D	V	F	V	252.512	Portion of
4	L	L	L	L	V	L	I	S	I	150.931	SEQ ID
7	L	V	L	I	S	I	C	W	A	34.588	NO: 3;
263	Y	L	I	H	P	T	K	L	T	34.279	each start
5	L	L	L	V	L	I	S	I	C	29.468	position is
151	V	V	A	L	D	L	Q	G	V	23.795	specified,
159	V	V	F	P	Y	F	P	R	L	22.339	the length
123	S	L	V	I	T	D	L	T	L	21.362	of peptide
84	L	T	S	D	Y	L	K	E	V	15.486	is 9 amino
32	I	Q	A	E	N	G	P	H	L	15.096	acids, the
298	I	L	G	Y	D	R	C	D	A	8.446	end
279	C	L	N	D	G	A	Q	I	A	8.351	position
290	G	Q	I	F	A	A	W	K	I	7.933	for each
291	Q	I	F	A	A	W	K	I	L	7.575	peptide is
144	G	L	E	D	D	T	V	V	V	7.483	the start
90	K	E	V	D	V	F	V	S	M	2.634	position
106	G	G	Y	Q	G	R	V	F	L	2.454	plus eight.
2	K	S	L	L	L	L	V	L	I	2.028
22	Y	T	L	D	H	D	R	A	I	2.022
257	F	N	G	R	F	Y	Y	L	I	1.786
186	A	V	I	A	S	F	D	Q	L	1.740
270	L	T	Y	D	E	A	V	Q	A	1.539
209	W	L	S	D	G	S	V	Q	Y	1.405
308	W	L	A	D	G	S	V	R	Y	1.405
343	K	L	Y	G	V	Y	C	F	R	1.377
34	A	E	N	G	P	H	L	L	V	1.352
76	K	I	R	I	K	W	T	K	L	1.328
152	V	A	L	D	L	Q	G	V	V	1.328
189	A	S	F	D	Q	L	Y	D	A	1.132
142	I	E	G	L	E	D	D	T	V	1.127
227	G	G	Q	N	T	V	P	G	V	1.044
181	C	L	D	Q	D	A	V	I	A	0.815
41	L	V	E	A	E	Q	A	K	V	0.662
137	Y	K	C	E	V	I	E	G	L	0.631
116	G	G	S	D	S	D	A	S	L	0.572
178	Q	Q	A	C	L	D	Q	D	A	0.504
306	A	G	W	L	A	D	G	S	V	0.490
207	A	G	W	L	S	D	G	S	V	0.490
179	Q	A	C	L	D	Q	D	A	V	0.473
324	R	C	S	P	T	E	A	A	V	0.454
346	G	V	Y	C	F	R	A	Y	N	0.436
180	A	C	L	D	Q	D	A	V	I	0.424
276	V	Q	A	C	L	N	D	G	A	0.420
193	Q	L	Y	D	A	W	R	G	G	0.332
284	A	Q	I	A	K	V	G	Q	I	0.316
86	S	D	Y	L	K	E	V	D	V	0.309
39	H	L	L	V	E	A	E	Q	A	0.306
96	V	S	M	G	Y	H	K	K	T	0.306
202	L	D	W	C	N	A	G	W	L	0.299
3	S	L	L	L	L	V	L	I	S	0.260
145	L	E	D	D	T	V	V	V	A	0.254
278	A	C	L	N	D	G	A	Q	I	0.252
281	N	D	G	A	Q	I	A	K	V	0.222
143	E	G	L	E	D	D	T	V	V	0.212
172	L	N	F	H	E	A	Q	Q	A	0.204
8	V	L	I	S	I	C	W	A	D	0.190
117	G	S	D	S	D	A	S	L	V	0.182
268	T	K	L	T	Y	D	E	A	V	0.175
256	N	F	N	G	R	F	Y	Y	L	0.155
223	R	E	P	C	G	G	Q	N	T	0.145
246	S	R	Y	D	V	F	C	F	T	0.142
156	L	Q	G	V	V	F	P	Y	F	0.134
81	W	T	K	L	T	S	D	Y	L	0.129
6	L	L	V	L	I	S	I	C	W	0.127
10	I	S	I	C	W	A	D	H	L	0.116
40	L	L	V	E	A	E	Q	A	K	0.104
24	L	D	H	D	R	A	I	H	I	0.101
287	A	K	V	G	Q	I	F	A	A	0.092
50	F	S	H	R	G	G	N	V	T	0.092
122	A	S	L	V	I	T	D	L	T	0.088
83	K	L	T	S	D	Y	L	K	E	0.078
36	N	G	P	H	L	L	V	E	A	0.075
155	D	L	Q	G	V	V	F	P	Y	0.075
166	R	L	G	R	Y	N	L	N	F	0.075
71	G	S	G	I	H	K	I	R	I	0.068
187	V	I	A	S	F	D	Q	L	Y	0.066
108	Y	Q	G	R	V	F	L	K	G	0.066
131	L	E	D	Y	G	R	Y	K	C	0.066
336	G	F	P	D	K	K	H	K	L	0.061
255	S	N	F	N	G	R	F	Y	Y	0.057
15	A	D	H	L	S	D	N	Y	T	0.057
199	R	G	G	L	D	W	C	N	A	0.055
141	V	I	E	G	L	E	D	D	T	0.055
97	S	M	G	Y	H	K	K	T	Y	0.054
121	D	A	S	L	V	I	T	D	L	0.051
262	Y	Y	L	I	H	P	T	K	L	0.050
164	F	P	R	L	G	R	Y	N	L	0.049
251	F	C	F	T	S	N	F	N	G	0.048
1	M	K	S	L	L	L	L	V	L	0.048
288	K	V	G	Q	I	F	A	A	W	0.043
57	V	T	L	P	C	K	F	Y	R	0.042
260	R	F	Y	Y	L	I	H	P	T	0.038
56	N	V	T	L	P	C	K	F	Y	0.036
231	T	V	P	G	V	R	N	Y	G	0.036
224	E	P	C	G	G	Q	N	T	V	0.034
53	R	G	G	N	V	T	L	P	C	0.032
334	F	V	G	F	P	D	K	K	H	0.030
201	G	L	D	W	C	N	A	G	W	0.030
9	L	I	S	I	C	W	A	D	H	0.030
58	T	L	P	C	K	F	Y	R	D	0.028
v.2-A2-9mers: 151P3D4
Pos	1	2	3	4	5	6	7	8	9	Score	SeqID
378	A	L	W	K	A	I	E	S	L	199.826	Portion of
284	W	L	P	L	R	T	P	W	T	188.536	SEQ ID
87	V	L	L	G	R	K	A	V	V	179.368	NO: 5;
234	F	I	F	K	T	I	A	P	L	114.985	each start
86	K	V	L	L	G	R	K	A	V	78.811	position is
165	C	L	S	G	A	P	H	E	V	69.552	specified,
88	L	L	G	R	K	A	V	V	V	48.478	the length
114	Y	L	A	F	L	H	K	R	M	22.853	of peptide
231	G	L	G	F	I	F	K	T	I	19.822	is 9 amino
201	Q	L	M	R	L	Q	K	Q	A	18.382	acids, the
52	K	D	F	G	H	V	Q	F	V	15.825	end
57	V	Q	F	V	G	S	Y	K	L	13.624	position
13	A	L	H	I	V	V	E	S	I	11.758	for each
230	R	G	L	G	F	I	F	K	T	9.124	peptide is
9	F	P	L	R	A	L	H	I	V	7.287	the start
67	Y	S	N	D	G	E	H	W	T	5.046	position
354	K	S	E	N	N	S	W	Y	V	4.195	plus eight.
100	G	I	N	I	S	G	S	F	C	3.757
38	L	V	P	T	K	V	T	G	I	3.569
30	K	Q	D	K	K	V	D	L	L	3.417
95	V	V	S	C	E	G	I	N	I	1.552
110	N	K	L	K	Y	L	A	F	L	1.389
68	S	N	D	G	E	H	W	T	V	1.362
138	R	I	F	W	R	Q	E	K	A	1.238
336	C	Q	G	Q	K	H	N	V	L	0.888
36	D	L	L	V	P	T	K	V	T	0.848
237	K	T	I	A	P	L	A	A	T	0.833
117	F	L	H	K	R	M	N	T	N	0.788
362	V	E	N	G	R	P	A	D	L	0.706
172	E	V	G	W	K	Y	Q	A	V	0.685
107	F	C	R	N	K	L	K	Y	L	0.617
35	V	D	L	L	V	P	T	K	V	0.608
81	K	Q	R	K	D	K	V	L	L	0.576
375	Y	C	G	A	L	W	K	A	I	0.533
93	A	V	V	V	S	C	E	G	I	0.447
308	S	P	Y	G	P	R	N	P	L	0.446
158	S	E	A	Y	K	K	V	C	L	0.415
27	Q	K	M	K	Q	D	K	K	V	0.357
175	W	K	Y	Q	A	V	T	A	T	0.350
33	K	K	V	D	L	L	V	P	T	0.342
232	L	G	F	I	F	K	T	I	A	0.318
173	V	G	W	K	Y	Q	A	V	T	0.281
289	T	P	W	T	R	P	S	S	C	0.269
242	L	A	A	T	R	A	T	R	I	0.246
279	A	S	P	A	A	W	L	P	L	0.237
29	M	K	Q	D	K	K	V	D	L	0.207
156	H	A	S	E	A	Y	K	K	V	0.202
133	F	Q	V	P	S	R	I	F	W	0.191
370	L	A	G	S	G	Y	C	G	A	0.176
262	S	S	A	H	R	P	P	A	L	0.139
104	S	G	S	F	C	R	N	K	L	0.139
249	R	I	G	H	P	G	G	R	T	0.133
37	L	L	V	P	T	K	V	T	G	0.127
131	Y	H	F	Q	V	P	S	R	I	0.123
399	R	K	A	E	N	G	P	H	L	0.122
239	I	A	P	L	A	A	T	R	A	0.117
43	V	T	G	I	I	T	Q	G	A	0.117
49	Q	G	A	K	D	F	G	H	V	0.112
227	G	S	P	R	G	L	G	F	I	0.112
299	T	S	S	S	T	Y	D	S	L	0.102
134	Q	V	P	S	R	I	F	W	R	0.096
382	A	I	E	S	L	E	E	G	L	0.092
194	I	H	Y	R	K	N	K	Q	L	0.081
268	P	A	L	S	A	R	A	P	V	0.079
306	S	L	S	P	Y	G	P	R	N	0.075
256	R	T	P	R	A	G	S	S	A	0.069
197	R	K	N	K	Q	L	M	R	L	0.068
400	K	A	E	N	G	P	H	L	L	0.066
270	L	S	A	R	A	P	V	P	A	0.055
111	K	L	K	Y	L	A	F	L	H	0.053
42	K	V	T	G	I	I	T	Q	G	0.052
393	K	Q	K	D	K	E	R	K	A	0.051
295	S	S	C	P	T	S	S	S	T	0.049
10	P	L	R	A	L	H	I	V	V	0.048
200	K	Q	L	M	R	L	Q	K	Q	0.045
48	T	Q	G	A	K	D	F	G	H	0.044
204	R	L	Q	K	Q	A	E	K	N	0.037
291	W	T	R	P	S	S	C	P	T	0.036
240	A	P	L	A	A	T	R	A	T	0.036
277	P	A	A	S	P	A	A	W	L	0.036
328	G	L	K	K	P	A	R	H	C	0.035
261	G	S	S	A	H	R	P	P	A	0.032
337	Q	G	Q	K	H	N	V	L	A	0.032
152	C	P	Q	G	H	A	S	E	A	0.032
325	G	G	G	G	L	K	K	P	A	0.032
274	A	P	V	P	A	A	S	P	A	0.032
266	R	P	P	A	L	S	A	R	A	0.032
236	F	K	T	I	A	P	L	A	A	0.032
302	S	T	Y	D	S	L	S	P	Y	0.031
59	F	V	G	S	Y	K	L	A	Y	0.030
205	L	Q	K	Q	A	E	K	N	M	0.030
64	K	L	A	Y	S	N	D	G	E	0.026
343	V	L	A	R	G	K	P	Q	R	0.025
163	K	V	C	L	S	G	A	P	H	0.023
207	K	Q	A	E	K	N	M	K	K	0.022
16	I	V	V	E	S	I	R	D	H	0.021
102	N	I	S	G	S	F	C	R	N	0.019
116	A	F	L	H	K	R	M	N	T	0.019
368	A	D	L	A	G	S	G	Y	C	0.018
371	A	G	S	G	Y	C	G	A	L	0.018

TABLE VIII

v.1-A2-10mers: 151P3D4

Pos

1

2

3

4

5

6

7

8

9

0

Score

SeqID

83

K

L

T

S

D

Y

L

K

E

V

559.894

Portion of

40

L

L

V

E

A

E

Q

A

K

V

484.777

SEQ ID

343

K

L

Y

G

V

Y

C

F

R

A

322.721

NO: 3;

6

L

L

V

L

I

S

I

C

W

A

106.837

each start

3

S

L

L

L

L

V

L

I

S

I

88.783

position is

193

Q

L

Y

D

A

W

R

G

G

L

36.436

specified,

4

L

L

L

L

V

L

I

S

I

C

29.468

the length

150

V

V

V

A

L

D

L

Q

G

V

23.795

of peptide

269

K

L

T

Y

D

E

A

V

Q

A

17.388

is 10

32

I

Q

A

E

N

G

P

H

L

L

15.096

amino

73

G

I

H

K

I

R

I

K

W

T

12.962

acids, the

48

K

V

F

S

H

R

G

G

N

V

10.245

end

297

K

I

L

G

Y

D

R

C

D

A

8.846

position

201

G

L

D

W

C

N

A

G

W

L

6.110

for each

255

S

N

F

N

G

R

F

Y

Y

L

5.392

peptide is

171

N

L

N

F

H

E

A

Q

Q

A

4.968

the start

326

S

P

T

E

A

A

V

R

F

V

4.710

position

23

T

L

D

H

D

R

A

I

H

I

4.173

plus nine.

285

Q

I

A

K

V

G

Q

I

F

A

3.757

209

W

L

S

D

G

S

V

Q

Y

P

3.556

158

G

V

V

F

P

Y

F

P

R

L

3.551

270

L

T

Y

D

E

A

V

Q

A

C

3.540

105

Y

G

G

Y

Q

G

R

V

F

L

3.528

178

Q

Q

A

C

L

D

Q

D

A

V

3.455

95

F

V

S

M

G

Y

H

K

K

T

2.999

145

L

E

D

D

T

V

V

V

A

L

2.664

9

L

I

S

I

C

W

A

D

H

L

2.447

116

G

G

S

D

S

D

A

S

L

V

1.861

290

G

Q

I

F

A

A

W

K

I

L

1.510

103

K

T

Y

G

G

Y

Q

G

R

V

1.406

223

R

E

P

C

G

G

Q

N

T

V

1.352

130

T

L

E

D

Y

G

R

Y

K

C

1.304

68

T

A

F

G

S

G

I

H

K

I

1.233

144

G

L

E

D

D

T

V

V

V

A

1.229

14

W

A

D

H

L

S

D

N

Y

T

1.047

226

C

G

G

Q

N

T

V

P

G

V

1.044

166

R

L

G

R

Y

N

L

N

F

H

0.943

142

I

E

G

L

E

D

D

T

V

V

0.943

335

V

G

F

P

D

K

K

H

K

L

0.877

289

V

G

Q

I

F

A

A

W

K

I

0.868

113

F

L

K

G

G

S

D

S

D

A

0.800

308

W

L

A

D

G

S

V

R

Y

P

0.711

280

L

N

D

G

A

Q

I

A

K

V

0.710

50

F

S

H

R

G

G

N

V

T

L

0.641

151

V

V

A

L

D

L

Q

G

V

V

0.551

122

A

S

L

V

I

T

D

L

T

L

0.516

141

V

I

E

G

L

E

D

D

T

V

0.510

177

A

Q

Q

A

C

L

D

Q

D

A

0.504

115

K

G

G

S

D

S

D

A

S

L

0.488

5

L

L

L

V

L

I

S

I

C

W

0.469

263

Y

L

I

H

P

T

K

L

T

Y

0.343

70

F

G

S

G

I

H

K

I

R

I

0.313

108

Y

Q

G

R

V

F

L

K

G

G

0.304

97

S

M

G

Y

H

K

K

T

Y

G

0.296

76

K

I

R

I

K

W

T

K

L

T

0.273

188

I

A

S

F

D

Q

L

Y

D

A

0.270

88

Y

L

K

E

V

D

V

F

V

S

0.269

196

D

A

W

R

G

G

L

D

W

C

0.266

8

V

L

I

S

I

C

W

A

D

H

0.215

275

A

V

Q

A

C

L

N

D

G

A

0.213

143

E

G

L

E

D

D

T

V

V

V

0.212

172

L

N

F

H

E

A

Q

Q

A

C

0.204

180

A

C

L

D

Q

D

A

V

I

A

0.202

90

K

E

V

D

V

F

V

S

M

G

0.182

85

T

S

D

Y

L

K

E

V

D

V

0.182

277

Q

A

C

L

N

D

G

A

Q

I

0.145

245

K

S

R

Y

D

V

F

C

F

T

0.135

340

K

K

H

K

L

Y

G

V

Y

C

0.133

206

N

A

G

W

L

S

D

G

S

V

0.126

31

H

I

Q

A

E

N

G

P

H

L

0.100

309

L

A

D

G

S

V

R

Y

P

I

0.099

140

E

V

I

E

G

L

E

D

D

T

0.098

288

K

V

G

Q

I

F

A

A

W

K

0.095

125

V

I

T

D

L

T

L

E

D

Y

0.080

153

A

L

D

L

Q

G

V

V

F

P

0.075

217

Y

P

I

T

K

P

R

E

P

C

0.073

181

C

L

D

Q

D

A

V

I

A

S

0.069

120

S

D

A

S

L

V

I

T

D

L

0.068

163

Y

F

P

R

L

G

R

Y

N

L

0.068

241

W

D

K

D

K

S

R

Y

D

V

0.064

298

I

L

G

Y

D

R

C

D

A

G

0.062

33

Q

A

E

N

G

P

H

L

L

V

0.062

7

L

V

L

I

S

I

C

W

A

D

0.062

279

C

L

N

D

G

A

Q

I

A

K

0.061

173

N

F

H

E

A

Q

Q

A

C

L

0.061

179

Q

A

C

L

D

Q

D

A

V

I

0.059

155

D

L

Q

G

V

V

F

P

Y

F

0.058

1

M

K

S

L

L

L

L

V

L

I

0.057

42

V

E

A

E

Q

A

K

V

F

S

0.056

65

R

D

P

T

A

F

G

S

G

I

0.055

286

I

A

K

V

G

Q

I

F

A

A

0.055

156

L

Q

G

V

V

F

P

Y

F

P

0.054

278

A

C

L

N

D

G

A

Q

I

A

0.049

345

Y

G

V

Y

C

F

R

A

Y

N

0.047

210

L

S

D

G

S

V

Q

Y

P

I

0.046

264

L

I

H

P

T

K

L

T

Y

D

0.044

261

F

Y

Y

L

I

H

P

T

K

L

0.044

283

G

A

Q

I

A

K

V

G

Q

I

0.043

56

N

V

T

L

P

C

K

F

Y

R

0.042

256

N

F

N

G

R

F

Y

Y

L

I

0.041

v.2-A2-10mers: 151P3D4

Pos

1

2

3

4

5

6

7

8

9

0

Score

SeqID

87

V

L

L

G

R

K

A

V

V

V

179.368

Portion of

67

Y

S

N

D

G

E

H

W

T

V

64.221

SEQ ID NO:

37

L

L

V

P

T

K

V

T

G

I

40.792

5; each start

86

K

V

L

L

G

R

K

A

V

V

32.313

position is

234

F

I

F

K

T

I

A

P

L

A

11.626

specified,

30

K

Q

D

K

K

V

D

L

L

V

9.873

the length of

34

K

V

D

L

L

V

P

T

K

V

8.520

peptide is 10

231

G

L

G

F

I

F

K

T

I

A

7.740

amino acids,

200

K

Q

L

M

R

L

Q

K

Q

A

6.523

the end

204

R

L

Q

K

Q

A

E

K

N

M

4.968

position for

269

A

L

S

A

R

A

P

V

P

A

4.968

each peptide

57

V

Q

F

V

G

S

Y

K

L

A

4.752

is the start

2

L

E

H

T

T

K

T

F

P

L

4.096

position plus

9

F

P

L

R

A

L

H

I

V

V

3.168

nine.

164

V

C

L

S

G

A

P

H

E

V

2.856

381

K

A

I

E

S

L

E

E

G

L

2.086

28

K

M

K

Q

D

K

K

V

D

L

1.890

7

K

T

F

P

L

R

A

L

H

I

1.876

373

S

G

Y

C

G

A

L

W

K

A

1.790

48

T

Q

G

A

K

D

F

G

H

V

1.742

94

V

V

V

S

C

E

G

I

N

I

1.552

42

K

V

T

G

I

I

T

Q

G

A

1.521

276

V

P

A

A

S

P

A

A

W

L

1.304

377

G

A

L

W

K

A

I

E

S

L

1.237

212

N

M

K

K

K

I

D

K

Y

T

1.036

238

T

I

A

P

L

A

A

T

R

A

0.683

115

L

A

F

L

H

K

R

M

N

T

0.651

183

T

L

E

E

K

R

K

E

K

A

0.639

12

R

A

L

H

I

V

V

E

S

I

0.604

369

D

L

A

G

S

G

Y

C

G

A

0.559

361

Y

V

E

N

G

R

P

A

D

L

0.550

284

W

L

P

L

R

T

P

W

T

R

0.514

133

F

Q

V

P

S

R

I

F

W

R

0.510

278

A

A

S

P

A

A

W

L

P

L

0.504

336

C

Q

G

Q

K

H

N

V

L

A

0.504

51

A

K

D

F

G

H

V

Q

F

V

0.489

230

R

G

L

G

F

I

F

K

T

I

0.479

173

V

G

W

K

Y

Q

A

V

T

A

0.458

175

W

K

Y

Q

A

V

T

A

T

L

0.437

59

F

V

G

S

Y

K

L

A

Y

S

0.379

353

P

K

S

E

N

N

S

W

Y

V

0.359

92

K

A

V

V

V

S

C

E

G

I

0.249

26

G

Q

K

M

K

Q

D

K

K

V

0.247

103

I

S

G

S

F

C

R

N

K

L

0.237

307

L

S

P

Y

G

P

R

N

P

L

0.237

29

M

K

Q

D

K

K

V

D

L

L

0.233

241

P

L

A

A

T

R

A

T

R

I

0.230

193

E

I

H

Y

R

K

N

K

Q

L

0.220

400

K

A

E

N

G

P

H

L

L

V

0.216

20

S

I

R

D

H

S

G

Q

K

M

0.213

106

S

F

C

R

N

K

L

K

Y

L

0.188

261

G

S

S

A

H

R

P

P

A

L

0.139

270

L

S

A

R

A

P

V

P

A

A

0.127

378

A

L

W

K

A

I

E

S

L

E

0.124

399

R

K

A

E

N

G

P

H

L

L

0.122

88

L

L

G

R

K

A

V

V

V

S

0.119

226

G

G

S

P

R

G

L

G

F

I

0.112

236

F

K

T

I

A

P

L

A

A

T

0.110

38

L

V

P

T

K

V

T

G

I

I

0.083

362

V

E

N

G

R

P

A

D

L

A

0.080

302

S

T

Y

D

S

L

S

P

Y

G

0.075

155

G

H

A

S

E

A

Y

K

K

V

0.072

273

R

A

P

V

P

A

A

S

P

A

0.069

288

R

T

P

W

T

R

P

S

S

C

0.069

263

S

A

H

R

P

P

A

L

S

A

0.069

171

H

E

V

G

W

K

Y

Q

A

V

0.069

117

F

L

H

K

R

M

N

T

N

P

0.069

114

Y

L

A

F

L

H

K

R

M

N

0.069

370

L

A

G

S

G

Y

C

G

A

L

0.066

56

H

V

Q

F

V

G

S

Y

K

L

0.064

109

R

N

K

L

K

Y

L

A

F

L

0.062

201

Q

L

M

R

L

Q

K

Q

A

E

0.055

207

K

Q

A

E

K

N

M

K

K

K

0.050

280

S

P

A

A

W

L

P

L

R

T

0.049

334

R

H

C

Q

G

Q

K

H

N

V

0.048

46

I

I

T

Q

G

A

K

D

F

G

0.047

8

T

F

P

L

R

A

L

H

I

V

0.046

239

I

A

P

L

A

A

T

R

A

T

0.035

233

G

F

I

F

K

T

I

A

P

L

0.034

64

K

L

A

Y

S

N

D

G

E

H

0.034

39

V

P

T

K

V

T

G

I

I

T

0.034

151

C

C

P

Q

G

H

A

S

E

A

0.032

260

A

G

S

S

A

H

R

P

P

A

0.032

324

S

G

G

G

G

L

K

K

P

A

0.032

274

A

P

V

P

A

A

S

P

A

A

0.032

223

S

P

G

G

G

S

P

R

G

L

0.028

35

V

D

L

L

V

P

T

K

V

T

0.027

343

V

L

A

R

G

K

P

Q

R

K

0.025

327

G

G

L

K

K

P

A

R

H

C

0.024

16

I

V

V

E

S

I

R

D

H

S

0.022

283

A

W

L

P

L

R

T

P

W

T

0.021

36

D

L

L

V

P

T

K

V

T

G

0.021

172

E

V

G

W

K

Y

Q

A

V

T

0.020

194

I

H

Y

R

K

N

K

Q

L

M

0.019

134

Q

V

P

S

R

I

F

W

R

Q

0.019

165

C

L

S

G

A

P

H

E

V

G

0.015

216

K

I

D

K

Y

T

E

S

P

G

0.014

99

E

G

I

N

I

S

G

S

F

C

0.013

100

G

I

N

I

S

G

S

F

C

R

0.012

77

Y

Q

D

E

K

Q

R

K

D

K

0.011

TABLE IX
v.1-A3-9mers: 151P3D4
Pos	1	2	3	4	5	6	7	8	9	Score	SeqID
343	K	L	Y	G	V	Y	C	F	R	135.000	Portion of
40	L	L	V	E	A	E	Q	A	K	45.000	SEQ ID
155	D	L	Q	G	V	V	F	P	Y	24.300	NO: 3;
166	R	L	G	R	Y	N	L	N	F	12.000	each start
158	G	V	V	F	P	Y	F	P	R	8.100	position is
130	T	L	E	D	Y	G	R	Y	K	6.000	specified,
103	K	T	Y	G	G	Y	Q	G	R	4.500	the length
159	V	V	F	P	Y	F	P	R	L	4.050	of peptide
4	L	L	L	L	V	L	I	S	I	4.050	is 9 amino
308	W	L	A	D	G	S	V	R	Y	4.000	acids, the
209	W	L	S	D	G	S	V	Q	Y	4.000	end
128	D	L	T	L	E	D	Y	G	R	3.600	position
68	T	A	F	G	S	G	I	H	K	3.000	for each
213	G	S	V	Q	Y	P	I	T	K	2.700	peptide is
153	A	L	D	L	Q	G	V	V	F	2.000	the start
95	F	V	S	M	G	Y	H	K	K	2.000	position
97	S	M	G	Y	H	K	K	T	Y	2.000	plus eight.
123	S	L	V	I	T	D	L	T	L	1.800
57	V	T	L	P	C	K	F	Y	R	1.350
187	V	I	A	S	F	D	Q	L	Y	1.200
264	L	I	H	P	T	K	L	T	Y	1.200
249	D	V	F	C	F	T	S	N	F	0.900
6	L	L	V	L	I	S	I	C	W	0.900
107	G	Y	Q	G	R	V	F	L	K	0.810
215	V	Q	Y	P	I	T	K	P	R	0.675
144	G	L	E	D	D	T	V	V	V	0.600
201	G	L	D	W	C	N	A	G	W	0.600
161	F	P	Y	F	P	R	L	G	R	0.600
312	G	S	V	R	Y	P	I	S	R	0.540
88	Y	L	K	E	V	D	V	F	V	0.450
5	L	L	L	V	L	I	S	I	C	0.450
3	S	L	L	L	L	V	L	I	S	0.360
56	N	V	T	L	P	C	K	F	Y	0.300
39	H	L	L	V	E	A	E	Q	A	0.300
285	Q	I	A	K	V	G	Q	I	F	0.300
332	V	R	F	V	G	F	P	D	K	0.300
126	I	T	D	L	T	L	E	D	Y	0.300
245	K	S	R	Y	D	V	F	C	F	0.270
156	L	Q	G	V	V	F	P	Y	F	0.270
186	A	V	I	A	S	F	D	Q	L	0.270
288	K	V	G	Q	I	F	A	A	W	0.270
290	G	Q	I	F	A	A	W	K	I	0.243
181	C	L	D	Q	D	A	V	I	A	0.200
23	T	L	D	H	D	R	A	I	H	0.200
279	C	L	N	D	G	A	Q	I	A	0.200
298	I	L	G	Y	D	R	C	D	A	0.200
235	V	R	N	Y	G	F	W	D	K	0.180
76	K	I	R	I	K	W	T	K	L	0.180
73	G	I	H	K	I	R	I	K	W	0.180
58	T	L	P	C	K	F	Y	R	D	0.180
228	G	Q	N	T	V	P	G	V	R	0.162
45	E	Q	A	K	V	F	S	H	R	0.162
261	F	Y	Y	L	I	H	P	T	K	0.150
291	Q	I	F	A	A	W	K	I	L	0.150
230	N	T	V	P	G	V	R	N	Y	0.135
8	V	L	I	S	I	C	W	A	D	0.135
75	H	K	I	R	I	K	W	T	K	0.135
333	R	F	V	G	F	P	D	K	K	0.135
129	L	T	L	E	D	Y	G	R	Y	0.135
280	L	N	D	G	A	Q	I	A	K	0.120
293	F	A	A	W	K	I	L	G	Y	0.120
255	S	N	F	N	G	R	F	Y	Y	0.120
83	K	L	T	S	D	Y	L	K	E	0.120
263	Y	L	I	H	P	T	K	L	T	0.113
54	G	G	N	V	T	L	P	C	K	0.090
94	V	F	V	S	M	G	Y	H	K	0.090
82	T	K	L	T	S	D	Y	L	K	0.090
253	F	T	S	N	F	N	G	R	F	0.090
346	G	V	Y	C	F	R	A	Y	N	0.090
335	V	G	F	P	D	K	K	H	K	0.075
289	V	G	Q	I	F	A	A	W	K	0.060
269	K	L	T	Y	D	E	A	V	Q	0.060
232	V	P	G	V	R	N	Y	G	F	0.060
234	G	V	R	N	Y	G	F	W	D	0.054
270	L	T	Y	D	E	A	V	Q	A	0.050
7	L	V	L	I	S	I	C	W	A	0.045
183	D	Q	D	A	V	I	A	S	F	0.041
148	D	T	V	V	V	A	L	D	L	0.041
14	W	A	D	H	L	S	D	N	Y	0.040
62	K	F	Y	R	D	P	T	A	F	0.030
239	G	F	W	D	K	D	K	S	R	0.030
237	N	Y	G	F	W	D	K	D	K	0.030
151	V	V	A	L	D	L	Q	G	V	0.030
326	S	P	T	E	A	A	V	R	F	0.030
81	W	T	K	L	T	S	D	Y	L	0.030
113	F	L	K	G	G	S	D	S	D	0.030
32	I	Q	A	E	N	G	P	H	L	0.027
342	H	K	L	Y	G	V	Y	C	F	0.027
284	A	Q	I	A	K	V	G	Q	I	0.024
84	L	T	S	D	Y	L	K	E	V	0.022
189	A	S	F	D	Q	L	Y	D	A	0.022
2	K	S	L	L	L	L	V	L	I	0.020
325	C	S	P	T	E	A	A	V	R	0.020
9	L	I	S	I	C	W	A	D	H	0.020
337	F	P	D	K	K	H	K	L	Y	0.020
171	N	L	N	F	H	E	A	Q	Q	0.020
41	L	V	E	A	E	Q	A	K	V	0.020
17	H	L	S	D	N	Y	T	L	D	0.020
55	G	N	V	T	L	P	C	K	F	0.018
92	V	D	V	F	V	S	M	G	Y	0.018
v.2-A3-9mers: 151P3D4
Pos	1	2	3	4	5	6	7	8	9	Score	SeqID
389	G	L	G	G	K	Q	K	D	K	45.000	Portion of
34	K	V	D	L	L	V	P	T	K	18.000	SEQ ID
183	T	L	E	E	K	R	K	E	K	15.000	NO: 5; each
385	S	L	E	E	G	L	G	G	K	13.500	start
212	N	M	K	K	K	I	D	K	Y	6.000	position is
207	K	Q	A	E	K	N	M	K	K	5.400	specified,
378	A	L	W	K	A	I	E	S	L	4.500	the length
231	G	L	G	F	I	F	K	T	I	4.050	of peptide
121	R	M	N	T	N	P	S	R	R	4.000	is 9 amino
343	V	L	A	R	G	K	P	Q	R	4.000	acids, the
179	A	V	T	A	T	L	E	E	K	3.000	end
56	H	V	Q	F	V	G	S	Y	K	3.000	position for
13	A	L	H	I	V	V	E	S	I	2.700	each
59	F	V	G	S	Y	K	L	A	Y	2.400	peptide is
338	G	Q	K	H	N	V	L	A	R	2.160	the start
26	G	Q	K	M	K	Q	D	K	K	1.800	position
111	K	L	K	Y	L	A	F	L	H	1.800	plus eight.
134	Q	V	P	S	R	I	F	W	R	1.800
302	S	T	Y	D	S	L	S	P	Y	1.500
75	T	V	Y	Q	D	E	K	Q	R	1.000
1	M	L	E	H	T	T	K	T	F	1.000
105	G	S	F	C	R	N	K	L	K	0.750
20	S	I	R	D	H	S	G	Q	K	0.600
112	L	K	Y	L	A	F	L	H	K	0.600
4	H	T	T	K	T	F	P	L	R	0.600
238	T	I	A	P	L	A	A	T	R	0.600
168	G	A	P	H	E	V	G	W	K	0.540
87	V	L	L	G	R	K	A	V	V	0.450
234	F	I	F	K	T	I	A	P	L	0.450
241	P	L	A	A	T	R	A	T	R	0.400
211	K	N	M	K	K	K	I	D	K	0.360
344	L	A	R	G	K	P	Q	R	K	0.300
165	C	L	S	G	A	P	H	E	V	0.300
57	V	Q	F	V	G	S	Y	K	L	0.270
169	A	P	H	E	V	G	W	K	Y	0.270
7	K	T	F	P	L	R	A	L	H	0.225
88	L	L	G	R	K	A	V	V	V	0.200
373	S	G	Y	C	G	A	L	W	K	0.200
180	V	T	A	T	L	E	E	K	R	0.200
155	G	H	A	S	E	A	Y	K	K	0.180
280	S	P	A	A	W	L	P	L	R	0.180
285	L	P	L	R	T	P	W	T	R	0.180
38	L	V	P	T	K	V	T	G	I	0.180
30	K	Q	D	K	K	V	D	L	L	0.162
208	Q	A	E	K	N	M	K	K	K	0.150
201	Q	L	M	R	L	Q	K	Q	A	0.150
358	N	S	W	Y	V	E	N	G	R	0.150
192	A	E	I	H	Y	R	K	N	K	0.135
95	V	V	S	C	E	G	I	N	I	0.120
284	W	L	P	L	R	T	P	W	T	0.100
46	I	I	T	Q	G	A	K	D	F	0.100
138	R	I	F	W	R	Q	E	K	A	0.100
114	Y	L	A	F	L	H	K	R	M	0.100
181	T	A	T	L	E	E	K	R	K	0.100
137	S	R	I	F	W	R	Q	E	K	0.090
306	S	L	S	P	Y	G	P	R	N	0.090
228	S	P	R	G	L	G	F	I	F	0.090
93	A	V	V	V	S	C	E	G	I	0.090
328	G	L	K	K	P	A	R	H	C	0.090
322	S	P	S	G	G	G	G	L	K	0.090
113	K	Y	L	A	F	L	H	K	R	0.081
308	S	P	Y	G	P	R	N	P	L	0.068
392	G	K	Q	K	D	K	E	R	K	0.060
73	H	W	T	V	Y	Q	D	E	K	0.060
382	A	I	E	S	L	E	E	G	L	0.060
64	K	L	A	Y	S	N	D	G	E	0.060
5	T	T	K	T	F	P	L	R	A	0.060
163	K	V	C	L	S	G	A	P	H	0.060
125	N	P	S	R	R	P	Y	H	F	0.060
100	G	I	N	I	S	G	S	F	C	0.060
81	K	Q	R	K	D	K	V	L	L	0.054
189	K	E	K	A	E	I	H	Y	R	0.054
237	K	T	I	A	P	L	A	A	T	0.051
55	G	H	V	Q	F	V	G	S	Y	0.049
37	L	L	V	P	T	K	V	T	G	0.045
86	K	V	L	L	G	R	K	A	V	0.045
190	E	K	A	E	I	H	Y	R	K	0.041
199	N	K	Q	L	M	R	L	Q	K	0.040
296	S	C	P	T	S	S	S	T	Y	0.040
10	P	L	R	A	L	H	I	V	V	0.040
101	I	N	I	S	G	S	F	C	R	0.036
36	D	L	L	V	P	T	K	V	T	0.034
323	P	S	G	G	G	G	L	K	K	0.030
103	I	S	G	S	F	C	R	N	K	0.030
203	M	R	L	Q	K	Q	A	E	K	0.030
117	F	L	H	K	R	M	N	T	N	0.030
28	K	M	K	Q	D	K	K	V	D	0.030
123	N	T	N	P	S	R	R	P	Y	0.030
369	D	L	A	G	S	G	Y	C	G	0.027
133	F	Q	V	P	S	R	I	F	W	0.027
84	K	D	K	V	L	L	G	R	K	0.027
42	K	V	T	G	I	I	T	Q	G	0.020
204	R	L	Q	K	Q	A	E	K	N	0.020
25	S	G	Q	K	M	K	Q	D	K	0.020
206	Q	K	Q	A	E	K	N	M	K	0.020
244	A	T	R	A	T	R	I	G	H	0.020
202	L	M	R	L	Q	K	Q	A	E	0.020
154	Q	G	H	A	S	E	A	Y	K	0.020
269	A	L	S	A	R	A	P	V	P	0.020
76	V	Y	Q	D	E	K	Q	R	K	0.020

TABLE X

v.1-A3-10mers: 151P3D4

Pos

1

2

3

4

5

6

7

8

9

0

Score

SeqID

234

G

V

R

N

Y

G

F

W

D

K

54.000

Portion

343

K

L

Y

G

V

Y

C

F

R

A

40.500

of SEQ

279

C

L

N

D

G

A

Q

I

A

K

40.000

ID NO:

39

H

L

L

V

E

A

E

Q

A

K

30.000

3; each

288

K

V

G

Q

I

F

A

A

W

K

18.000

start

263

Y

L

I

H

P

T

K

L

T

Y

12.000

position

93

D

V

F

V

S

M

G

Y

H

K

9.000

is

331

A

V

R

F

V

G

F

P

D

K

6.000

specified,

155

D

L

Q

G

V

V

F

P

Y

F

4.050

the

3

S

L

L

L

L

V

L

I

S

I

4.050

length of

81

W

T

K

L

T

S

D

Y

L

K

3.000

peptide is

106

G

G

Y

Q

G

R

V

F

L

K

2.700

10 amino

193

Q

L

Y

D

A

W

R

G

G

L

2.700

acids, the

158

G

V

V

F

P

Y

F

P

R

L

2.430

end

186

A

V

I

A

S

F

D

Q

L

Y

1.800

position

144

G

L

E

D

D

T

V

V

V

A

1.800

for each

83

K

L

T

S

D

Y

L

K

E

V

1.350

peptide is

23

T

L

D

H

D

R

A

I

H

I

1.200

the start

17

H

L

S

D

N

Y

T

L

D

H

1.200

position

56

N

V

T

L

P

C

K

F

Y

R

1.200

plus nine.

334

F

V

G

F

P

D

K

K

H

K

1.000

5

L

L

L

V

L

I

S

I

C

W

0.900

231

T

V

P

G

V

R

N

Y

G

F

0.900

129

L

T

L

E

D

Y

G

R

Y

K

0.675

125

V

I

T

D

L

T

L

E

D

Y

0.600

130

T

L

E

D

Y

G

R

Y

K

C

0.600

294

A

A

W

K

I

L

G

Y

D

R

0.600

269

K

L

T

Y

D

E

A

V

Q

A

0.600

251

F

C

F

T

S

N

F

N

G

R

0.600

201

G

L

D

W

C

N

A

G

W

L

0.540

88

Y

L

K

E

V

D

V

F

V

S

0.540

4

L

L

L

L

V

L

I

S

I

C

0.450

236

R

N

Y

G

F

W

D

K

D

K

0.450

40

L

L

V

E

A

E

Q

A

K

V

0.450

6

L

L

V

L

I

S

I

C

W

A

0.450

91

E

V

D

V

F

V

S

M

G

Y

0.360

128

D

L

T

L

E

D

Y

G

R

Y

0.360

113

F

L

K

G

G

S

D

S

D

A

0.300

214

S

V

Q

Y

P

I

T

K

P

R

0.300

8

V

L

I

S

I

C

W

A

D

H

0.300

332

V

R

F

V

G

F

P

D

K

K

0.300

166

R

L

G

R

Y

N

L

N

F

H

0.300

181

C

L

D

Q

D

A

V

I

A

S

0.240

103

K

T

Y

G

G

Y

Q

G

R

V

0.203

171

N

L

N

F

H

E

A

Q

Q

A

0.200

67

P

T

A

F

G

S

G

I

H

K

0.200

9

L

I

S

I

C

W

A

D

H

L

0.180

260

R

F

Y

Y

L

I

H

P

T

K

0.150

270

L

T

Y

D

E

A

V

Q

A

C

0.150

284

A

Q

I

A

K

V

G

Q

I

F

0.135

297

K

I

L

G

Y

D

R

C

D

A

0.135

41

L

V

E

A

E

Q

A

K

V

F

0.100

74

I

H

K

I

R

I

K

W

T

K

0.090

161

F

P

Y

F

P

R

L

G

R

Y

0.090

48

K

V

F

S

H

R

G

G

N

V

0.090

154

L

D

L

Q

G

V

V

F

P

Y

0.081

68

T

A

F

G

S

G

I

H

K

I

0.068

239

G

F

W

D

K

D

K

S

R

Y

0.060

324

R

C

S

P

T

E

A

A

V

R

0.060

313

S

V

R

Y

P

I

S

R

P

R

0.060

153

A

L

D

L

Q

G

V

V

F

P

0.060

291

Q

I

F

A

A

W

K

I

L

G

0.060

254

T

S

N

F

N

G

R

F

Y

Y

0.060

209

W

L

S

D

G

S

V

Q

Y

P

0.060

31

H

I

Q

A

E

N

G

P

H

L

0.060

341

K

H

K

L

Y

G

V

Y

C

F

0.054

255

S

N

F

N

G

R

F

Y

Y

L

0.054

44

A

E

Q

A

K

V

F

S

H

R

0.054

123

S

L

V

I

T

D

L

T

L

E

0.045

71

G

S

G

I

H

K

I

R

I

K

0.045

150

V

V

V

A

L

D

L

Q

G

V

0.045

76

K

I

R

I

K

W

T

K

L

T

0.045

309

L

A

D

G

S

V

R

Y

P

I

0.041

290

G

Q

I

F

A

A

W

K

I

L

0.041

285

Q

I

A

K

V

G

Q

I

F

A

0.040

212

D

G

S

V

Q

Y

P

I

T

K

0.036

53

R

G

G

N

V

T

L

P

C

K

0.030

94

V

F

V

S

M

G

Y

H

K

K

0.030

314

V

R

Y

P

I

S

R

P

R

R

0.030

141

V

I

E

G

L

E

D

D

T

V

0.030

152

V

A

L

D

L

Q

G

V

V

F

0.030

86

S

D

Y

L

K

E

V

D

V

F

0.030

55

G

N

V

T

L

P

C

K

F

Y

0.027

157

Q

G

V

V

F

P

Y

F

P

R

0.027

32

I

Q

A

E

N

G

P

H

L

L

0.027

73

G

I

H

K

I

R

I

K

W

T

0.022

96

V

S

M

G

Y

H

K

K

T

Y

0.022

57

V

T

L

P

C

K

F

Y

R

D

0.020

210

L

S

D

G

S

V

Q

Y

P

I

0.020

298

I

L

G

Y

D

R

C

D

A

G

0.020

111

R

V

F

L

K

G

G

S

D

S

0.020

97

S

M

G

Y

H

K

K

T

Y

G

0.020

275

A

V

Q

A

C

L

N

D

G

A

0.020

253

F

T

S

N

F

N

G

R

F

Y

0.020

306

A

G

W

L

A

D

G

S

V

R

0.020

79

I

K

W

T

K

L

T

S

D

Y

0.020

208

G

W

L

S

D

G

S

V

Q

Y

0.018

307

G

W

L

A

D

G

S

V

R

Y

0.018

127

T

D

L

T

L

E

D

Y

G

R

0.018

328

T

E

A

A

V

R

F

V

G

F

0.018

v.2-A3-10mers: 151P3D4

Pos

1

2

3

4

5

6

7

8

9

0

Score

SeqID

111

K

L

K

Y

L

A

F

L

H

K

360.000

Portion of

202

L

M

R

L

Q

K

Q

A

E

K

20.000

SEQ ID

343

V

L

A

R

G

K

P

Q

R

K

20.000

NO: 5;

284

W

L

P

L

R

T

P

W

T

R

12.000

each start

75

T

V

Y

Q

D

E

K

Q

R

K

10.000

position is

13

A

L

H

I

V

V

E

S

I

R

6.000

specified,

37

L

L

V

P

T

K

V

T

G

I

4.050

the length

100

G

I

N

I

S

G

S

F

C

R

3.600

of peptide

207

K

Q

A

E

K

N

M

K

K

K

2.025

is 10

228

S

P

R

G

L

G

F

I

F

K

1.800

amino

28

K

M

K

Q

D

K

K

V

D

L

1.800

acids, the

231

G

L

G

F

I

F

K

T

I

A

1.800

end

7

K

T

F

P

L

R

A

L

H

I

1.350

position

133

F

Q

V

P

S

R

I

F

W

R

1.215

for each

182

A

T

L

E

E

K

R

K

E

K

1.125

peptide is

237

K

T

I

A

P

L

A

A

T

R

0.900

the start

191

K

A

E

I

H

Y

R

K

N

K

0.900

position

102

N

I

S

G

S

F

C

R

N

K

0.900

plus nine.

189

K

E

K

A

E

I

H

Y

R

K

0.810

372

G

S

G

Y

C

G

A

L

W

K

0.600

322

S

P

S

G

G

G

G

L

K

K

0.600

342

N

V

L

A

R

G

K

P

Q

R

0.600

105

G

S

F

C

R

N

K

L

K

Y

0.600

129

R

P

Y

H

F

Q

V

P

S

R

0.600

205

L

Q

K

Q

A

E

K

N

M

K

0.600

168

G

A

P

H

E

V

G

W

K

Y

0.540

180

V

T

A

T

L

E

E

K

R

K

0.500

178

Q

A

V

T

A

T

L

E

E

K

0.450

87

V

L

L

G

R

K

A

V

V

V

0.450

45

G

I

I

T

Q

G

A

K

D

F

0.450

77

Y

Q

D

E

K

Q

R

K

D

K

0.450

179

A

V

T

A

T

L

E

E

K

R

0.400

183

T

L

E

E

K

R

K

E

K

A

0.300

43

V

T

G

I

I

T

Q

G

A

K

0.300

33

K

K

V

D

L

L

V

P

T

K

0.270

198

K

N

K

Q

L

M

R

L

Q

K

0.240

269

A

L

S

A

R

A

P

V

P

A

0.200

64

K

L

A

Y

S

N

D

G

E

H

0.180

94

V

V

V

S

C

E

G

I

N

I

0.180

56

H

V

Q

F

V

G

S

Y

K

L

0.180

331

K

P

A

R

H

C

Q

G

Q

K

0.180

74

W

T

V

Y

Q

D

E

K

Q

R

0.150

234

F

I

F

K

T

I

A

P

L

A

0.150

378

A

L

W

K

A

I

E

S

L

E

0.150

55

G

H

V

Q

F

V

G

S

Y

K

0.135

42

K

V

T

G

I

I

T

Q

G

A

0.135

352

K

P

K

S

E

N

N

S

W

Y

0.120

311

G

P

R

N

P

L

P

N

P

R

0.120

88

L

L

G

R

K

A

V

V

V

S

0.120

24

H

S

G

Q

K

M

K

Q

D

K

0.100

204

R

L

Q

K

Q

A

E

K

N

M

0.100

279

A

S

P

A

A

W

L

P

L

R

0.090

34

K

V

D

L

L

V

P

T

K

V

0.090

369

D

L

A

G

S

G

Y

C

G

A

0.090

112

L

K

Y

L

A

F

L

H

K

R

0.090

86

K

V

L

L

G

R

K

A

V

V

0.090

389

G

L

G

G

K

Q

K

D

K

E

0.090

227

G

S

P

R

G

L

G

F

I

F

0.090

72

E

H

W

T

V

Y

Q

D

E

K

0.090

212

N

M

K

K

K

I

D

K

Y

T

0.075

391

G

G

K

Q

K

D

K

E

R

K

0.060

154

Q

G

H

A

S

E

A

Y

K

K

0.060

153

P

Q

G

H

A

S

E

A

Y

K

0.060

50

G

A

K

D

F

G

H

V

Q

F

0.060

152

C

P

Q

G

H

A

S

E

A

Y

0.060

240

A

P

L

A

A

T

R

A

T

R

0.060

361

Y

V

E

N

G

R

P

A

D

L

0.060

241

P

L

A

A

T

R

A

T

R

I

0.060

247

A

T

R

I

G

H

P

G

G

R

0.060

328

G

L

K

K

P

A

R

H

C

Q

0.060

4

H

T

T

K

T

F

P

L

R

A

0.060

211

K

N

M

K

K

K

I

D

K

Y

0.054

58

Q

F

V

G

S

Y

K

L

A

Y

0.054

30

K

Q

D

K

K

V

D

L

L

V

0.054

47

I

T

Q

G

A

K

D

F

G

H

0.045

165

C

L

S

G

A

P

H

E

V

G

0.045

386

L

E

E

G

L

G

G

K

Q

K

0.045

381

K

A

I

E

S

L

E

E

G

L

0.041

377

G

A

L

W

K

A

I

E

S

L

0.041

12

R

A

L

H

I

V

V

E

S

I

0.041

257

T

P

R

A

G

S

S

A

H

R

0.040

366

R

P

A

D

L

A

G

S

G

Y

0.040

206

Q

K

Q

A

E

K

N

M

K

K

0.040

187

K

R

K

E

K

A

E

I

H

Y

0.036

384

E

S

L

E

E

G

L

G

G

K

0.030

136

P

S

R

I

F

W

R

Q

E

K

0.030

295

S

S

C

P

T

S

S

S

T

Y

0.030

301

S

S

T

Y

D

S

L

S

P

Y

0.030

201

Q

L

M

R

L

Q

K

Q

A

E

0.030

238

T

I

A

P

L

A

A

T

R

A

0.030

321

H

S

P

S

G

G

G

G

L

K

0.030

38

L

V

P

T

K

V

T

G

I

I

0.027

167

S

G

A

P

H

E

V

G

W

K

0.027

92

K

A

V

V

V

S

C

E

G

I

0.027

134

Q

V

P

S

R

I

F

W

R

Q

0.027

337

Q

G

Q

K

H

N

V

L

A

R

0.024

1

M

L

E

H

T

T

K

T

F

P

0.020

117

F

L

H

K

R

M

N

T

N

P

0.020

20

S

I

R

D

H

S

G

Q

K

M

0.020

25

S

G

Q

K

M

K

Q

D

K

K

0.020

TABLE XI
v.1-A11-9mers: 151P3D4
Pos	1	2	3	4	5	6	7	8	9	Score	SeqID
158	G	V	V	F	P	Y	F	P	R	5.400	Portion of
107	G	Y	Q	G	R	V	F	L	K	3.600	SEQ ID
95	F	V	S	M	G	Y	H	K	K	2.000	NO: 3; each
103	K	T	Y	G	G	Y	Q	G	R	1.200	start
57	V	T	L	P	C	K	F	Y	R	0.900	position is
333	R	F	V	G	F	P	D	K	K	0.900	specified,
68	T	A	F	G	S	G	I	H	K	0.800	the length
261	F	Y	Y	L	I	H	P	T	K	0.800	of peptide
94	V	F	V	S	M	G	Y	H	K	0.600	is 9 amino
40	L	L	V	E	A	E	Q	A	K	0.600	acids, the
343	K	L	Y	G	V	Y	C	F	R	0.480	end
228	G	Q	N	T	V	P	G	V	R	0.360	position for
315	R	Y	P	I	S	R	P	R	R	0.240	each
237	N	Y	G	F	W	D	K	D	K	0.200	peptide is
213	G	S	V	Q	Y	P	I	T	K	0.180	the start
161	F	P	Y	F	P	R	L	G	R	0.160	position
239	G	F	W	D	K	D	K	S	R	0.120	plus eight.
215	V	Q	Y	P	I	T	K	P	R	0.120
280	L	N	D	G	A	Q	I	A	K	0.080
75	H	K	I	R	I	K	W	T	K	0.060
82	T	K	L	T	S	D	Y	L	K	0.060
54	G	G	N	V	T	L	P	C	K	0.060
288	K	V	G	Q	I	F	A	A	W	0.060
290	G	Q	I	F	A	A	W	K	I	0.054
128	D	L	T	L	E	D	Y	G	R	0.048
130	T	L	E	D	Y	G	R	Y	K	0.040
252	C	F	T	S	N	F	N	G	R	0.040
332	V	R	F	V	G	F	P	D	K	0.040
235	V	R	N	Y	G	F	W	D	K	0.040
159	V	V	F	P	Y	F	P	R	L	0.040
312	G	S	V	R	Y	P	I	S	R	0.036
45	E	Q	A	K	V	F	S	H	R	0.036
186	A	V	I	A	S	F	D	Q	L	0.030
7	L	V	L	I	S	I	C	W	A	0.030
73	G	I	H	K	I	R	I	K	W	0.024
166	R	L	G	R	Y	N	L	N	F	0.024
270	L	T	Y	D	E	A	V	Q	A	0.020
335	V	G	F	P	D	K	K	H	K	0.020
151	V	V	A	L	D	L	Q	G	V	0.020
289	V	G	Q	I	F	A	A	W	K	0.020
41	L	V	E	A	E	Q	A	K	V	0.020
307	G	W	L	A	D	G	S	V	R	0.018
234	G	V	R	N	Y	G	F	W	D	0.018
129	L	T	L	E	D	Y	G	R	Y	0.015
201	G	L	D	W	C	N	A	G	W	0.012
346	G	V	Y	C	F	R	A	Y	N	0.012
169	R	Y	N	L	N	F	H	E	A	0.012
4	L	L	L	L	V	L	I	S	I	0.012
249	D	V	F	C	F	T	S	N	F	0.012
6	L	L	V	L	I	S	I	C	W	0.012
144	G	L	E	D	D	T	V	V	V	0.012
300	G	Y	D	R	C	D	A	G	W	0.012
76	K	I	R	I	K	W	T	K	L	0.012
48	K	V	F	S	H	R	G	G	N	0.012
62	K	F	Y	R	D	P	T	A	F	0.012
111	R	V	F	L	K	G	G	S	D	0.012
123	S	L	V	I	T	D	L	T	L	0.012
344	L	Y	G	V	Y	C	F	R	A	0.012
93	D	V	F	V	S	M	G	Y	H	0.012
253	F	T	S	N	F	N	G	R	F	0.010
56	N	V	T	L	P	C	K	F	Y	0.010
334	F	V	G	F	P	D	K	K	H	0.010
126	I	T	D	L	T	L	E	D	Y	0.010
81	W	T	K	L	T	S	D	Y	L	0.010
148	D	T	V	V	V	A	L	D	L	0.009
284	A	Q	I	A	K	V	G	Q	I	0.009
264	L	I	H	P	T	K	L	T	Y	0.008
295	A	W	K	I	L	G	Y	D	R	0.008
316	Y	P	I	S	R	P	R	R	R	0.006
178	Q	Q	A	C	L	D	Q	D	A	0.006
324	R	C	S	P	T	E	A	A	V	0.006
150	V	V	V	A	L	D	L	Q	G	0.006
276	V	Q	A	C	L	N	D	G	A	0.006
32	I	Q	A	E	N	G	P	H	L	0.006
331	A	V	R	F	V	G	F	P	D	0.006
262	Y	Y	L	I	H	P	T	K	L	0.006
39	H	L	L	V	E	A	E	Q	A	0.006
156	L	Q	G	V	V	F	P	Y	F	0.006
336	G	F	P	D	K	K	H	K	L	0.006
84	L	T	S	D	Y	L	K	E	V	0.005
20	D	N	Y	T	L	D	H	D	R	0.005
9	L	I	S	I	C	W	A	D	H	0.004
104	T	Y	G	G	Y	Q	G	R	V	0.004
325	C	S	P	T	E	A	A	V	R	0.004
293	F	A	A	W	K	I	L	G	Y	0.004
291	Q	I	F	A	A	W	K	I	L	0.004
256	N	F	N	G	R	F	Y	Y	L	0.004
164	F	P	R	L	G	R	Y	N	L	0.004
232	V	P	G	V	R	N	Y	G	F	0.004
298	I	L	G	Y	D	R	C	D	A	0.004
209	W	L	S	D	G	S	V	Q	Y	0.004
153	A	L	D	L	Q	G	V	V	F	0.004
279	C	L	N	D	G	A	Q	I	A	0.004
286	I	A	K	V	G	Q	I	F	A	0.004
194	L	Y	D	A	W	R	G	G	L	0.004
191	F	D	Q	L	Y	D	A	W	R	0.004
181	C	L	D	Q	D	A	V	I	A	0.004
31	H	I	Q	A	E	N	G	P	H	0.004
308	W	L	A	D	G	S	V	R	Y	0.004
88	Y	L	K	E	V	D	V	F	V	0.004
v.2-A11-9mers: 151P3D4
Pos	1	2	3	4	5	6	7	8	9	Score	SeqID
34	K	V	D	L	L	V	P	T	K	6.000	Portion of
207	K	Q	A	E	K	N	M	K	K	3.600	SEQ ID
56	H	V	Q	F	V	G	S	Y	K	2.000	NO: 5;
179	A	V	T	A	T	L	E	E	K	2.000	each start
26	G	Q	K	M	K	Q	D	K	K	1.800	position is
134	Q	V	P	S	R	I	F	W	R	1.200	specified,
338	G	Q	K	H	N	V	L	A	R	0.720	the length
389	G	L	G	G	K	Q	K	D	K	0.600	of peptide
168	G	A	P	H	E	V	G	W	K	0.600	is 9 amino
211	K	N	M	K	K	K	I	D	K	0.480	acids, the
75	T	V	Y	Q	D	E	K	Q	R	0.400	end
385	S	L	E	E	G	L	G	G	K	0.400	position
76	V	Y	Q	D	E	K	Q	R	K	0.400	for each
20	S	I	R	D	H	S	G	Q	K	0.400	peptide is
113	K	Y	L	A	F	L	H	K	R	0.360	the start
121	R	M	N	T	N	P	S	R	R	0.240	position
322	S	P	S	G	G	G	G	L	K	0.200	plus eight.
344	L	A	R	G	K	P	Q	R	K	0.200
4	H	T	T	K	T	F	P	L	R	0.200
183	T	L	E	E	K	R	K	E	K	0.200
180	V	T	A	T	L	E	E	K	R	0.200
155	G	H	A	S	E	A	Y	K	K	0.120
285	L	P	L	R	T	P	W	T	R	0.120
208	Q	A	E	K	N	M	K	K	K	0.100
181	T	A	T	L	E	E	K	R	K	0.100
238	T	I	A	P	L	A	A	T	R	0.080
343	V	L	A	R	G	K	P	Q	R	0.080
373	S	G	Y	C	G	A	L	W	K	0.080
112	L	K	Y	L	A	F	L	H	K	0.080
84	K	D	K	V	L	L	G	R	K	0.060
105	G	S	F	C	R	N	K	L	K	0.060
392	G	K	Q	K	D	K	E	R	K	0.060
7	K	T	F	P	L	R	A	L	H	0.060
163	K	V	C	L	S	G	A	P	H	0.060
86	K	V	L	L	G	R	K	A	V	0.045
192	A	E	I	H	Y	R	K	N	K	0.045
280	S	P	A	A	W	L	P	L	R	0.040
95	V	V	S	C	E	G	I	N	I	0.040
199	N	K	Q	L	M	R	L	Q	K	0.040
59	F	V	G	S	Y	K	L	A	Y	0.040
101	I	N	I	S	G	S	F	C	R	0.036
111	K	L	K	Y	L	A	F	L	H	0.036
189	K	E	K	A	E	I	H	Y	R	0.036
22	R	D	H	S	G	Q	K	M	K	0.030
346	R	G	K	P	Q	R	K	P	K	0.030
203	M	R	L	Q	K	Q	A	E	K	0.030
44	T	G	I	I	T	Q	G	A	K	0.030
137	S	R	I	F	W	R	Q	E	K	0.030
256	R	T	P	R	A	G	S	S	A	0.030
93	A	V	V	V	S	C	E	G	I	0.030
83	R	K	D	K	V	L	L	G	R	0.024
120	K	R	M	N	T	N	P	S	R	0.024
138	R	I	F	W	R	Q	E	K	A	0.024
57	V	Q	F	V	G	S	Y	K	L	0.024
374	G	Y	C	G	A	L	W	K	A	0.024
5	T	T	K	T	F	P	L	R	A	0.020
25	S	G	Q	K	M	K	Q	D	K	0.020
332	P	A	R	H	C	Q	G	Q	K	0.020
38	L	V	P	T	K	V	T	G	I	0.020
206	Q	K	Q	A	E	K	N	M	K	0.020
244	A	T	R	A	T	R	I	G	H	0.020
302	S	T	Y	D	S	L	S	P	Y	0.020
73	H	W	T	V	Y	Q	D	E	K	0.020
154	Q	G	H	A	S	E	A	Y	K	0.020
81	K	Q	R	K	D	K	V	L	L	0.018
133	F	Q	V	P	S	R	I	F	W	0.018
48	T	Q	G	A	K	D	F	G	H	0.018
30	K	Q	D	K	K	V	D	L	L	0.018
326	G	G	G	L	K	K	P	A	R	0.012
251	G	H	P	G	G	R	T	P	R	0.012
176	K	Y	Q	A	V	T	A	T	L	0.012
190	E	K	A	E	I	H	Y	R	K	0.012
78	Q	D	E	K	Q	R	K	D	K	0.010
43	V	T	G	I	I	T	Q	G	A	0.010
387	E	E	G	L	G	G	K	Q	K	0.009
241	P	L	A	A	T	R	A	T	R	0.008
130	P	Y	H	F	Q	V	P	S	R	0.008
378	A	L	W	K	A	I	E	S	L	0.008
358	N	S	W	Y	V	E	N	G	R	0.008
196	Y	R	K	N	K	Q	L	M	R	0.008
234	F	I	F	K	T	I	A	P	L	0.008
14	L	H	I	V	V	E	S	I	R	0.006
391	G	G	K	Q	K	D	K	E	R	0.006
340	K	H	N	V	L	A	R	G	K	0.006
248	T	R	I	G	H	P	G	G	R	0.006
87	V	L	L	G	R	K	A	V	V	0.006
172	E	V	G	W	K	Y	Q	A	V	0.006
400	K	A	E	N	G	P	H	L	L	0.006
352	K	P	K	S	E	N	N	S	W	0.006
42	K	V	T	G	I	I	T	Q	G	0.006
228	S	P	R	G	L	G	F	I	F	0.006
231	G	L	G	F	I	F	K	T	I	0.006
336	C	Q	G	Q	K	H	N	V	L	0.006
266	R	P	P	A	L	S	A	R	A	0.006
237	K	T	I	A	P	L	A	A	T	0.005
323	P	S	G	G	G	G	L	K	K	0.004
229	P	R	G	L	G	F	I	F	K	0.004
169	A	P	H	E	V	G	W	K	Y	0.004
308	S	P	Y	G	P	R	N	P	L	0.004
106	S	F	C	R	N	K	L	K	Y	0.004

TABLE XII

v.1-A11-10mers: 151P3D4

Pos

1

2

3

4

5

6

7

8

9

0

Score

SeqID

234

G

V

R

N

Y

G

F

W

D

K

12.000

Portion of

288

K

V

G

Q

I

F

A

A

W

K

6.000

SEQ ID

93

D

V

F

V

S

M

G

Y

H

K

2.400

NO: 3; each

81

W

T

K

L

T

S

D

Y

L

K

2.000

start

331

A

V

R

F

V

G

F

P

D

K

2.000

position is

260

R

F

Y

Y

L

I

H

P

T

K

1.200

specified,

56

N

V

T

L

P

C

K

F

Y

R

1.200

the length

334

F

V

G

F

P

D

K

K

H

K

1.000

of peptide

279

C

L

N

D

G

A

Q

I

A

K

0.800

is 10 amino

39

H

L

L

V

E

A

E

Q

A

K

0.600

acids, the

106

G

G

Y

Q

G

R

V

F

L

K

0.360

end

94

V

F

V

S

M

G

Y

H

K

K

0.300

position for

67

P

T

A

F

G

S

G

I

H

K

0.200

each

214

S

V

Q

Y

P

I

T

K

P

R

0.200

peptide is

294

A

A

W

K

I

L

G

Y

D

R

0.160

the start

129

L

T

L

E

D

Y

G

R

Y

K

0.150

position

236

R

N

Y

G

F

W

D

K

D

K

0.120

plus nine.

324

R

C

S

P

T

E

A

A

V

R

0.120

48

K

V

F

S

H

R

G

G

N

V

0.120

158

G

V

V

F

P

Y

F

P

R

L

0.090

160

V

F

P

Y

F

P

R

L

G

R

0.080

251

F

C

F

T

S

N

F

N

G

R

0.080

343

K

L

Y

G

V

Y

C

F

R

A

0.072

53

R

G

G

N

V

T

L

P

C

K

0.060

103

K

T

Y

G

G

Y

Q

G

R

V

0.060

74

I

H

K

I

R

I

K

W

T

K

0.040

190

S

F

D

Q

L

Y

D

A

W

R

0.040

231

T

V

P

G

V

R

N

Y

G

F

0.040

332

V

R

F

V

G

F

P

D

K

K

0.040

313

S

V

R

Y

P

I

S

R

P

R

0.040

186

A

V

I

A

S

F

D

Q

L

Y

0.030

150

V

V

V

A

L

D

L

Q

G

V

0.030

315

R

Y

P

I

S

R

P

R

R

R

0.024

275

A

V

Q

A

C

L

N

D

G

A

0.020

69

A

F

G

S

G

I

H

K

I

R

0.020

151

V

V

A

L

D

L

Q

G

V

V

0.020

157

Q

G

V

V

F

P

Y

F

P

R

0.018

297

K

I

L

G

Y

D

R

C

D

A

0.018

22

Y

T

L

D

H

D

R

A

I

H

0.015

290

G

Q

I

F

A

A

W

K

I

L

0.013

102

K

K

T

Y

G

G

Y

Q

G

R

0.012

127

T

D

L

T

L

E

D

Y

G

R

0.012

227

G

G

Q

N

T

V

P

G

V

R

0.012

111

R

V

F

L

K

G

G

S

D

S

0.012

136

R

Y

K

C

E

V

I

E

G

L

0.012

300

G

Y

D

R

C

D

A

G

W

L

0.012

44

A

E

Q

A

K

V

F

S

H

R

0.012

91

E

V

D

V

F

V

S

M

G

Y

0.012

239

G

F

W

D

K

D

K

S

R

Y

0.012

263

Y

L

I

H

P

T

K

L

T

Y

0.012

144

G

L

E

D

D

T

V

V

V

A

0.012

212

D

G

S

V

Q

Y

P

I

T

K

0.012

166

R

L

G

R

Y

N

L

N

F

H

0.012

5

L

L

L

V

L

I

S

I

C

W

0.012

3

S

L

L

L

L

V

L

I

S

I

0.012

201

G

L

D

W

C

N

A

G

W

L

0.012

99

G

Y

H

K

K

T

Y

G

G

Y

0.012

269

K

L

T

Y

D

E

A

V

Q

A

0.012

41

L

V

E

A

E

Q

A

K

V

F

0.010

284

A

Q

I

A

K

V

G

Q

I

F

0.009

306

A

G

W

L

A

D

G

S

V

R

0.008

314

V

R

Y

P

I

S

R

P

R

R

0.008

23

T

L

D

H

D

R

A

I

H

I

0.008

17

H

L

S

D

N

Y

T

L

D

H

0.008

261

F

Y

Y

L

I

H

P

T

K

L

0.008

285

Q

I

A

K

V

G

Q

I

F

A

0.008

193

Q

L

Y

D

A

W

R

G

G

L

0.008

71

G

S

G

I

H

K

I

R

I

K

0.006

342

H

K

L

Y

G

V

Y

C

F

R

0.006

7

L

V

L

I

S

I

C

W

A

D

0.006

124

L

V

I

T

D

L

T

L

E

D

0.006

286

I

A

K

V

G

Q

I

F

A

A

0.006

6

L

L

V

L

I

S

I

C

W

A

0.006

149

T

V

V

V

A

L

D

L

Q

G

0.006

178

Q

Q

A

C

L

D

Q

D

A

V

0.006

32

I

Q

A

E

N

G

P

H

L

L

0.006

8

V

L

I

S

I

C

W

A

D

H

0.006

40

L

L

V

E

A

E

Q

A

K

V

0.006

283

G

A

Q

I

A

K

V

G

Q

I

0.006

177

A

Q

Q

A

C

L

D

Q

D

A

0.006

83

K

L

T

S

D

Y

L

K

E

V

0.006

333

R

F

V

G

F

P

D

K

K

H

0.005

19

S

D

N

Y

T

L

D

H

D

R

0.004

9

L

I

S

I

C

W

A

D

H

L

0.004

188

I

A

S

F

D

Q

L

Y

D

A

0.004

163

Y

F

P

R

L

G

R

Y

N

L

0.004

256

N

F

N

G

R

F

Y

Y

L

I

0.004

171

N

L

N

F

H

E

A

Q

Q

A

0.004

271

T

Y

D

E

A

V

Q

A

C

L

0.004

125

V

I

T

D

L

T

L

E

D

Y

0.004

33

Q

A

E

N

G

P

H

L

L

V

0.004

31

H

I

Q

A

E

N

G

P

H

L

0.004

292

I

F

A

A

W

K

I

L

G

Y

0.004

113

F

L

K

G

G

S

D

S

D

A

0.004

68

T

A

F

G

S

G

I

H

K

I

0.004

309

L

A

D

G

S

V

R

Y

P

I

0.004

161

F

P

Y

F

P

R

L

G

R

Y

0.004

238

Y

G

F

W

D

K

D

K

S

R

0.004

141

V

I

E

G

L

E

D

D

T

V

0.004

336

G

F

P

D

K

K

H

K

L

Y

0.003

v.2-A11-10mers: 151P3D4

Pos

1

2

3

4

5

6

7

8

9

0

Score

SeqID

75

T

V

Y

Q

D

E

K

Q

R

K

4.000

Portion of

111

K

L

K

Y

L

A

F

L

H

K

2.400

SEQ ID

43

V

T

G

I

I

T

Q

G

A

K

1.000

NO: 5;

207

K

Q

A

E

K

N

M

K

K

K

0.900

each start

237

K

T

I

A

P

L

A

A

T

R

0.900

position is

182

A

T

L

E

E

K

R

K

E

K

0.750

specified,

100

G

I

N

I

S

G

S

F

C

R

0.720

the length

205

L

Q

K

Q

A

E

K

N

M

K

0.600

of peptide

342

N

V

L

A

R

G

K

P

Q

R

0.600

is 10

331

K

P

A

R

H

C

Q

G

Q

K

0.600

amino

133

F

Q

V

P

S

R

I

F

W

R

0.540

acids, the

180

V

T

A

T

L

E

E

K

R

K

0.500

end

343

V

L

A

R

G

K

P

Q

R

K

0.400

position

228

S

P

R

G

L

G

F

I

F

K

0.400

for each

322

S

P

S

G

G

G

G

L

K

K

0.400

peptide is

202

L

M

R

L

Q

K

Q

A

E

K

0.400

the start

179

A

V

T

A

T

L

E

E

K

R

0.400

position

189

K

E

K

A

E

I

H

Y

R

K

0.360

plus nine.

178

Q

A

V

T

A

T

L

E

E

K

0.300

191

K

A

E

I

H

Y

R

K

N

K

0.300

77

Y

Q

D

E

K

Q

R

K

D

K

0.300

198

K

N

K

Q

L

M

R

L

Q

K

0.240

129

R

P

Y

H

F

Q

V

P

S

R

0.240

247

A

T

R

I

G

H

P

G

G

R

0.200

195

H

Y

R

K

N

K

Q

L

M

R

0.160

284

W

L

P

L

R

T

P

W

T

R

0.160

74

W

T

V

Y

Q

D

E

K

Q

R

0.150

372

G

S

G

Y

C

G

A

L

W

K

0.120

311

G

P

R

N

P

L

P

N

P

R

0.120

7

K

T

F

P

L

R

A

L

H

I

0.120

55

G

H

V

Q

F

V

G

S

Y

K

0.090

33

K

K

V

D

L

L

V

P

T

K

0.090

86

K

V

L

L

G

R

K

A

V

V

0.090

13

A

L

H

I

V

V

E

S

I

R

0.080

391

G

G

K

Q

K

D

K

E

R

K

0.060

153

P

Q

G

H

A

S

E

A

Y

K

0.060

83

R

K

D

K

V

L

L

G

R

K

0.060

94

V

V

V

S

C

E

G

I

N

I

0.060

34

K

V

D

L

L

V

P

T

K

V

0.060

42

K

V

T

G

I

I

T

Q

G

A

0.060

240

A

P

L

A

A

T

R

A

T

R

0.060

206

Q

K

Q

A

E

K

N

M

K

K

0.040

154

Q

G

H

A

S

E

A

Y

K

K

0.040

102

N

I

S

G

S

F

C

R

N

K

0.040

257

T

P

R

A

G

S

S

A

H

R

0.040

56

H

V

Q

F

V

G

S

Y

K

L

0.040

30

K

Q

D

K

K

V

D

L

L

V

0.036

386

L

E

E

G

L

G

G

K

Q

K

0.030

256

R

T

P

R

A

G

S

S

A

H

0.030

47

I

T

Q

G

A

K

D

F

G

H

0.030

120

K

R

M

N

T

N

P

S

R

R

0.024

25

S

G

Q

K

M

K

Q

D

K

K

0.020

38

L

V

P

T

K

V

T

G

I

I

0.020

167

S

G

A

P

H

E

V

G

W

K

0.020

321

H

S

P

S

G

G

G

G

L

K

0.020

4

H

T

T

K

T

F

P

L

R

A

0.020

24

H

S

G

Q

K

M

K

Q

D

K

0.020

361

Y

V

E

N

G

R

P

A

D

L

0.020

200

K

Q

L

M

R

L

Q

K

Q

A

0.013

188

R

K

E

K

A

E

I

H

Y

R

0.012

325

G

G

G

G

L

K

K

P

A

R

0.012

64

K

L

A

Y

S

N

D

G

E

H

0.012

210

E

K

N

M

K

K

K

I

D

K

0.012

400

K

A

E

N

G

P

H

L

L

V

0.012

72

E

H

W

T

V

Y

Q

D

E

K

0.012

231

G

L

G

F

I

F

K

T

I

A

0.012

28

K

M

K

Q

D

K

K

V

D

L

0.012

221

T

E

S

P

G

G

G

S

P

R

0.012

168

G

A

P

H

E

V

G

W

K

Y

0.012

104

S

G

S

F

C

R

N

K

L

K

0.010

123

N

T

N

P

S

R

R

P

Y

H

0.010

21

I

R

D

H

S

G

Q

K

M

K

0.010

345

A

R

G

K

P

Q

R

K

P

K

0.010

45

G

I

I

T

Q

G

A

K

D

F

0.009

19

E

S

I

R

D

H

S

G

Q

K

0.009

26

G

Q

K

M

K

Q

D

K

K

V

0.009

113

K

Y

L

A

F

L

H

K

R

M

0.009

233

G

F

I

F

K

T

I

A

P

L

0.009

92

K

A

V

V

V

S

C

E

G

I

0.009

12

R

A

L

H

I

V

V

E

S

I

0.009

377

G

A

L

W

K

A

I

E

S

L

0.009

384

E

S

L

E

E

G

L

G

G

K

0.009

381

K

A

I

E

S

L

E

E

G

L

0.009

82

Q

R

K

D

K

V

L

L

G

R

0.008

234

F

I

F

K

T

I

A

P

L

A

0.008

337

Q

G

Q

K

H

N

V

L

A

R

0.008

357

N

N

S

W

Y

V

E

N

G

R

0.008

112

L

K

Y

L

A

F

L

H

K

R

0.008

374

G

Y

C

G

A

L

W

K

A

I

0.006

163

K

V

C

L

S

G

A

P

H

E

0.006

9

F

P

L

R

A

L

H

I

V

V

0.006

352

K

P

K

S

E

N

N

S

W

Y

0.006

50

G

A

K

D

F

G

H

V

Q

F

0.006

336

C

Q

G

Q

K

H

N

V

L

A

0.006

37

L

L

V

P

T

K

V

T

G

I

0.006

204

R

L

Q

K

Q

A

E

K

N

M

0.006

58

Q

F

V

G

S

Y

K

L

A

Y

0.006

57

V

Q

F

V

G

S

Y

K

L

A

0.006

366

R

P

A

D

L

A

G

S

G

Y

0.006

273

R

A

P

V

P

A

A

S

P

A

0.006

TABLE XIII
v.1-A24-9mers: 151P3D4
Pos	1	2	3	4	5	6	7	8	9	Score	SeqID
262	Y	Y	L	I	H	P	T	K	L	330.000	Portion of
194	L	Y	D	A	W	R	G	G	L	200.000	SEQ ID
87	D	Y	L	K	E	V	D	V	F	150.000	NO: 3; each
336	G	F	P	D	K	K	H	K	L	39.600	start
256	N	F	N	G	R	F	Y	Y	L	36.000	position is
62	K	F	Y	R	D	P	T	A	F	20.000	specified,
169	R	Y	N	L	N	F	H	E	A	19.800	the length
247	R	Y	D	V	F	C	F	T	S	10.000	of peptide
76	K	I	R	I	K	W	T	K	L	8.800	is 9 amino
148	D	T	V	V	V	A	L	D	L	8.400	acids, the
271	T	Y	D	E	A	V	Q	A	C	7.200	end
186	A	V	I	A	S	F	D	Q	L	7.200	position for
10	I	S	I	C	W	A	D	H	L	6.000	each
33	Q	A	E	N	G	P	H	L	L	6.000	peptide is
123	S	L	V	I	T	D	L	T	L	6.000	the start
159	V	V	F	P	Y	F	P	R	L	5.760	position
121	D	A	S	L	V	I	T	D	L	5.600	plus eight.
133	D	Y	G	R	Y	K	C	E	V	5.500
69	A	F	G	S	G	I	H	K	I	5.500
344	L	Y	G	V	Y	C	F	R	A	5.000
300	G	Y	D	R	C	D	A	G	W	5.000
21	N	Y	T	L	D	H	D	R	A	5.000
104	T	Y	G	G	Y	Q	G	R	V	5.000
32	I	Q	A	E	N	G	P	H	L	4.800
116	G	G	S	D	S	D	A	S	L	4.800
245	K	S	R	Y	D	V	F	C	F	4.000
164	F	P	R	L	G	R	Y	N	L	4.000
166	R	L	G	R	Y	N	L	N	F	4.000
81	W	T	K	L	T	S	D	Y	L	4.000
291	Q	I	F	A	A	W	K	I	L	4.000
106	G	G	Y	Q	G	R	V	F	L	4.000
55	G	N	V	T	L	P	C	K	F	3.960
2	K	S	L	L	L	L	V	L	I	3.600
156	L	Q	G	V	V	F	P	Y	F	3.360
285	Q	I	A	K	V	G	Q	I	F	3.360
183	D	Q	D	A	V	I	A	S	F	2.800
329	E	A	A	V	R	F	V	G	F	2.400
326	S	P	T	E	A	A	V	R	F	2.400
4	L	L	L	L	V	L	I	S	I	2.100
249	D	V	F	C	F	T	S	N	F	2.000
232	V	P	G	V	R	N	Y	G	F	2.000
105	Y	G	G	Y	Q	G	R	V	F	2.000
253	F	T	S	N	F	N	G	R	F	2.000
153	A	L	D	L	Q	G	V	V	F	2.000
22	Y	T	L	D	H	D	R	A	I	1.800
180	A	C	L	D	Q	D	A	V	I	1.800
290	G	Q	I	F	A	A	W	K	I	1.650
284	A	Q	I	A	K	V	G	Q	I	1.500
278	A	C	L	N	D	G	A	Q	I	1.500
315	R	Y	P	I	S	R	P	R	R	1.500
260	R	F	Y	Y	L	I	H	P	T	1.200
136	R	Y	K	C	E	V	I	E	G	1.100
134	Y	G	R	Y	K	C	E	V	I	1.000
71	G	S	G	I	H	K	I	R	I	1.000
257	F	N	G	R	F	Y	Y	L	I	1.000
66	D	P	T	A	F	G	S	G	I	1.000
163	Y	F	P	R	L	G	R	Y	N	0.900
272	Y	D	E	A	V	Q	A	C	L	0.840
112	V	F	L	K	G	G	S	D	S	0.750
216	Q	Y	P	I	T	K	P	R	E	0.750
107	G	Y	Q	G	R	V	F	L	K	0.750
173	N	F	H	E	A	Q	Q	A	C	0.720
261	F	Y	Y	L	I	H	P	T	K	0.700
137	Y	K	C	E	V	I	E	G	L	0.672
190	S	F	D	Q	L	Y	D	A	W	0.600
250	V	F	C	F	T	S	N	F	N	0.600
162	P	Y	F	P	R	L	G	R	Y	0.600
63	F	Y	R	D	P	T	A	F	G	0.600
16	D	H	L	S	D	N	Y	T	L	0.600
174	F	H	E	A	Q	Q	A	C	L	0.600
146	E	D	D	T	V	V	V	A	L	0.560
99	G	Y	H	K	K	T	Y	G	G	0.500
237	N	Y	G	F	W	D	K	D	K	0.500
49	V	F	S	H	R	G	G	N	V	0.500
1	M	K	S	L	L	L	L	V	L	0.480
28	R	A	I	H	I	Q	A	E	N	0.462
51	S	H	R	G	G	N	V	T	L	0.400
243	K	D	K	S	R	Y	D	V	F	0.400
202	L	D	W	C	N	A	G	W	L	0.400
301	Y	D	R	C	D	A	G	W	L	0.400
288	K	V	G	Q	I	F	A	A	W	0.336
90	K	E	V	D	V	F	V	S	M	0.302
342	H	K	L	Y	G	V	Y	C	F	0.300
53	R	G	G	N	V	T	L	P	C	0.280
324	R	C	S	P	T	E	A	A	V	0.240
42	V	E	A	E	Q	A	K	V	F	0.240
80	K	W	T	K	L	T	S	D	Y	0.240
152	V	A	L	D	L	Q	G	V	V	0.216
279	C	L	N	D	G	A	Q	I	A	0.216
155	D	L	Q	G	V	V	F	P	Y	0.210
122	A	S	L	V	I	T	D	L	T	0.210
6	L	L	V	L	I	S	I	C	W	0.210
199	R	G	G	L	D	W	C	N	A	0.200
48	K	V	F	S	H	R	G	G	N	0.200
320	R	P	R	R	R	C	S	P	T	0.200
115	K	G	G	S	D	S	D	A	S	0.200
78	R	I	K	W	T	K	L	T	S	0.200
36	N	G	P	H	L	L	V	E	A	0.198
345	Y	G	V	Y	C	F	R	A	Y	0.180
129	L	T	L	E	D	Y	G	R	Y	0.180
v.2-A24-9mers: 151P3D4
Pos	1	2	3	4	5	6	7	8	9	Score	SeqID
176	K	Y	Q	A	V	T	A	T	L	840.000	Portion of
195	H	Y	R	K	N	K	Q	L	M	30.000	SEQ ID NO:
132	H	F	Q	V	P	S	R	I	F	15.000	5; each start
400	K	A	E	N	G	P	H	L	L	12.000	position is
360	W	Y	V	E	N	G	R	P	A	9.000	specified,
81	K	Q	R	K	D	K	V	L	L	8.000	the length of
30	K	Q	D	K	K	V	D	L	L	8.000	peptide is 9
8	T	F	P	L	R	A	L	H	I	7.500	amino acids,
382	A	I	E	S	L	E	E	G	L	7.200	the end
279	A	S	P	A	A	W	L	P	L	6.000	position for
321	H	S	P	S	G	G	G	G	L	6.000	each peptide
374	G	Y	C	G	A	L	W	K	A	5.500	is the start
104	S	G	S	F	C	R	N	K	L	5.280	position plus
66	A	Y	S	N	D	G	E	H	W	5.000	eight.
336	C	Q	G	Q	K	H	N	V	L	4.800
308	S	P	Y	G	P	R	N	P	L	4.800
57	V	Q	F	V	G	S	Y	K	L	4.400
99	E	G	I	N	I	S	G	S	F	4.200
107	F	C	R	N	K	L	K	Y	L	4.000
234	F	I	F	K	T	I	A	P	L	4.000
378	A	L	W	K	A	I	E	S	L	4.000
109	R	N	K	L	K	Y	L	A	F	4.000
299	T	S	S	S	T	Y	D	S	L	4.000
371	A	G	S	G	Y	C	G	A	L	4.000
262	S	S	A	H	R	P	P	A	L	4.000
1	M	L	E	H	T	T	K	T	F	3.000
226	G	G	S	P	R	G	L	G	F	2.400
228	S	P	R	G	L	G	F	I	F	2.400
46	I	I	T	Q	G	A	K	D	F	2.000
125	N	P	S	R	R	P	Y	H	F	2.000
231	G	L	G	F	I	F	K	T	I	1.680
113	K	Y	L	A	F	L	H	K	R	1.650
227	G	S	P	R	G	L	G	F	I	1.500
38	L	V	P	T	K	V	T	G	I	1.500
93	A	V	V	V	S	C	E	G	I	1.500
39	V	P	T	K	V	T	G	I	I	1.400
13	A	L	H	I	V	V	E	S	I	1.400
375	Y	C	G	A	L	W	K	A	I	1.200
219	K	Y	T	E	S	P	G	G	G	1.200
197	R	K	N	K	Q	L	M	R	L	1.200
76	V	Y	Q	D	E	K	Q	R	K	1.080
95	V	V	S	C	E	G	I	N	I	1.000
242	L	A	A	T	R	A	T	R	I	1.000
399	R	K	A	E	N	G	P	H	L	0.960
58	Q	F	V	G	S	Y	K	L	A	0.750
116	A	F	L	H	K	R	M	N	T	0.750
29	M	K	Q	D	K	K	V	D	L	0.720
160	A	Y	K	K	V	C	L	S	G	0.700
235	I	F	K	T	I	A	P	L	A	0.700
114	Y	L	A	F	L	H	K	R	M	0.600
362	V	E	N	G	R	P	A	D	L	0.600
110	N	K	L	K	Y	L	A	F	L	0.600
303	T	Y	D	S	L	S	P	Y	G	0.600
80	E	K	Q	R	K	D	K	V	L	0.600
106	S	F	C	R	N	K	L	K	Y	0.550
205	L	Q	K	Q	A	E	K	N	M	0.500
62	S	Y	K	L	A	Y	S	N	D	0.500
12	R	A	L	H	I	V	V	E	S	0.462
3	E	H	T	T	K	T	F	P	L	0.400
158	S	E	A	Y	K	K	V	C	L	0.400
277	P	A	A	S	P	A	A	W	L	0.400
224	P	G	G	G	S	P	R	G	L	0.400
194	I	H	Y	R	K	N	K	Q	L	0.400
6	T	K	T	F	P	L	R	A	L	0.400
266	R	P	P	A	L	S	A	R	A	0.360
191	K	A	E	I	H	Y	R	K	N	0.330
204	R	L	Q	K	Q	A	E	K	N	0.330
230	R	G	L	G	F	I	F	K	T	0.330
86	K	V	L	L	G	R	K	A	V	0.300
354	K	S	E	N	N	S	W	Y	V	0.300
288	R	T	P	W	T	R	P	S	S	0.300
142	R	Q	E	K	A	D	G	G	S	0.300
237	K	T	I	A	P	L	A	A	T	0.300
256	R	T	P	R	A	G	S	S	A	0.300
393	K	Q	K	D	K	E	R	K	A	0.264
352	K	P	K	S	E	N	N	S	W	0.240
138	R	I	F	W	R	Q	E	K	A	0.220
283	A	W	L	P	L	R	T	P	W	0.216
17	V	V	E	S	I	R	D	H	S	0.210
293	R	P	S	S	C	P	T	S	S	0.200
249	R	I	G	H	P	G	G	R	T	0.200
51	A	K	D	F	G	H	V	Q	F	0.200
129	R	P	Y	H	F	Q	V	P	S	0.200
169	A	P	H	E	V	G	W	K	Y	0.185
316	L	P	N	P	R	H	S	P	S	0.180
67	Y	S	N	D	G	E	H	W	T	0.180
201	Q	L	M	R	L	Q	K	Q	A	0.180
133	F	Q	V	P	S	R	I	F	W	0.180
123	N	T	N	P	S	R	R	P	Y	0.180
274	A	P	V	P	A	A	S	P	A	0.180
314	N	P	L	P	N	P	R	H	S	0.180
43	V	T	G	I	I	T	Q	G	A	0.168
152	C	P	Q	G	H	A	S	E	A	0.165
356	E	N	N	S	W	Y	V	E	N	0.165
377	G	A	L	W	K	A	I	E	S	0.165
335	H	C	Q	G	Q	K	H	N	V	0.150
94	V	V	V	S	C	E	G	I	N	0.150
100	G	I	N	I	S	G	S	F	C	0.150
87	V	L	L	G	R	K	A	V	V	0.150
239	I	A	P	L	A	A	T	R	A	0.150

TABLE XIV

v.1-A24-10mers: 151P3D4

Pos

1

2

3

4

5

6

7

8

9

0

Score

SeqID

136

R

Y

K

C

E

V

I

E

G

L

560.000

Portion of

271

T

Y

D

E

A

V

Q

A

C

L

336.000

SEQ ID

261

F

Y

Y

L

I

H

P

T

K

L

220.000

NO: 3;

300

G

Y

D

R

C

D

A

G

W

L

200.000

each start

104

T

Y

G

G

Y

Q

G

R

V

F

100.000

position is

133

D

Y

G

R

Y

K

C

E

V

I

50.000

specified,

21

N

Y

T

L

D

H

D

R

A

I

50.000

the length

163

Y

F

P

R

L

G

R

Y

N

L

30.000

of peptide

173

N

F

H

E

A

Q

Q

A

C

L

24.000

is 10

247

R

Y

D

V

F

C

F

T

S

N

12.000

amino

87

D

Y

L

K

E

V

D

V

F

V

10.500

acids, the

252

C

F

T

S

N

F

N

G

R

F

10.000

end

115

K

G

G

S

D

S

D

A

S

L

8.000

position

80

K

W

T

K

L

T

S

D

Y

L

8.000

for each

256

N

F

N

G

R

F

Y

Y

L

I

7.500

peptide is

262

Y

Y

L

I

H

P

T

K

L

T

7.500

the start

158

G

V

V

F

P

Y

F

P

R

L

7.200

position

185

D

A

V

I

A

S

F

D

Q

L

7.200

plus nine.

344

L

Y

G

V

Y

C

F

R

A

Y

6.000

122

A

S

L

V

I

T

D

L

T

L

6.000

63

F

Y

R

D

P

T

A

F

G

S

6.000

31

H

I

Q

A

E

N

G

P

H

L

6.000

290

G

Q

I

F

A

A

W

K

I

L

6.000

237

N

Y

G

F

W

D

K

D

K

S

5.500

335

V

G

F

P

D

K

K

H

K

L

5.280

155

D

L

Q

G

V

V

F

P

Y

F

5.040

284

A

Q

I

A

K

V

G

Q

I

F

5.040

99

G

Y

H

K

K

T

Y

G

G

Y

5.000

32

I

Q

A

E

N

G

P

H

L

L

4.800

255

S

N

F

N

G

R

F

Y

Y

L

4.800

193

Q

L

Y

D

A

W

R

G

G

L

4.800

105

Y

G

G

Y

Q

G

R

V

F

L

4.000

50

F

S

H

R

G

G

N

V

T

L

4.000

201

G

L

D

W

C

N

A

G

W

L

4.000

9

L

I

S

I

C

W

A

D

H

L

4.000

54

G

G

N

V

T

L

P

C

K

F

3.960

152

V

A

L

D

L

Q

G

V

V

F

3.600

41

L

V

E

A

E

Q

A

K

V

F

3.000

231

T

V

P

G

V

R

N

Y

G

F

3.000

325

C

S

P

T

E

A

A

V

R

F

3.000

3

S

L

L

L

L

V

L

I

S

I

2.100

289

V

G

Q

I

F

A

A

W

K

I

1.650

169

R

Y

N

L

N

F

H

E

A

Q

1.500

283

G

A

Q

I

A

K

V

G

Q

I

1.500

315

R

Y

P

I

S

R

P

R

R

R

1.500

309

L

A

D

G

S

V

R

Y

P

I

1.400

210

L

S

D

G

S

V

Q

Y

P

I

1.400

107

G

Y

Q

G

R

V

F

L

K

G

1.386

68

T

A

F

G

S

G

I

H

K

I

1.100

23

T

L

D

H

D

R

A

I

H

I

1.000

277

Q

A

C

L

N

D

G

A

Q

I

1.000

117

G

S

D

S

D

A

S

L

V

I

1.000

70

F

G

S

G

I

H

K

I

R

I

1.000

179

Q

A

C

L

D

Q

D

A

V

I

1.000

336

G

F

P

D

K

K

H

K

L

Y

0.900

216

Q

Y

P

I

T

K

P

R

E

P

0.825

162

P

Y

F

P

R

L

G

R

Y

N

0.720

145

L

E

D

D

T

V

V

V

A

L

0.672

75

H

K

I

R

I

K

W

T

K

L

0.660

239

G

F

W

D

K

D

K

S

R

Y

0.600

49

V

F

S

H

R

G

G

N

V

T

0.600

120

S

D

A

S

L

V

I

T

D

L

0.560

147

D

D

T

V

V

V

A

L

D

L

0.560

182

L

D

Q

D

A

V

I

A

S

F

0.504

194

L

Y

D

A

W

R

G

G

L

D

0.500

292

I

F

A

A

W

K

I

L

G

Y

0.500

15

A

D

H

L

S

D

N

Y

T

L

0.400

341

K

H

K

L

Y

G

V

Y

C

F

0.400

2

K

S

L

L

L

L

V

L

I

S

0.360

245

K

S

R

Y

D

V

F

C

F

T

0.336

65

R

D

P

T

A

F

G

S

G

I

0.300

297

K

I

L

G

Y

D

R

C

D

A

0.300

248

Y

D

V

F

C

F

T

S

N

F

0.300

328

T

E

A

A

V

R

F

V

G

F

0.240

221

K

P

R

E

P

C

G

G

Q

N

0.240

72

S

G

I

H

K

I

R

I

K

W

0.231

83

K

L

T

S

D

Y

L

K

E

V

0.220

177

A

Q

Q

A

C

L

D

Q

D

A

0.216

140

E

V

I

E

G

L

E

D

D

T

0.216

5

L

L

L

V

L

I

S

I

C

W

0.210

269

K

L

T

Y

D

E

A

V

Q

A

0.200

61

C

K

F

Y

R

D

P

T

A

F

0.200

48

K

V

F

S

H

R

G

G

N

V

0.200

343

K

L

Y

G

V

Y

C

F

R

A

0.200

103

K

T

Y

G

G

Y

Q

G

R

V

0.200

76

K

I

R

I

K

W

T

K

L

T

0.200

111

R

V

F

L

K

G

G

S

D

S

0.200

244

D

K

S

R

Y

D

V

F

C

F

0.200

242

D

K

D

K

S

R

Y

D

V

F

0.200

86

S

D

Y

L

K

E

V

D

V

F

0.200

130

T

L

E

D

Y

G

R

Y

K

C

0.198

40

L

L

V

E

A

E

Q

A

K

V

0.198

180

A

C

L

D

Q

D

A

V

I

A

0.180

278

A

C

L

N

D

G

A

Q

I

A

0.180

275

A

V

Q

A

C

L

N

D

G

A

0.180

4

L

L

L

L

V

L

I

S

I

C

0.180

143

E

G

L

E

D

D

T

V

V

V

0.180

150

V

V

V

A

L

D

L

Q

G

V

0.180

144

G

L

E

D

D

T

V

V

V

A

0.180

200

G

G

L

D

W

C

N

A

G

W

0.180

v.2-A24-10mers: 151P3D4

Pos

1

2

3

4

5

6

7

8

9

0

Score

SeqID

113

K

Y

L

A

F

L

H

K

R

M

90.000

Portion of

374

G

Y

C

G

A

L

W

K

A

I

60.000

SEQ ID

233

G

F

I

F

K

T

I

A

P

L

30.000

NO: 5;

106

S

F

C

R

N

K

L

K

Y

L

20.000

each start

381

K

A

I

E

S

L

E

E

G

L

17.280

position is

219

K

Y

T

E

S

P

G

G

G

S

12.000

specified,

109

R

N

K

L

K

Y

L

A

F

L

8.000

the length

28

K

M

K

Q

D

K

K

V

D

L

8.000

of peptide

335

H

C

Q

G

Q

K

H

N

V

L

7.200

is 10

307

L

S

P

Y

G

P

R

N

P

L

7.200

amino

130

P

Y

H

F

Q

V

P

S

R

I

7.000

acids, the

56

H

V

Q

F

V

G

S

Y

K

L

6.600

end

361

Y

V

E

N

G

R

P

A

D

L

6.000

position

157

A

S

E

A

Y

K

K

V

C

L

6.000

for each

377

G

A

L

W

K

A

I

E

S

L

6.000

peptide is

103

I

S

G

S

F

C

R

N

K

L

5.280

the start

230

R

G

L

G

F

I

F

K

T

I

5.040

position

160

A

Y

K

K

V

C

L

S

G

A

5.000

plus nine.

66

A

Y

S

N

D

G

E

H

W

T

5.000

278

A

A

S

P

A

A

W

L

P

L

4.800

12

R

A

L

H

I

V

V

E

S

I

4.200

276

V

P

A

A

S

P

A

A

W

L

4.000

261

G

S

S

A

H

R

P

P

A

L

4.000

223

S

P

G

G

G

S

P

R

G

L

4.000

193

E

I

H

Y

R

K

N

K

Q

L

4.000

370

L

A

G

S

G

Y

C

G

A

L

4.000

5

T

T

K

T

F

P

L

R

A

L

4.000

227

G

S

P

R

G

L

G

F

I

F

3.600

124

T

N

P

S

R

R

P

Y

H

F

3.000

92

K

A

V

V

V

S

C

E

G

I

3.000

45

G

I

I

T

Q

G

A

K

D

F

3.000

50

G

A

K

D

F

G

H

V

Q

F

2.400

7

K

T

F

P

L

R

A

L

H

I

2.400

38

L

V

P

T

K

V

T

G

I

I

2.100

225

G

G

G

S

P

R

G

L

G

F

2.000

37

L

L

V

P

T

K

V

T

G

I

1.800

208

Q

A

E

K

N

M

K

K

K

I

1.650

94

V

V

V

S

C

E

G

I

N

I

1.500

204

R

L

Q

K

Q

A

E

K

N

M

1.500

176

K

Y

Q

A

V

T

A

T

L

E

1.500

226

G

G

S

P

R

G

L

G

F

I

1.200

76

V

Y

Q

D

E

K

Q

R

K

D

0.990

320

R

H

S

P

S

G

G

G

G

L

0.960

399

R

K

A

E

N

G

P

H

L

L

0.960

116

A

F

L

H

K

R

M

N

T

N

0.900

360

W

Y

V

E

N

G

R

P

A

D

0.900

20

S

I

R

D

H

S

G

Q

K

M

0.792

8

T

F

P

L

R

A

L

H

I

V

0.750

132

H

F

Q

V

P

S

R

I

F

W

0.750

58

Q

F

V

G

S

Y

K

L

A

Y

0.750

29

M

K

Q

D

K

K

V

D

L

L

0.720

80

E

K

Q

R

K

D

K

V

L

L

0.600

53

D

F

G

H

V

Q

F

V

G

S

0.600

309

P

Y

G

P

R

N

P

L

P

N

0.600

62

S

Y

K

L

A

Y

S

N

D

G

0.600

175

W

K

Y

Q

A

V

T

A

T

L

0.560

195

H

Y

R

K

N

K

Q

L

M

R

0.500

303

T

Y

D

S

L

S

P

Y

G

P

0.500

235

I

F

K

T

I

A

P

L

A

A

0.500

196

Y

R

K

N

K

Q

L

M

R

L

0.400

398

E

R

K

A

E

N

G

P

H

L

0.400

79

D

E

K

Q

R

K

D

K

V

L

0.400

2

L

E

H

T

T

K

T

F

P

L

0.400

298

P

T

S

S

S

T

Y

D

S

L

0.400

200

K

Q

L

M

R

L

Q

K

Q

A

0.360

42

K

V

T

G

I

I

T

Q

G

A

0.336

211

K

N

M

K

K

K

I

D

K

Y

0.330

348

K

P

Q

R

K

P

K

S

E

N

0.330

34

K

V

D

L

L

V

P

T

K

V

0.308

273

R

A

P

V

P

A

A

S

P

A

0.300

400

K

A

E

N

G

P

H

L

L

V

0.300

142

R

Q

E

K

A

D

G

G

S

C

0.300

313

R

N

P

L

P

N

P

R

H

S

0.300

86

K

V

L

L

G

R

K

A

V

V

0.300

288

R

T

P

W

T

R

P

S

S

C

0.300

108

C

R

N

K

L

K

Y

L

A

F

0.300

98

C

E

G

I

N

I

S

G

S

F

0.280

30

K

Q

D

K

K

V

D

L

L

V

0.280

346

R

G

K

P

Q

R

K

P

K

S

0.264

16

I

V

V

E

S

I

R

D

H

S

0.252

366

R

P

A

D

L

A

G

S

G

Y

0.240

168

G

A

P

H

E

V

G

W

K

Y

0.231

293

R

P

S

S

C

P

T

S

S

S

0.200

131

Y

H

F

Q

V

P

S

R

I

F

0.200

352

K

P

K

S

E

N

N

S

W

Y

0.200

183

T

L

E

E

K

R

K

E

K

A

0.198

67

Y

S

N

D

G

E

H

W

T

V

0.180

274

A

P

V

P

A

A

S

P

A

A

0.180

283

A

W

L

P

L

R

T

P

W

T

0.180

9

F

P

L

R

A

L

H

I

V

V

0.180

101

I

N

I

S

G

S

F

C

R

N

0.180

151

C

C

P

Q

G

H

A

S

E

A

0.165

164

V

C

L

S

G

A

P

H

E

V

0.165

87

V

L

L

G

R

K

A

V

V

V

0.150

305

D

S

L

S

P

Y

G

P

R

N

0.150

97

S

C

E

G

I

N

I

S

G

S

0.150

99

E

G

I

N

I

S

G

S

F

C

0.150

152

C

P

Q

G

H

A

S

E

A

Y

0.150

327

G

G

L

K

K

P

A

R

H

C

0.150

239

I

A

P

L

A

A

T

R

A

T

0.150

TABLE XV
v.1-B7-9mers: 151P3D4
Pos	1	2	3	4	5	6	7	8	9	Score	SeqID
164	F	P	R	L	G	R	Y	N	L	1200.000	Portion of
186	A	V	I	A	S	F	D	Q	L	60.000	SEQ ID
76	K	I	R	I	K	W	T	K	L	40.000	NO: 3;
159	V	V	F	P	Y	F	P	R	L	20.000	each start
320	R	P	R	R	R	C	S	P	T	20.000	position is
121	D	A	S	L	V	I	T	D	L	12.000	specified,
66	D	P	T	A	F	G	S	G	I	8.000	the length
106	G	G	Y	Q	G	R	V	F	L	6.000	of peptide
148	D	T	V	V	V	A	L	D	L	4.000	is 9 amino
81	W	T	K	L	T	S	D	Y	L	4.000	acids, the
51	S	H	R	G	G	N	V	T	L	4.000	end
134	Y	G	R	Y	K	C	E	V	I	4.000	position
116	G	G	S	D	S	D	A	S	L	4.000	for each
224	E	P	C	G	G	Q	N	T	V	4.000	peptide is
123	S	L	V	I	T	D	L	T	L	4.000	the start
10	I	S	I	C	W	A	D	H	L	4.000	position
291	Q	I	F	A	A	W	K	I	L	4.000	plus eight.
32	I	Q	A	E	N	G	P	H	L	4.000
301	Y	D	R	C	D	A	G	W	L	4.000
33	Q	A	E	N	G	P	H	L	L	3.600
221	K	P	R	E	P	C	G	G	Q	3.000
331	A	V	R	F	V	G	F	P	D	1.500
180	A	C	L	D	Q	D	A	V	I	1.200
278	A	C	L	N	D	G	A	Q	I	1.200
284	A	Q	I	A	K	V	G	Q	I	1.200
151	V	V	A	L	D	L	Q	G	V	1.000
313	S	V	R	Y	P	I	S	R	P	0.750
207	A	G	W	L	S	D	G	S	V	0.600
152	V	A	L	D	L	Q	G	V	V	0.600
179	Q	A	C	L	D	Q	D	A	V	0.600
306	A	G	W	L	A	D	G	S	V	0.600
234	G	V	R	N	Y	G	F	W	D	0.500
7	L	V	L	I	S	I	C	W	A	0.500
161	F	P	Y	F	P	R	L	G	R	0.450
4	L	L	L	L	V	L	I	S	I	0.400
22	Y	T	L	D	H	D	R	A	I	0.400
137	Y	K	C	E	V	I	E	G	L	0.400
256	N	F	N	G	R	F	Y	Y	L	0.400
202	L	D	W	C	N	A	G	W	L	0.400
326	S	P	T	E	A	A	V	R	F	0.400
71	G	S	G	I	H	K	I	R	I	0.400
16	D	H	L	S	D	N	Y	T	L	0.400
1	M	K	S	L	L	L	L	V	L	0.400
290	G	Q	I	F	A	A	W	K	I	0.400
336	G	F	P	D	K	K	H	K	L	0.400
2	K	S	L	L	L	L	V	L	I	0.400
257	F	N	G	R	F	Y	Y	L	I	0.400
262	Y	Y	L	I	H	P	T	K	L	0.400
232	V	P	G	V	R	N	Y	G	F	0.400
286	I	A	K	V	G	Q	I	F	A	0.300
41	L	V	E	A	E	Q	A	K	V	0.300
122	A	S	L	V	I	T	D	L	T	0.300
189	A	S	F	D	Q	L	Y	D	A	0.300
318	I	S	R	P	R	R	R	C	S	0.300
197	A	W	R	G	G	L	D	W	C	0.300
96	V	S	M	G	Y	H	K	K	T	0.300
324	R	C	S	P	T	E	A	A	V	0.200
88	Y	L	K	E	V	D	V	F	V	0.200
217	Y	P	I	T	K	P	R	E	P	0.200
316	Y	P	I	S	R	P	R	R	R	0.200
37	G	P	H	L	L	V	E	A	E	0.200
59	L	P	C	K	F	Y	R	D	P	0.200
245	K	S	R	Y	D	V	F	C	F	0.200
227	G	G	Q	N	T	V	P	G	V	0.200
266	H	P	T	K	L	T	Y	D	E	0.200
84	L	T	S	D	Y	L	K	E	V	0.200
143	E	G	L	E	D	D	T	V	V	0.200
310	A	D	G	S	V	R	Y	P	I	0.180
194	L	Y	D	A	W	R	G	G	L	0.180
263	Y	L	I	H	P	T	K	L	T	0.150
275	A	V	Q	A	C	L	N	D	G	0.150
298	I	L	G	Y	D	R	C	D	A	0.150
346	G	V	Y	C	F	R	A	Y	N	0.150
56	N	V	T	L	P	C	K	F	Y	0.150
48	K	V	F	S	H	R	G	G	N	0.150
69	A	F	G	S	G	I	H	K	I	0.120
337	F	P	D	K	K	H	K	L	Y	0.120
146	E	D	D	T	V	V	V	A	L	0.120
174	F	H	E	A	Q	Q	A	C	L	0.120
272	Y	D	E	A	V	Q	A	C	L	0.120
249	D	V	F	C	F	T	S	N	F	0.100
172	L	N	F	H	E	A	Q	Q	A	0.100
322	R	R	R	C	S	P	T	E	A	0.100
90	K	E	V	D	V	F	V	S	M	0.100
50	F	S	H	R	G	G	N	V	T	0.100
279	C	L	N	D	G	A	Q	I	A	0.100
26	H	D	R	A	I	H	I	Q	A	0.100
167	L	G	R	Y	N	L	N	F	H	0.100
5	L	L	L	V	L	I	S	I	C	0.100
36	N	G	P	H	L	L	V	E	A	0.100
270	L	T	Y	D	E	A	V	Q	A	0.100
178	Q	Q	A	C	L	D	Q	D	A	0.100
109	Q	G	R	V	F	L	K	G	G	0.100
199	R	G	G	L	D	W	C	N	A	0.100
288	K	V	G	Q	I	F	A	A	W	0.100
212	D	G	S	V	Q	Y	P	I	T	0.100
258	N	G	R	F	Y	Y	L	I	H	0.100
39	H	L	L	V	E	A	E	Q	A	0.100
276	V	Q	A	C	L	N	D	G	A	0.100
53	R	G	G	N	V	T	L	P	C	0.100
v.2-B7-9mers: 151P3D4
Pos	1	2	3	4	5	6	7	8	9	Score	SeqID
308	S	P	Y	G	P	R	N	P	L	180.000	Portion
81	K	Q	R	K	D	K	V	L	L	40.000	of SEQ
107	F	C	R	N	K	L	K	Y	L	40.000	ID NO:
279	A	S	P	A	A	W	L	P	L	12.000	5; each
378	A	L	W	K	A	I	E	S	L	12.000	start
371	A	G	S	G	Y	C	G	A	L	12.000	position
39	V	P	T	K	V	T	G	I	I	8.000	is
240	A	P	L	A	A	T	R	A	T	6.000	specified,
104	S	G	S	F	C	R	N	K	L	6.000	the
93	A	V	V	V	S	C	E	G	I	6.000	length of
274	A	P	V	P	A	A	S	P	A	6.000	peptide is
271	S	A	R	A	P	V	P	A	A	4.500	9 amino
336	C	Q	G	Q	K	H	N	V	L	4.000	acids, the
299	T	S	S	S	T	Y	D	S	L	4.000	end
234	F	I	F	K	T	I	A	P	L	4.000	position
262	S	S	A	H	R	P	P	A	L	4.000	for each
228	S	P	R	G	L	G	F	I	F	4.000	peptide is
57	V	Q	F	V	G	S	Y	K	L	4.000	the start
9	F	P	L	R	A	L	H	I	V	4.000	position
321	H	S	P	S	G	G	G	G	L	4.000	plus
400	K	A	E	N	G	P	H	L	L	3.600	eight.
382	A	I	E	S	L	E	E	G	L	3.600
311	G	P	R	N	P	L	P	N	P	3.000
38	L	V	P	T	K	V	T	G	I	2.000
318	N	P	R	H	S	P	S	G	G	2.000
95	V	V	S	C	E	G	I	N	I	2.000
266	R	P	P	A	L	S	A	R	A	2.000
289	T	P	W	T	R	P	S	S	C	2.000
257	T	P	R	A	G	S	S	A	H	2.000
252	H	P	G	G	R	T	P	R	A	2.000
152	C	P	Q	G	H	A	S	E	A	2.000
277	P	A	A	S	P	A	A	W	L	1.800
86	K	V	L	L	G	R	K	A	V	1.500
13	A	L	H	I	V	V	E	S	I	1.200
169	A	P	H	E	V	G	W	K	Y	1.200
30	K	Q	D	K	K	V	D	L	L	1.200
242	L	A	A	T	R	A	T	R	I	1.200
291	W	T	R	P	S	S	C	P	T	1.000
114	Y	L	A	F	L	H	K	R	M	1.000
205	L	Q	K	Q	A	E	K	N	M	1.000
195	H	Y	R	K	N	K	Q	L	M	1.000
172	E	V	G	W	K	Y	Q	A	V	1.000
6	T	K	T	F	P	L	R	A	L	0.600
156	H	A	S	E	A	Y	K	K	V	0.600
264	A	H	R	P	P	A	L	S	A	0.450
254	G	G	R	T	P	R	A	G	S	0.450
244	A	T	R	A	T	R	I	G	H	0.450
362	V	E	N	G	R	P	A	D	L	0.400
29	M	K	Q	D	K	K	V	D	L	0.400
3	E	H	T	T	K	T	F	P	L	0.400
316	L	P	N	P	R	H	S	P	S	0.400
129	R	P	Y	H	F	Q	V	P	S	0.400
110	N	K	L	K	Y	L	A	F	L	0.400
186	E	K	R	K	E	K	A	E	I	0.400
125	N	P	S	R	R	P	Y	H	F	0.400
375	Y	C	G	A	L	W	K	A	I	0.400
176	K	Y	Q	A	V	T	A	T	L	0.400
399	R	K	A	E	N	G	P	H	L	0.400
227	G	S	P	R	G	L	G	F	I	0.400
293	R	P	S	S	C	P	T	S	S	0.400
276	V	P	A	A	S	P	A	A	W	0.400
352	K	P	K	S	E	N	N	S	W	0.400
231	G	L	G	F	I	F	K	T	I	0.400
80	E	K	Q	R	K	D	K	V	L	0.400
224	P	G	G	G	S	P	R	G	L	0.400
314	N	P	L	P	N	P	R	H	S	0.400
197	R	K	N	K	Q	L	M	R	L	0.400
194	I	H	Y	R	K	N	K	Q	L	0.400
158	S	E	A	Y	K	K	V	C	L	0.400
239	I	A	P	L	A	A	T	R	A	0.300
247	A	T	R	I	G	H	P	G	G	0.300
344	L	A	R	G	K	P	Q	R	K	0.300
201	Q	L	M	R	L	Q	K	Q	A	0.300
370	L	A	G	S	G	Y	C	G	A	0.300
297	C	P	T	S	S	S	T	Y	D	0.200
280	S	P	A	A	W	L	P	L	R	0.200
285	L	P	L	R	T	P	W	T	R	0.200
335	H	C	Q	G	Q	K	H	N	V	0.200
366	R	P	A	D	L	A	G	S	G	0.200
49	Q	G	A	K	D	F	G	H	V	0.200
89	L	G	R	K	A	V	V	V	S	0.200
322	S	P	S	G	G	G	G	L	K	0.200
127	S	R	R	P	Y	H	F	Q	V	0.200
88	L	L	G	R	K	A	V	V	V	0.200
135	V	P	S	R	I	F	W	R	Q	0.200
331	K	P	A	R	H	C	Q	G	Q	0.200
10	P	L	R	A	L	H	I	V	V	0.200
87	V	L	L	G	R	K	A	V	V	0.200
348	K	P	Q	R	K	P	K	S	E	0.200
223	S	P	G	G	G	S	P	R	G	0.200
165	C	L	S	G	A	P	H	E	V	0.200
363	E	N	G	R	P	A	D	L	A	0.150
149	G	S	C	C	P	Q	G	H	A	0.150
179	A	V	T	A	T	L	E	E	K	0.150
237	K	T	I	A	P	L	A	A	T	0.150
249	R	I	G	H	P	G	G	R	T	0.150
261	G	S	S	A	H	R	P	P	A	0.150
36	D	L	L	V	P	T	K	V	T	0.150
328	G	L	K	K	P	A	R	H	C	0.150
282	A	A	W	L	P	L	R	T	P	0.135

TABLE XVI

v.1-B7-10mers: 151P3D4

Pos

1

2

3

4

5

6

7

8

9

0

Score

SeqID

158

G

V

V

F

P

Y

F

P

R

L

20.000

Portion of

185

D

A

V

I

A

S

F

D

Q

L

12.000

SEQ ID

122

A

S

L

V

I

T

D

L

T

L

12.000

NO: 3;

105

Y

G

G

Y

Q

G

R

V

F

L

6.000

each start

193

Q

L

Y

D

A

W

R

G

G

L

6.000

position is

316

Y

P

I

S

R

P

R

R

R

C

4.500

specified,

217

Y

P

I

T

K

P

R

E

P

C

4.500

the length

335

V

G

F

P

D

K

K

H

K

L

4.000

of peptide

9

L

I

S

I

C

W

A

D

H

L

4.000

is 10

255

S

N

F

N

G

R

F

Y

Y

L

4.000

amino

32

I

Q

A

E

N

G

P

H

L

L

4.000

acids, the

221

K

P

R

E

P

C

G

G

Q

N

4.000

end

50

F

S

H

R

G

G

N

V

T

L

4.000

position

290

G

Q

I

F

A

A

W

K

I

L

4.000

for each

115

K

G

G

S

D

S

D

A

S

L

4.000

peptide is

164

F

P

R

L

G

R

Y

N

L

N

4.000

the start

31

H

I

Q

A

E

N

G

P

H

L

4.000

position

326

S

P

T

E

A

A

V

R

F

V

4.000

plus nine.

59

L

P

C

K

F

Y

R

D

P

T

3.000

320

R

P

R

R

R

C

S

P

T

E

2.000

266

H

P

T

K

L

T

Y

D

E

A

2.000

331

A

V

R

F

V

G

F

P

D

K

1.500

275

A

V

Q

A

C

L

N

D

G

A

1.500

179

Q

A

C

L

D

Q

D

A

V

I

1.200

15

A

D

H

L

S

D

N

Y

T

L

1.200

277

Q

A

C

L

N

D

G

A

Q

I

1.200

283

G

A

Q

I

A

K

V

G

Q

I

1.200

201

G

L

D

W

C

N

A

G

W

L

1.200

68

T

A

F

G

S

G

I

H

K

I

1.200

48

K

V

F

S

H

R

G

G

N

V

1.000

151

V

V

A

L

D

L

Q

G

V

V

1.000

150

V

V

V

A

L

D

L

Q

G

V

1.000

245

K

S

R

Y

D

V

F

C

F

T

1.000

76

K

I

R

I

K

W

T

K

L

T

1.000

305

D

A

G

W

L

A

D

G

S

V

0.600

206

N

A

G

W

L

S

D

G

S

V

0.600

163

Y

F

P

R

L

G

R

Y

N

L

0.600

309

L

A

D

G

S

V

R

Y

P

I

0.540

234

G

V

R

N

Y

G

F

W

D

K

0.500

140

E

V

I

E

G

L

E

D

D

T

0.500

95

F

V

S

M

G

Y

H

K

K

T

0.500

313

S

V

R

Y

P

I

S

R

P

R

0.500

70

F

G

S

G

I

H

K

I

R

I

0.400

161

F

P

Y

F

P

R

L

G

R

Y

0.400

136

R

Y

K

C

E

V

I

E

G

L

0.400

147

D

D

T

V

V

V

A

L

D

L

0.400

173

N

F

H

E

A

Q

Q

A

C

L

0.400

232

V

P

G

V

R

N

Y

G

F

W

0.400

289

V

G

Q

I

F

A

A

W

K

I

0.400

75

H

K

I

R

I

K

W

T

K

L

0.400

261

F

Y

Y

L

I

H

P

T

K

L

0.400

3

S

L

L

L

L

V

L

I

S

I

0.400

120

S

D

A

S

L

V

I

T

D

L

0.400

80

K

W

T

K

L

T

S

D

Y

L

0.400

286

I

A

K

V

G

Q

I

F

A

A

0.300

121

D

A

S

L

V

I

T

D

L

T

0.300

186

A

V

I

A

S

F

D

Q

L

Y

0.300

188

I

A

S

F

D

Q

L

Y

D

A

0.300

180

A

C

L

D

Q

D

A

V

I

A

0.300

196

D

A

W

R

G

G

L

D

W

C

0.300

177

A

Q

Q

A

C

L

D

Q

D

A

0.300

278

A

C

L

N

D

G

A

Q

I

A

0.300

33

Q

A

E

N

G

P

H

L

L

V

0.270

66

D

P

T

A

F

G

S

G

I

H

0.200

226

C

G

G

Q

N

T

V

P

G

V

0.200

224

E

P

C

G

G

Q

N

T

V

P

0.200

116

G

G

S

D

S

D

A

S

L

V

0.200

109

Q

G

R

V

F

L

K

G

G

S

0.200

37

G

P

H

L

L

V

E

A

E

Q

0.200

178

Q

Q

A

C

L

D

Q

D

A

V

0.200

143

E

G

L

E

D

D

T

V

V

V

0.200

103

K

T

Y

G

G

Y

Q

G

R

V

0.200

40

L

L

V

E

A

E

Q

A

K

V

0.200

83

K

L

T

S

D

Y

L

K

E

V

0.200

297

K

I

L

G

Y

D

R

C

D

A

0.150

318

I

S

R

P

R

R

R

C

S

P

0.150

322

R

R

R

C

S

P

T

E

A

A

0.150

271

T

Y

D

E

A

V

Q

A

C

L

0.120

145

L

E

D

D

T

V

V

V

A

L

0.120

117

G

S

D

S

D

A

S

L

V

I

0.120

210

L

S

D

G

S

V

Q

Y

P

I

0.120

300

G

Y

D

R

C

D

A

G

W

L

0.120

23

T

L

D

H

D

R

A

I

H

I

0.120

167

L

G

R

Y

N

L

N

F

H

E

0.100

249

D

V

F

C

F

T

S

N

F

N

0.100

269

K

L

T

Y

D

E

A

V

Q

A

0.100

73

G

I

H

K

I

R

I

K

W

T

0.100

6

L

L

V

L

I

S

I

C

W

A

0.100

35

E

N

G

P

H

L

L

V

E

A

0.100

20

D

N

Y

T

L

D

H

D

R

A

0.100

270

L

T

Y

D

E

A

V

Q

A

C

0.100

285

Q

I

A

K

V

G

Q

I

F

A

0.100

111

R

V

F

L

K

G

G

S

D

S

0.100

172

L

N

F

H

E

A

Q

Q

A

C

0.100

171

N

L

N

F

H

E

A

Q

Q

A

0.100

134

Y

G

R

Y

K

C

E

V

I

E

0.100

113

F

L

K

G

G

S

D

S

D

A

0.100

343

K

L

Y

G

V

Y

C

F

R

A

0.100

4

L

L

L

L

V

L

I

S

I

C

0.100

231

T

V

P

G

V

R

N

Y

G

F

0.100

v.2-B7-10mers: 151P3D4

Pos

1

2

3

4

5

6

7

8

9

0

Score

SeqID

276

V

P

A

A

S

P

A

A

W

L

120.000

Portion of

223

S

P

G

G

G

S

P

R

G

L

80.000

SEQ ID

278

A

A

S

P

A

A

W

L

P

L

36.000

NO: 5; each

56

H

V

Q

F

V

G

S

Y

K

L

20.000

start

377

G

A

L

W

K

A

I

E

S

L

12.000

position is

370

L

A

G

S

G

Y

C

G

A

L

12.000

specified,

381

K

A

I

E

S

L

E

E

G

L

12.000

the length

20

S

I

R

D

H

S

G

Q

K

M

10.000

of peptide

307

L

S

P

Y

G

P

R

N

P

L

9.000

is 10 amino

5

T

T

K

T

F

P

L

R

A

L

6.000

acids, the

361

Y

V

E

N

G

R

P

A

D

L

6.000

end

103

I

S

G

S

F

C

R

N

K

L

6.000

position for

274

A

P

V

P

A

A

S

P

A

A

6.000

each

109

R

N

K

L

K

Y

L

A

F

L

4.000

peptide is

335

H

C

Q

G

Q

K

H

N

V

L

4.000

the start

261

G

S

S

A

H

R

P

P

A

L

4.000

position

28

K

M

K

Q

D

K

K

V

D

L

4.000

plus nine.

9

F

P

L

R

A

L

H

I

V

V

4.000

193

E

I

H

Y

R

K

N

K

Q

L

4.000

157

A

S

E

A

Y

K

K

V

C

L

3.600

318

N

P

R

H

S

P

S

G

G

G

3.000

39

V

P

T

K

V

T

G

I

I

T

2.000

94

V

V

V

S

C

E

G

I

N

I

2.000

228

S

P

R

G

L

G

F

I

F

K

2.000

311

G

P

R

N

P

L

P

N

P

R

2.000

38

L

V

P

T

K

V

T

G

I

I

2.000

257

T

P

R

A

G

S

S

A

H

R

2.000

280

S

P

A

A

W

L

P

L

R

T

2.000

92

K

A

V

V

V

S

C

E

G

I

1.200

12

R

A

L

H

I

V

V

E

S

I

1.200

89

L

G

R

K

A

V

V

V

S

C

1.000

107

F

C

R

N

K

L

K

Y

L

A

1.000

204

R

L

Q

K

Q

A

E

K

N

M

1.000

86

K

V

L

L

G

R

K

A

V

V

1.000

240

A

P

L

A

A

T

R

A

T

R

0.900

169

A

P

H

E

V

G

W

K

Y

Q

0.600

348

K

P

Q

R

K

P

K

S

E

N

0.600

267

P

P

A

L

S

A

R

A

P

V

0.600

293

R

P

S

S

C

P

T

S

S

S

0.600

271

S

A

R

A

P

V

P

A

A

S

0.600

42

K

V

T

G

I

I

T

Q

G

A

0.500

172

E

V

G

W

K

Y

Q

A

V

T

0.500

115

L

A

F

L

H

K

R

M

N

T

0.450

260

A

G

S

S

A

H

R

P

P

A

0.450

263

S

A

H

R

P

P

A

L

S

A

0.450

344

L

A

R

G

K

P

Q

R

K

P

0.450

314

N

P

L

P

N

P

R

H

S

P

0.450

226

G

G

S

P

R

G

L

G

F

I

0.400

106

S

F

C

R

N

K

L

K

Y

L

0.400

398

E

R

K

A

E

N

G

P

H

L

0.400

366

R

P

A

D

L

A

G

S

G

Y

0.400

2

L

E

H

T

T

K

T

F

P

L

0.400

175

W

K

Y

Q

A

V

T

A

T

L

0.400

152

C

P

Q

G

H

A

S

E

A

Y

0.400

79

D

E

K

Q

R

K

D

K

V

L

0.400

399

R

K

A

E

N

G

P

H

L

L

0.400

320

R

H

S

P

S

G

G

G

G

L

0.400

297

C

P

T

S

S

S

T

Y

D

S

0.400

298

P

T

S

S

S

T

Y

D

S

L

0.400

233

G

F

I

F

K

T

I

A

P

L

0.400

196

Y

R

K

N

K

Q

L

M

R

L

0.400

230

R

G

L

G

F

I

F

K

T

I

0.400

7

K

T

F

P

L

R

A

L

H

I

0.400

80

E

K

Q

R

K

D

K

V

L

L

0.400

352

K

P

K

S

E

N

N

S

W

Y

0.400

29

M

K

Q

D

K

K

V

D

L

L

0.400

37

L

L

V

P

T

K

V

T

G

I

0.400

208

Q

A

E

K

N

M

K

K

K

I

0.360

239

I

A

P

L

A

A

T

R

A

T

0.300

34

K

V

D

L

L

V

P

T

K

V

0.300

289

T

P

W

T

R

P

S

S

C

P

0.300

125

N

P

S

R

R

P

Y

H

F

Q

0.300

156

H

A

S

E

A

Y

K

K

V

C

0.300

247

A

T

R

I

G

H

P

G

G

R

0.300

244

A

T

R

A

T

R

I

G

H

P

0.300

269

A

L

S

A

R

A

P

V

P

A

0.300

285

L

P

L

R

T

P

W

T

R

P

0.300

93

A

V

V

V

S

C

E

G

I

N

0.300

273

R

A

P

V

P

A

A

S

P

A

0.300

282

A

A

W

L

P

L

R

T

P

W

0.270

400

K

A

E

N

G

P

H

L

L

V

0.270

291

W

T

R

P

S

S

C

P

T

S

0.200

26

G

Q

K

M

K

Q

D

K

K

V

0.200

164

V

C

L

S

G

A

P

H

E

V

0.200

252

H

P

G

G

R

T

P

R

A

G

0.200

322

S

P

S

G

G

G

G

L

K

K

0.200

308

S

P

Y

G

P

R

N

P

L

P

0.200

87

V

L

L

G

R

K

A

V

V

V

0.200

67

Y

S

N

D

G

E

H

W

T

V

0.200

129

R

P

Y

H

F

Q

V

P

S

R

0.200

331

K

P

A

R

H

C

Q

G

Q

K

0.200

254

G

G

R

T

P

R

A

G

S

S

0.200

126

P

S

R

R

P

Y

H

F

Q

V

0.200

364

N

G

R

P

A

D

L

A

G

S

0.200

266

R

P

P

A

L

S

A

R

A

P

0.200

48

T

Q

G

A

K

D

F

G

H

V

0.200

316

L

P

N

P

R

H

S

P

S

G

0.200

135

V

P

S

R

I

F

W

R

Q

E

0.200

179

A

V

T

A

T

L

E

E

K

R

0.150

327

G

G

L

K

K

P

A

R

H

C

0.150

TABLE XVII
v.1-B35-9mers: 151P3D4
Pos	1	2	3	4	5	6	7	8	9	Score	SeqID
164	F	P	R	L	G	R	Y	N	L	60.000	Portion of
245	K	S	R	Y	D	V	F	C	F	45.000	SEQ ID
326	S	P	T	E	A	A	V	R	F	40.000	NO: 3;
232	V	P	G	V	R	N	Y	G	F	20.000	each start
320	R	P	R	R	R	C	S	P	T	12.000	position is
337	F	P	D	K	K	H	K	L	Y	12.000	specified,
254	T	S	N	F	N	G	R	F	Y	10.000	the length
66	D	P	T	A	F	G	S	G	I	8.000	of peptide
76	K	I	R	I	K	W	T	K	L	6.000	is 9 amino
293	F	A	A	W	K	I	L	G	Y	6.000	acids, the
129	L	T	L	E	D	Y	G	R	Y	6.000	end
10	I	S	I	C	W	A	D	H	L	5.000	position
209	W	L	S	D	G	S	V	Q	Y	4.000	for each
308	W	L	A	D	G	S	V	R	Y	4.000	peptide is
224	E	P	C	G	G	Q	N	T	V	4.000	the start
2	K	S	L	L	L	L	V	L	I	4.000	position
81	W	T	K	L	T	S	D	Y	L	3.000	plus eight.
121	D	A	S	L	V	I	T	D	L	3.000
329	E	A	A	V	R	F	V	G	F	3.000
221	K	P	R	E	P	C	G	G	Q	2.400
187	V	I	A	S	F	D	Q	L	Y	2.000
230	N	T	V	P	G	V	R	N	Y	2.000
255	S	N	F	N	G	R	F	Y	Y	2.000
71	G	S	G	I	H	K	I	R	I	2.000
345	Y	G	V	Y	C	F	R	A	Y	2.000
166	R	L	G	R	Y	N	L	N	F	2.000
116	G	G	S	D	S	D	A	S	L	2.000
264	L	I	H	P	T	K	L	T	Y	2.000
97	S	M	G	Y	H	K	K	T	Y	2.000
56	N	V	T	L	P	C	K	F	Y	2.000
155	D	L	Q	G	V	V	F	P	Y	2.000
32	I	Q	A	E	N	G	P	H	L	2.000
14	W	A	D	H	L	S	D	N	Y	1.800
196	D	A	W	R	G	G	L	D	W	1.500
318	I	S	R	P	R	R	R	C	S	1.500
134	Y	G	R	Y	K	C	E	V	I	1.200
88	Y	L	K	E	V	D	V	F	V	1.200
152	V	A	L	D	L	Q	G	V	V	1.200
106	G	G	Y	Q	G	R	V	F	L	1.000
148	D	T	V	V	V	A	L	D	L	1.000
189	A	S	F	D	Q	L	Y	D	A	1.000
186	A	V	I	A	S	F	D	Q	L	1.000
253	F	T	S	N	F	N	G	R	F	1.000
123	S	L	V	I	T	D	L	T	L	1.000
55	G	N	V	T	L	P	C	K	F	1.000
159	V	V	F	P	Y	F	P	R	L	1.000
285	Q	I	A	K	V	G	Q	I	F	1.000
156	L	Q	G	V	V	F	P	Y	F	1.000
249	D	V	F	C	F	T	S	N	F	1.000
291	Q	I	F	A	A	W	K	I	L	1.000
105	Y	G	G	Y	Q	G	R	V	F	1.000
288	K	V	G	Q	I	F	A	A	W	1.000
179	Q	A	C	L	D	Q	D	A	V	0.900
286	I	A	K	V	G	Q	I	F	A	0.900
33	Q	A	E	N	G	P	H	L	L	0.900
90	K	E	V	D	V	F	V	S	M	0.800
22	Y	T	L	D	H	D	R	A	I	0.800
180	A	C	L	D	Q	D	A	V	I	0.800
278	A	C	L	N	D	G	A	Q	I	0.600
243	K	D	K	S	R	Y	D	V	F	0.600
100	Y	H	K	K	T	Y	G	G	Y	0.600
78	R	I	K	W	T	K	L	T	S	0.600
143	E	G	L	E	D	D	T	V	V	0.600
28	R	A	I	H	I	Q	A	E	N	0.600
126	I	T	D	L	T	L	E	D	Y	0.600
96	V	S	M	G	Y	H	K	K	T	0.500
122	A	S	L	V	I	T	D	L	T	0.500
6	L	L	V	L	I	S	I	C	W	0.500
50	F	S	H	R	G	G	N	V	T	0.500
73	G	I	H	K	I	R	I	K	W	0.500
301	Y	D	R	C	D	A	G	W	L	0.450
117	G	S	D	S	D	A	S	L	V	0.450
84	L	T	S	D	Y	L	K	E	V	0.400
80	K	W	T	K	L	T	S	D	Y	0.400
284	A	Q	I	A	K	V	G	Q	I	0.400
324	R	C	S	P	T	E	A	A	V	0.400
257	F	N	G	R	F	Y	Y	L	I	0.400
4	L	L	L	L	V	L	I	S	I	0.400
290	G	Q	I	F	A	A	W	K	I	0.400
340	K	K	H	K	L	Y	G	V	Y	0.400
153	A	L	D	L	Q	G	V	V	F	0.300
305	D	A	G	W	L	A	D	G	S	0.300
199	R	G	G	L	D	W	C	N	A	0.300
115	K	G	G	S	D	S	D	A	S	0.300
151	V	V	A	L	D	L	Q	G	V	0.300
51	S	H	R	G	G	N	V	T	L	0.300
206	N	A	G	W	L	S	D	G	S	0.300
62	K	F	Y	R	D	P	T	A	F	0.300
183	D	Q	D	A	V	I	A	S	F	0.300
270	L	T	Y	D	E	A	V	Q	A	0.300
42	V	E	A	E	Q	A	K	V	F	0.200
53	R	G	G	N	V	T	L	P	C	0.200
59	L	P	C	K	F	Y	R	D	P	0.200
306	A	G	W	L	A	D	G	S	V	0.200
137	Y	K	C	E	V	I	E	G	L	0.200
227	G	G	Q	N	T	V	P	G	V	0.200
37	G	P	H	L	L	V	E	A	E	0.200
161	F	P	Y	F	P	R	L	G	R	0.200
336	G	F	P	D	K	K	H	K	L	0.200
48	K	V	F	S	H	R	G	G	N	0.200
v.2-B35-9mers: 151P3D4
Pos	1	2	3	4	5	6	7	8	9	Score	SeqID
352	K	P	K	S	E	N	N	S	W	90.000	Portion
169	A	P	H	E	V	G	W	K	Y	80.000	of SEQ
228	S	P	R	G	L	G	F	I	F	60.000	ID NO:
308	S	P	Y	G	P	R	N	P	L	20.000	5; each
125	N	P	S	R	R	P	Y	H	F	20.000	start
276	V	P	A	A	S	P	A	A	W	10.000	position
81	K	Q	R	K	D	K	V	L	L	9.000	is
39	V	P	T	K	V	T	G	I	I	8.000	specified,
205	L	Q	K	Q	A	E	K	N	M	6.000	the
212	N	M	K	K	K	I	D	K	Y	6.000	length of
109	R	N	K	L	K	Y	L	A	F	6.000	peptide is
299	T	S	S	S	T	Y	D	S	L	5.000	9 amino
262	S	S	A	H	R	P	P	A	L	5.000	acids, the
321	H	S	P	S	G	G	G	G	L	5.000	end
279	A	S	P	A	A	W	L	P	L	5.000	position
302	S	T	Y	D	S	L	S	P	Y	4.000	for each
129	R	P	Y	H	F	Q	V	P	S	4.000	peptide is
266	R	P	P	A	L	S	A	R	A	4.000	the start
9	F	P	L	R	A	L	H	I	V	4.000	position
293	R	P	S	S	C	P	T	S	S	4.000	plus
107	F	C	R	N	K	L	K	Y	L	3.000	eight.
372	G	S	G	Y	C	G	A	L	W	2.500
316	L	P	N	P	R	H	S	P	S	2.000
274	A	P	V	P	A	A	S	P	A	2.000
152	C	P	Q	G	H	A	S	E	A	2.000
252	H	P	G	G	R	T	P	R	A	2.000
296	S	C	P	T	S	S	S	T	Y	2.000
240	A	P	L	A	A	T	R	A	T	2.000
114	Y	L	A	F	L	H	K	R	M	2.000
227	G	S	P	R	G	L	G	F	I	2.000
123	N	T	N	P	S	R	R	P	Y	2.000
59	F	V	G	S	Y	K	L	A	Y	2.000
289	T	P	W	T	R	P	S	S	C	2.000
314	N	P	L	P	N	P	R	H	S	2.000
400	K	A	E	N	G	P	H	L	L	1.800
242	L	A	A	T	R	A	T	R	I	1.200
393	K	Q	K	D	K	E	R	K	A	1.200
156	H	A	S	E	A	Y	K	K	V	1.200
371	A	G	S	G	Y	C	G	A	L	1.000
99	E	G	I	N	I	S	G	S	F	1.000
336	C	Q	G	Q	K	H	N	V	L	1.000
104	S	G	S	F	C	R	N	K	L	1.000
234	F	I	F	K	T	I	A	P	L	1.000
378	A	L	W	K	A	I	E	S	L	1.000
57	V	Q	F	V	G	S	Y	K	L	1.000
46	I	I	T	Q	G	A	K	D	F	1.000
226	G	G	S	P	R	G	L	G	F	1.000
96	V	S	C	E	G	I	N	I	S	1.000
67	Y	S	N	D	G	E	H	W	T	1.000
271	S	A	R	A	P	V	P	A	A	0.900
366	R	P	A	D	L	A	G	S	G	0.800
257	T	P	R	A	G	S	S	A	H	0.600
318	N	P	R	H	S	P	S	G	G	0.600
195	H	Y	R	K	N	K	Q	L	M	0.600
95	V	V	S	C	E	G	I	N	I	0.600
12	R	A	L	H	I	V	V	E	S	0.600
354	K	S	E	N	N	S	W	Y	V	0.600
311	G	P	R	N	P	L	P	N	P	0.600
30	K	Q	D	K	K	V	D	L	L	0.600
261	G	S	S	A	H	R	P	P	A	0.500
300	S	S	S	T	Y	D	S	L	S	0.500
270	L	S	A	R	A	P	V	P	A	0.500
167	S	G	A	P	H	E	V	G	W	0.500
295	S	S	C	P	T	S	S	S	T	0.500
149	G	S	C	C	P	Q	G	H	A	0.500
61	G	S	Y	K	L	A	Y	S	N	0.500
133	F	Q	V	P	S	R	I	F	W	0.500
69	N	D	G	E	H	W	T	V	Y	0.400
13	A	L	H	I	V	V	E	S	I	0.400
231	G	L	G	F	I	F	K	T	I	0.400
38	L	V	P	T	K	V	T	G	I	0.400
375	Y	C	G	A	L	W	K	A	I	0.400
348	K	P	Q	R	K	P	K	S	E	0.400
86	K	V	L	L	G	R	K	A	V	0.400
93	A	V	V	V	S	C	E	G	I	0.400
399	R	K	A	E	N	G	P	H	L	0.400
331	K	P	A	R	H	C	Q	G	Q	0.400
328	G	L	K	K	P	A	R	H	C	0.300
277	P	A	A	S	P	A	A	W	L	0.300
239	I	A	P	L	A	A	T	R	A	0.300
89	L	G	R	K	A	V	V	V	S	0.300
49	Q	G	A	K	D	F	G	H	V	0.300
382	A	I	E	S	L	E	E	G	L	0.300
254	G	G	R	T	P	R	A	G	S	0.300
291	W	T	R	P	S	S	C	P	T	0.300
377	G	A	L	W	K	A	I	E	S	0.300
263	S	A	H	R	P	P	A	L	S	0.300
159	E	A	Y	K	K	V	C	L	S	0.300
1	M	L	E	H	T	T	K	T	F	0.300
370	L	A	G	S	G	Y	C	G	A	0.300
115	L	A	F	L	H	K	R	M	N	0.300
5	T	T	K	T	F	P	L	R	A	0.300
230	R	G	L	G	F	I	F	K	T	0.200
280	S	P	A	A	W	L	P	L	R	0.200
138	R	I	F	W	R	Q	E	K	A	0.200
322	S	P	S	G	G	G	G	L	K	0.200
288	R	T	P	W	T	R	P	S	S	0.200
297	C	P	T	S	S	S	T	Y	D	0.200
249	R	I	G	H	P	G	G	R	T	0.200
204	R	L	Q	K	Q	A	E	K	N	0.200

TABLE XVIII

v.1-B35-10mers: 151P3D4

Pos

1

2

3

4

5

6

7

8

9

0

Score

SeqID

161

F

P

Y

F

P

R

L

G

R

Y

40.000

Portion

221

K

P

R

E

P

C

G

G

Q

N

24.000

of SEQ

254

T

S

N

F

N

G

R

F

Y

Y

10.000

ID NO:

96

V

S

M

G

Y

H

K

K

T

Y

10.000

3; each

232

V

P

G

V

R

N

Y

G

F

W

10.000

start

326

S

P

T

E

A

A

V

R

F

V

8.000

position

164

F

P

R

L

G

R

Y

N

L

N

6.000

is

152

V

A

L

D

L

Q

G

V

V

F

6.000

specified,

122

A

S

L

V

I

T

D

L

T

L

5.000

the

325

C

S

P

T

E

A

A

V

R

F

5.000

length of

189

A

S

F

D

Q

L

Y

D

A

W

5.000

peptide is

50

F

S

H

R

G

G

N

V

T

L

5.000

10 amino

125

V

I

T

D

L

T

L

E

D

Y

4.000

acids, the

185

D

A

V

I

A

S

F

D

Q

L

3.000

end

128

D

L

T

L

E

D

Y

G

R

Y

3.000

position

245

K

S

R

Y

D

V

F

C

F

T

3.000

for each

55

G

N

V

T

L

P

C

K

F

Y

2.000

peptide is

115

K

G

G

S

D

S

D

A

S

L

2.000

the start

59

L

P

C

K

F

Y

R

D

P

T

2.000

position

217

Y

P

I

T

K

P

R

E

P

C

2.000

plus nine.

229

Q

N

T

V

P

G

V

R

N

Y

2.000

253

F

T

S

N

F

N

G

R

F

Y

2.000

32

I

Q

A

E

N

G

P

H

L

L

2.000

193

Q

L

Y

D

A

W

R

G

G

L

2.000

263

Y

L

I

H

P

T

K

L

T

Y

2.000

186

A

V

I

A

S

F

D

Q

L

Y

2.000

316

Y

P

I

S

R

P

R

R

R

C

2.000

266

H

P

T

K

L

T

Y

D

E

A

2.000

277

Q

A

C

L

N

D

G

A

Q

I

1.800

68

T

A

F

G

S

G

I

H

K

I

1.200

179

Q

A

C

L

D

Q

D

A

V

I

1.200

283

G

A

Q

I

A

K

V

G

Q

I

1.200

320

R

P

R

R

R

C

S

P

T

E

1.200

284

A

Q

I

A

K

V

G

Q

I

F

1.000

335

V

G

F

P

D

K

K

H

K

L

1.000

299

L

G

Y

D

R

C

D

A

G

W

1.000

105

Y

G

G

Y

Q

G

R

V

F

L

1.000

290

G

Q

I

F

A

A

W

K

I

L

1.000

255

S

N

F

N

G

R

F

Y

Y

L

1.000

158

G

V

V

F

P

Y

F

P

R

L

1.000

231

T

V

P

G

V

R

N

Y

G

F

1.000

2

K

S

L

L

L

L

V

L

I

S

1.000

200

G

G

L

D

W

C

N

A

G

W

1.000

31

H

I

Q

A

E

N

G

P

H

L

1.000

54

G

G

N

V

T

L

P

C

K

F

1.000

9

L

I

S

I

C

W

A

D

H

L

1.000

155

D

L

Q

G

V

V

F

P

Y

F

1.000

88

Y

L

K

E

V

D

V

F

V

S

0.900

286

I

A

K

V

G

Q

I

F

A

A

0.900

91

E

V

D

V

F

V

S

M

G

Y

0.600

210

L

S

D

G

S

V

Q

Y

P

I

0.600

305

D

A

G

W

L

A

D

G

S

V

0.600

136

R

Y

K

C

E

V

I

E

G

L

0.600

206

N

A

G

W

L

S

D

G

S

V

0.600

117

G

S

D

S

D

A

S

L

V

I

0.600

339

D

K

K

H

K

L

Y

G

V

Y

0.600

143

E

G

L

E

D

D

T

V

V

V

0.600

116

G

G

S

D

S

D

A

S

L

V

0.600

239

G

F

W

D

K

D

K

S

R

Y

0.600

76

K

I

R

I

K

W

T

K

L

T

0.600

341

K

H

K

L

Y

G

V

Y

C

F

0.600

40

L

L

V

E

A

E

Q

A

K

V

0.600

10

I

S

I

C

W

A

D

H

L

S

0.500

5

L

L

L

V

L

I

S

I

C

W

0.500

72

S

G

I

H

K

I

R

I

K

W

0.500

103

K

T

Y

G

G

Y

Q

G

R

V

0.400

336

G

F

P

D

K

K

H

K

L

Y

0.400

13

C

W

A

D

H

L

S

D

N

Y

0.400

48

K

V

F

S

H

R

G

G

N

V

0.400

3

S

L

L

L

L

V

L

I

S

I

0.400

289

V

G

Q

I

F

A

A

W

K

I

0.400

70

F

G

S

G

I

H

K

I

R

I

0.400

83

K

L

T

S

D

Y

L

K

E

V

0.400

309

L

A

D

G

S

V

R

Y

P

I

0.360

297

K

I

L

G

Y

D

R

C

D

A

0.300

109

Q

G

R

V

F

L

K

G

G

S

0.300

269

K

L

T

Y

D

E

A

V

Q

A

0.300

180

A

C

L

D

Q

D

A

V

I

A

0.300

201

G

L

D

W

C

N

A

G

W

L

0.300

121

D

A

S

L

V

I

T

D

L

T

0.300

41

L

V

E

A

E

Q

A

K

V

F

0.300

196

D

A

W

R

G

G

L

D

W

C

0.300

188

I

A

S

F

D

Q

L

Y

D

A

0.300

150

V

V

V

A

L

D

L

Q

G

V

0.300

178

Q

Q

A

C

L

D

Q

D

A

V

0.300

113

F

L

K

G

G

S

D

S

D

A

0.300

85

T

S

D

Y

L

K

E

V

D

V

0.300

111

R

V

F

L

K

G

G

S

D

S

0.200

151

V

V

A

L

D

L

Q

G

V

V

0.200

344

L

Y

G

V

Y

C

F

R

A

Y

0.200

343

K

L

Y

G

V

Y

C

F

R

A

0.200

307

G

W

L

A

D

G

S

V

R

Y

0.200

292

I

F

A

A

W

K

I

L

G

Y

0.200

80

K

W

T

K

L

T

S

D

Y

L

0.200

182

L

D

Q

D

A

V

I

A

S

F

0.200

66

D

P

T

A

F

G

S

G

I

H

0.200

270

L

T

Y

D

E

A

V

Q

A

C

0.200

99

G

Y

H

K

K

T

Y

G

G

Y

0.200

226

C

G

G

Q

N

T

V

P

G

V

0.200

224

E

P

C

G

G

Q

N

T

V

P

0.200

v.2-B35-10mers: 151P3D4

Pos

1

2

3

4

5

6

7

8

9

0

Score

SeqID

352

K

P

K

S

E

N

N

S

W

Y

240.000

Portion of

366

R

P

A

D

L

A

G

S

G

Y

160.000

SEQ ID

152

C

P

Q

G

H

A

S

E

A

Y

40.000

NO: 5;

276

V

P

A

A

S

P

A

A

W

L

20.000

each start

223

S

P

G

G

G

S

P

R

G

L

20.000

position is

50

G

A

K

D

F

G

H

V

Q

F

18.000

specified,

20

S

I

R

D

H

S

G

Q

K

M

12.000

the length

381

K

A

I

E

S

L

E

E

G

L

12.000

of peptide

301

S

S

T

Y

D

S

L

S

P

Y

10.000

is 10

105

G

S

F

C

R

N

K

L

K

Y

10.000

amino

295

S

S

C

P

T

S

S

S

T

Y

10.000

acids, the

109

R

N

K

L

K

Y

L

A

F

L

6.000

end

168

G

A

P

H

E

V

G

W

K

Y

6.000

position

28

K

M

K

Q

D

K

K

V

D

L

6.000

for each

227

G

S

P

R

G

L

G

F

I

F

5.000

peptide is

261

G

S

S

A

H

R

P

P

A

L

5.000

the start

307

L

S

P

Y

G

P

R

N

P

L

5.000

position

103

I

S

G

S

F

C

R

N

K

L

5.000

plus nine.

348

K

P

Q

R

K

P

K

S

E

N

4.000

9

F

P

L

R

A

L

H

I

V

V

4.000

211

K

N

M

K

K

K

I

D

K

Y

4.000

293

R

P

S

S

C

P

T

S

S

S

4.000

204

R

L

Q

K

Q

A

E

K

N

M

4.000

67

Y

S

N

D

G

E

H

W

T

V

3.000

370

L

A

G

S

G

Y

C

G

A

L

3.000

278

A

A

S

P

A

A

W

L

P

L

3.000

377

G

A

L

W

K

A

I

E

S

L

3.000

5

T

T

K

T

F

P

L

R

A

L

3.000

166

L

S

G

A

P

H

E

V

G

W

2.500

187

K

R

K

E

K

A

E

I

H

Y

2.400

12

R

A

L

H

I

V

V

E

S

I

2.400

92

K

A

V

V

V

S

C

E

G

I

2.400

65

L

A

Y

S

N

D

G

E

H

W

2.250

39

V

P

T

K

V

T

G

I

I

T

2.000

297

C

P

T

S

S

S

T

Y

D

S

2.000

280

S

P

A

A

W

L

P

L

R

T

2.000

274

A

P

V

P

A

A

S

P

A

A

2.000

54

F

G

H

V

Q

F

V

G

S

Y

2.000

122

M

N

T

N

P

S

R

R

P

Y

2.000

282

A

A

W

L

P

L

R

T

P

W

1.500

157

A

S

E

A

Y

K

K

V

C

L

1.500

56

H

V

Q

F

V

G

S

Y

K

L

1.000

193

E

I

H

Y

R

K

N

K

Q

L

1.000

45

G

I

I

T

Q

G

A

K

D

F

1.000

225

G

G

G

S

P

R

G

L

G

F

1.000

335

H

C

Q

G

Q

K

H

N

V

L

1.000

124

T

N

P

S

R

R

P

Y

H

F

1.000

271

S

A

R

A

P

V

P

A

A

S

0.900

7

K

T

F

P

L

R

A

L

H

I

0.800

230

R

G

L

G

F

I

F

K

T

I

0.800

68

S

N

D

G

E

H

W

T

V

Y

0.600

311

G

P

R

N

P

L

P

N

P

R

0.600

94

V

V

V

S

C

E

G

I

N

I

0.600

273

R

A

P

V

P

A

A

S

P

A

0.600

228

S

P

R

G

L

G

F

I

F

K

0.600

156

H

A

S

E

A

Y

K

K

V

C

0.600

257

T

P

R

A

G

S

S

A

H

R

0.600

346

R

G

K

P

Q

R

K

P

K

S

0.600

26

G

Q

K

M

K

Q

D

K

K

V

0.600

318

N

P

R

H

S

P

S

G

G

G

0.600

371

A

G

S

G

Y

C

G

A

L

W

0.500

299

T

S

S

S

T

Y

D

S

L

S

0.500

149

G

S

C

C

P

Q

G

H

A

S

0.500

305

D

S

L

S

P

Y

G

P

R

N

0.500

270

L

S

A

R

A

P

V

P

A

A

0.500

262

S

S

A

H

R

P

P

A

L

S

0.500

364

N

G

R

P

A

D

L

A

G

S

0.450

86

K

V

L

L

G

R

K

A

V

V

0.400

399

R

K

A

E

N

G

P

H

L

L

0.400

226

G

G

S

P

R

G

L

G

F

I

0.400

266

R

P

P

A

L

S

A

R

A

P

0.400

37

L

L

V

P

T

K

V

T

G

I

0.400

129

R

P

Y

H

F

Q

V

P

S

R

0.400

113

K

Y

L

A

F

L

H

K

R

M

0.400

169

A

P

H

E

V

G

W

K

Y

Q

0.400

38

L

V

P

T

K

V

T

G

I

I

0.400

267

P

P

A

L

S

A

R

A

P

V

0.400

331

K

P

A

R

H

C

Q

G

Q

K

0.400

208

Q

A

E

K

N

M

K

K

K

I

0.360

400

K

A

E

N

G

P

H

L

L

V

0.360

79

D

E

K

Q

R

K

D

K

V

L

0.300

107

F

C

R

N

K

L

K

Y

L

A

0.300

115

L

A

F

L

H

K

R

M

N

T

0.300

398

E

R

K

A

E

N

G

P

H

L

0.300

239

I

A

P

L

A

A

T

R

A

T

0.300

361

Y

V

E

N

G

R

P

A

D

L

0.300

291

W

T

R

P

S

S

C

P

T

S

0.300

263

S

A

H

R

P

P

A

L

S

A

0.300

212

N

M

K

K

K

I

D

K

Y

T

0.300

196

Y

R

K

N

K

Q

L

M

R

L

0.300

254

G

G

R

T

P

R

A

G

S

S

0.300

126

P

S

R

R

P

Y

H

F

Q

V

0.300

89

L

G

R

K

A

V

V

V

S

C

0.300

48

T

Q

G

A

K

D

F

G

H

V

0.300

314

N

P

L

P

N

P

R

H

S

P

0.200

194

I

H

Y

R

K

N

K

Q

L

M

0.200

322

S

P

S

G

G

G

G

L

K

K

0.200

164

V

C

L

S

G

A

P

H

E

V

0.200

288

R

T

P

W

T

R

P

S

S

C

0.200

42

K

V

T

G

I

I

T

Q

G

A

0.200

TABLE XIX
Frequently Occurring Motifs
	avrg. %
Name	identity	Description	Potential Function
zf-C2H2	34%	Zinc finger, C2H2 type	Nucleic acid-binding protein functions
			as transcription factor, nuclear location
			probable
cytochrome_b_N	68%	Cytochrome b(N-	membrane bound oxidase, generate
		terminal)/b6/petB	superoxide
ig	19%	Immunoglobulin	domains are one hundred amino acids
		domain	long and include a conserved
			intradomain disulfide bond.
WD40	18%	WD domain, G-beta	tandem repeats of about 40 residues,
		repeat	each containing a Trp-Asp motif.
			Function in signal transduction and
			protein interaction
PDZ	23%	PDZ domain	may function in targeting signaling
			molecules to sub-membranous sites
LRR	28%	Leucine Rich Repeat	short sequence motifs involved in
			protein-protein interactions
pkinase	23%	Protein kinase domain	conserved catalytic core common to
			both serine/threonine and tyrosine
			protein kinases containing an ATP
			binding site and a catalytic site
PH	16%	PH domain	pleckstrin homology involved in
			intracellular signaling or as constituents
			of the cytoskeleton
EGF	34%	EGF-like domain	30-40 amino-acid long found in the
			extracellular domain of membrane-
			bound proteins or in secreted proteins
rvt	49%	Reverse transcriptase
		(RNA-dependent DNA
		polymerase)
ank	25%	Ank repeat	Cytoplasmic protein, associates integral
			membrane proteins to the cytoskeleton
oxidored_q1	32%	NADH-	membrane associated. Involved in
		Ubiquinone/plastoquinone	proton translocation across the
		(complex I), various	membrane
		chains
efhand	24%	EF hand	calcium-binding domain, consists of a12 residue
			loop flanked on both sides by a 12 residue alpha-
			helical domain
rvp	79%	Retroviral aspartyl	Aspartyl or acid proteases, centered on a
		protease	catalytic aspartyl residue
Collagen	42%	Collagen triple helix	extracellular structural proteins involved in
		repeat (20 copies)	formation of connective tissue. The sequence
			consists of the G-X-Y and the polypeptide chains
			forms a triple helix.
fn3	20%	Fibronectin type III	Located in the extracellular ligand-binding
		domain	region of receptors and is about 200 amino acid
			residues long with two pairs of cysteines
			involved in disulfide bonds
7tm_1	19%	7 transmembrane	seven hydrophobic transmembrane regions, with
		receptor (rhodopsin	the N-terminus located extracellularly while the
		family)	C-terminus is cytoplasmic. Signal through G
			proteins

TABLE XX
Motifs and Post-translational Modifications of 151P3D4
N-glycosylation site.
21-24   NYTL
56-59   NVTL
cAMP- and cGMP-dependent protein kinase phosphorylation site
323-326 RRcS
Protein kinase C phosphorylation site
51-53   ShR
313-315 SvR
Casein kinase II phosphorylation site
118-121 SdsD
130-133 TleD
246-249 SryD
271-274 TydE
326-329 SptE
N-myristoylation site
54-59   GGnvTL
106-111 GGyqGR
116-121 GGsdSD
201-206 GLdwCN
227-232 GGqnTV
283-288 GAqiAK
290-295 GQifAA

TABLE XXI
Protein Properties of 151P3D4
	Bioinformatic	URL located on the World
151P3D4 V.1	Program	Wide Web at:	Outcome
ORF	ORF finder		bp316-1380 (includes stop)
Protein length			354 aa
Transmembrane	TM Pred	.ch.embnet.org/	no TM
region	HMMTop	.enzim.hu/hmmtop/	no TM, intracellular
	Sosui	.genome.ad.jp/SOSui/	no TM, soluble protein
	TMHMM	.cbs.dtu.dk/services/TMHMM	no TM
Signal Peptide	Signal P	.cbs.dtu.dk/services/SignalP/	yes
pI	pI/MW tool	.expasy.ch/tools/	7.1
Molecular	pI/MW tool	.expasy.ch/tools/	40.1 kDa
weight
Localization	PSORT	/psort.nibb.ac.jp/	53% outside, 51% lysosome
	PSORT II	psort.nibb.ac.jp/	66% extracellular, 11%
			cytoplasmic
Motifs	Pfam	.sanger.ac.uk/Pfam/	Ig domain, extracellular link
			domain
	Prints	.biochem.ucl.ac.uk/	Link module
	Blocks	.blocks.fhcrc.org/	Link motif, C-type lectin
			domain, receptor tyrosine
			kinase class III
151P3D4 V.2	Bioinformatic	URL located on the World
	Program	Wide Web at:	Outcome
ORF	ORF finder		bp1-2166 (includes stop)
Protein length			721aa
Transmembrane	TM Pred	.ch.embnet.org/	no TM
region	HMMTop	.enzim.hu/hmmtop/	no TM, extracellular
	Sosui	.genome.ad.jp/SOSui/	no TM, soluble protein
	TMHMM	.cbs.dtu.dk/services/TMHMM	no TM
Signal Peptide	Signal P	.cbs.dtu.dk/services/SignalP/	none
pI	pI/MW tool	.expasy.ch/tools/	pI9.6
Molecular	pI/MW tool	.expasy.ch/tools/	80.7 kDa
weight
Localization	PSORT	psort.nibb.ac.jp/	82% nucleus, 42% peroxisome
	PSORT II	psort.nibb.ac.jp/	52% nuclear, 26% cytoplasmic
Motifs	Pfam	.sanger.ac.uk/Pfam/	F5/8 type C domain, Ig domain
			extracellular link domain
	Prints	.biochem.ucl.ac.uk/	link module signature
	Blocks	.blocks.fhcrc.org/	Link motif, coagulation factor
			5/8 type c domain (FA58C),
			ribosomal protein L13, C-type
			lectin domain, receptor
			tyrosine kinase class III

TABLE XXII
151P3D4 v.1
HLA Peptide
Scoring Results A1 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
126	I	T	D	L	T	L	E	D	Y	31	Portion
230	N	T	V	P	G	V	R	N	Y	28	of SEQ
337	F	P	D	K	K	H	K	L	Y	28	ID NO:
240	F	W	D	K	D	K	S	R	Y	26	3; each
14	W	A	D	H	L	S	D	N	Y	25	start
264	L	I	H	P	T	K	L	T	Y	25	position
293	F	A	A	W	K	I	L	G	Y	22	is
18	L	S	D	N	Y	T	L	D	H	21	specified,
129	L	T	L	E	D	Y	G	R	Y	21	the length
155	D	L	Q	G	V	V	F	P	Y	20	of
254	T	S	N	F	N	G	R	F	Y	20	peptide is
255	S	N	F	N	G	R	F	Y	Y	20	9 amino
345	Y	G	V	Y	C	F	R	A	Y	20	acids, the
162	P	Y	F	P	R	L	G	R	Y	19	end
92	V	D	V	F	V	S	M	G	Y	18	position
187	V	I	A	S	F	D	Q	L	Y	18	for each
209	W	L	S	D	G	S	V	Q	Y	18	peptide is
303	R	C	D	A	G	W	L	A	D	18	the start
308	W	L	A	D	G	S	V	R	Y	18	position
97	S	M	G	Y	H	K	K	T	Y	17	plus
100	Y	H	K	K	T	Y	G	G	Y	17	eight.
327	P	T	E	A	A	V	R	F	V	17
56	N	V	T	L	P	C	K	F	Y	16
64	Y	R	D	P	T	A	F	G	S	16
117	G	S	D	S	D	A	S	L	V	16
153	A	L	D	L	Q	G	V	V	F	16
210	L	S	D	G	S	V	Q	Y	P	16
340	K	K	H	K	L	Y	G	V	Y	16
80	K	W	T	K	L	T	S	D	Y	15
85	T	S	D	Y	L	K	E	V	D	15
108	Y	Q	G	R	V	F	L	K	G	15
131	L	E	D	Y	G	R	Y	K	C	15
222	P	R	E	P	C	G	G	Q	N	15
280	L	N	D	G	A	Q	I	A	K	15
33	Q	A	E	N	G	P	H	L	L	14
119	D	S	D	A	S	L	V	I	T	14
148	D	T	V	V	V	A	L	D	L	14
272	Y	D	E	A	V	Q	A	C	L	14
130	T	L	E	D	Y	G	R	Y	K	13
146	E	D	D	T	V	V	V	A	L	13
174	F	H	E	A	Q	Q	A	C	L	13
23	T	L	D	H	D	R	A	I	H	12
41	L	V	E	A	E	Q	A	K	V	12
89	L	K	E	V	D	V	F	V	S	12
91	E	V	D	V	F	V	S	M	G	12
138	K	C	E	V	I	E	G	L	E	12
141	V	I	E	G	L	E	D	D	T	12
144	G	L	E	D	D	T	V	V	V	12
145	L	E	D	D	T	V	V	V	A	12
183	D	Q	D	A	V	I	A	S	F	12
190	S	F	D	Q	L	Y	D	A	W	12
201	G	L	D	W	C	N	A	G	W	12
309	L	A	D	G	S	V	R	Y	P	12
34	A	E	N	G	P	H	L	L	V	11
35	E	N	G	P	H	L	L	V	E	11
57	V	T	L	P	C	K	F	Y	R	11
181	C	L	D	Q	D	A	V	I	A	11
194	L	Y	D	A	W	R	G	G	L	11
242	D	K	D	K	S	R	Y	D	V	11
271	T	Y	D	E	A	V	Q	A	C	11
3	S	L	L	L	L	V	L	I	S	10
25	D	H	D	R	A	I	H	I	Q	10
43	E	A	E	Q	A	K	V	F	S	10
219	I	T	K	P	R	E	P	C	G	10
247	R	Y	D	V	F	C	F	T	S	10
300	G	Y	D	R	C	D	A	G	W	10
50	F	S	H	R	G	G	N	V	T	9
83	K	L	T	S	D	Y	L	K	E	9
96	V	S	M	G	Y	H	K	K	T	9
103	K	T	Y	G	G	Y	Q	G	R	9
118	S	D	S	D	A	S	L	V	I	9
123	S	L	V	I	T	D	L	T	L	9
159	V	V	F	P	Y	F	P	R	L	9
161	F	P	Y	F	P	R	L	G	R	9
166	R	L	G	R	Y	N	L	N	F	9
196	D	A	W	R	G	G	L	D	W	9
213	G	S	V	Q	Y	P	I	T	K	9
312	G	S	V	R	Y	P	I	S	R	9
318	I	S	R	P	R	R	R	C	S	9
22	Y	T	L	D	H	D	R	A	I	8
53	R	G	G	N	V	T	L	P	C	8
67	P	T	A	F	G	S	G	I	H	8
71	G	S	G	I	H	K	I	R	I	8
204	W	C	N	A	G	W	L	S	D	8
253	F	T	S	N	F	N	G	R	F	8
1	M	K	S	L	L	L	L	V	L	7
4	L	L	L	L	V	L	I	S	I	7
73	G	I	H	K	I	R	I	K	W	7
84	L	T	S	D	Y	L	K	E	V	7
120	S	D	A	S	L	V	I	T	D	7
122	A	S	L	V	I	T	D	L	T	7
125	V	I	T	D	L	T	L	E	D	7
139	C	E	V	I	E	G	L	E	D	7
150	V	V	V	A	L	D	L	Q	G	7
189	A	S	F	D	Q	L	Y	D	A	7
246	S	R	Y	D	V	F	C	F	T	7
258	N	G	R	F	Y	Y	L	I	H	7
2	K	S	L	L	L	L	V	L	I	6
12	I	C	W	A	D	H	L	S	D	6
51	S	H	R	G	G	N	V	T	L	6
68	T	A	F	G	S	G	I	H	K	6
78	R	I	K	W	T	K	L	T	S	6
81	W	T	K	L	T	S	D	Y	L	6
105	Y	G	G	Y	Q	G	R	V	F	6
176	E	A	Q	Q	A	C	L	D	Q	6
188	I	A	S	F	D	Q	L	Y	D	6
235	V	R	N	Y	G	F	W	D	K	6
263	Y	L	I	H	P	T	K	L	T	6
267	P	T	K	L	T	Y	D	E	A	6
270	L	T	Y	D	E	A	V	Q	A	6
274	E	A	V	Q	A	C	L	N	D	6
286	I	A	K	V	G	Q	I	F	A	6
292	I	F	A	A	W	K	I	L	G	6
332	V	R	F	V	G	F	P	D	K	6
338	P	D	K	K	H	K	L	Y	G	6
6	L	L	V	L	I	S	I	C	W	5
45	E	Q	A	K	V	F	S	H	R	5
69	A	F	G	S	G	I	H	K	I	5
88	Y	L	K	E	V	D	V	F	V	5
90	K	E	V	D	V	F	V	S	M	5
95	F	V	S	M	G	Y	H	K	K	5
113	F	L	K	G	G	S	D	S	D	5
136	R	Y	K	C	E	V	I	E	G	5
147	D	D	T	V	V	V	A	L	D	5
156	L	Q	G	V	V	F	P	Y	F	5
182	L	D	Q	D	A	V	I	A	S	5
195	Y	D	A	W	R	G	G	L	D	5
214	S	V	Q	Y	P	I	T	K	P	5
215	V	Q	Y	P	I	T	K	P	R	5
225	P	C	G	G	Q	N	T	V	P	5
245	K	S	R	Y	D	V	F	C	F	5
248	Y	D	V	F	C	F	T	S	N	5
259	G	R	F	Y	Y	L	I	H	P	5
314	V	R	Y	P	I	S	R	P	R	5
325	C	S	P	T	E	A	A	V	R	5
335	V	G	F	P	D	K	K	H	K	5
10	I	S	I	C	W	A	D	H	L	4
11	S	I	C	W	A	D	H	L	S	4
24	L	D	H	D	R	A	I	H	I	4
26	H	D	R	A	I	H	I	Q	A	4
42	V	E	A	E	Q	A	K	V	F	4
52	H	R	G	G	N	V	T	L	P	4
58	T	L	P	C	K	F	Y	R	D	4
107	G	Y	Q	G	R	V	F	L	K	4
112	V	F	L	K	G	G	S	D	S	4
137	Y	K	C	E	V	I	E	G	L	4
164	F	P	R	L	G	R	Y	N	L	4
175	H	E	A	Q	Q	A	C	L	D	4
180	A	C	L	D	Q	D	A	V	I	4
186	A	V	I	A	S	F	D	Q	L	4
197	A	W	R	G	G	L	D	W	C	4
211	S	D	G	S	V	Q	Y	P	I	4
231	T	V	P	G	V	R	N	Y	G	4
238	Y	G	F	W	D	K	D	K	S	4
256	N	F	N	G	R	F	Y	Y	L	4
262	Y	Y	L	I	H	P	T	K	L	4
273	D	E	A	V	Q	A	C	L	N	4
281	N	D	G	A	Q	I	A	K	V	4
287	A	K	V	G	Q	I	F	A	A	4
310	A	D	G	S	V	R	Y	P	I	4
324	R	C	S	P	T	E	A	A	V	4
328	T	E	A	A	V	R	F	V	G	4
331	A	V	R	F	V	G	F	P	D	4
334	F	V	G	F	P	D	K	K	H	4
343	K	L	Y	G	V	Y	C	F	R	4
17	H	L	S	D	N	Y	T	L	D	3
29	A	I	H	I	Q	A	E	N	G	3
65	R	D	P	T	A	F	G	S	G	3
102	K	K	T	Y	G	G	Y	Q	G	3
106	G	G	Y	Q	G	R	V	F	L	3
134	Y	G	R	Y	K	C	E	V	I	3
154	L	D	L	Q	G	V	V	F	P	3
160	V	F	P	Y	F	P	R	L	G	3
163	Y	F	P	R	L	G	R	Y	N	3
165	P	R	L	G	R	Y	N	L	N	3
169	R	Y	N	L	N	F	H	E	A	3
203	D	W	C	N	A	G	W	L	S	3
223	R	E	P	C	G	G	Q	N	T	3
224	E	P	C	G	G	Q	N	T	V	3
228	G	Q	N	T	V	P	G	V	R	3
236	R	N	Y	G	F	W	D	K	D	3
252	C	F	T	S	N	F	N	G	R	3
257	F	N	G	R	F	Y	Y	L	I	3
279	C	L	N	D	G	A	Q	I	A	3
285	Q	I	A	K	V	G	Q	I	F	3
288	K	V	G	Q	I	F	A	A	W	3
302	D	R	C	D	A	G	W	L	A	3
313	S	V	R	Y	P	I	S	R	P	3
319	S	R	P	R	R	R	C	S	P	3
329	E	A	A	V	R	F	V	G	F	3
333	R	F	V	G	F	P	D	K	K	3
342	H	K	L	Y	G	V	Y	C	F	3
8	V	L	I	S	I	C	W	A	D	2
19	S	D	N	Y	T	L	D	H	D	2
38	P	H	L	L	V	E	A	E	Q	2
44	A	E	Q	A	K	V	F	S	H	2
49	V	F	S	H	R	G	G	N	V	2
55	G	N	V	T	L	P	C	K	F	2
60	P	C	K	F	Y	R	D	P	T	2
63	F	Y	R	D	P	T	A	F	G	2
70	F	G	S	G	I	H	K	I	R	2
72	S	G	I	H	K	I	R	I	K	2
76	K	I	R	I	K	W	T	K	L	2
77	I	R	I	K	W	T	K	L	T	2
82	T	K	L	T	S	D	Y	L	K	2
86	S	D	Y	L	K	E	V	D	V	2
87	D	Y	L	K	E	V	D	V	F	2
94	V	F	V	S	M	G	Y	H	K	2
101	H	K	K	T	Y	G	G	Y	Q	2
104	T	Y	G	G	Y	Q	G	R	V	2
121	D	A	S	L	V	I	T	D	L	2
124	L	V	I	T	D	L	T	L	E	2
140	E	V	I	E	G	L	E	D	D	2
149	T	V	V	V	A	L	D	L	Q	2
152	V	A	L	D	L	Q	G	V	V	2
170	Y	N	L	N	F	H	E	A	Q	2
191	F	D	Q	L	Y	D	A	W	R	2
208	G	W	L	S	D	G	S	V	Q	2
212	D	G	S	V	Q	Y	P	I	T	2
217	Y	P	I	T	K	P	R	E	P	2
218	P	I	T	K	P	R	E	P	C	2
229	Q	N	T	V	P	G	V	R	N	2
232	V	P	G	V	R	N	Y	G	F	2
234	G	V	R	N	Y	G	F	W	D	2
251	F	C	F	T	S	N	F	N	G	2
269	K	L	T	Y	D	E	A	V	Q	2
276	V	Q	A	C	L	N	D	G	A	2
278	A	C	L	N	D	G	A	Q	I	2
284	A	Q	I	A	K	V	G	Q	I	2
290	G	Q	I	F	A	A	W	K	I	2
295	A	W	K	I	L	G	Y	D	R	2
296	W	K	I	L	G	Y	D	R	C	2
297	K	I	L	G	Y	D	R	C	D	2
298	I	L	G	Y	D	R	C	D	A	2
301	Y	D	R	C	D	A	G	W	L	2
307	G	W	L	A	D	G	S	V	R	2
316	Y	P	I	S	R	P	R	R	R	2
317	P	I	S	R	P	R	R	R	C	2
326	S	P	T	E	A	A	V	R	F	2
330	A	A	V	R	F	V	G	F	P	2
336	G	F	P	D	K	K	H	K	L	2
341	K	H	K	L	Y	G	V	Y	C	2
5	L	L	L	V	L	I	S	I	C	1
15	A	D	H	L	S	D	N	Y	T	1
16	D	H	L	S	D	N	Y	T	L	1
31	H	I	Q	A	E	N	G	P	H	1
32	I	Q	A	E	N	G	P	H	L	1
37	G	P	H	L	L	V	E	A	E	1
39	H	L	L	V	E	A	E	Q	A	1
40	L	L	V	E	A	E	Q	A	K	1
47	A	K	V	F	S	H	R	G	G	1
48	K	V	F	S	H	R	G	G	N	1
66	D	P	T	A	F	G	S	G	I	1
111	R	V	F	L	K	G	G	S	D	1
114	L	K	G	G	S	D	S	D	A	1
128	D	L	T	L	E	D	Y	G	R	1
132	E	D	Y	G	R	Y	K	C	E	1
133	D	Y	G	R	Y	K	C	E	V	1
143	E	G	L	E	D	D	T	V	V	1
151	V	V	A	L	D	L	Q	G	V	1
158	G	V	V	F	P	Y	F	P	R	1
168	G	R	Y	N	L	N	F	H	E	1
171	N	L	N	F	H	E	A	Q	Q	1
177	A	Q	Q	A	C	L	D	Q	D	1
193	Q	L	Y	D	A	W	R	G	G	1
198	W	R	G	G	L	D	W	C	N	1
205	C	N	A	G	W	L	S	D	G	1
207	A	G	W	L	S	D	G	S	V	1
221	K	P	R	E	P	C	G	G	Q	1
227	G	G	Q	N	T	V	P	G	V	1
243	K	D	K	S	R	Y	D	V	F	1
244	D	K	S	R	Y	D	V	F	C	1
250	V	F	C	F	T	S	N	F	N	1
261	F	Y	Y	L	I	H	P	T	K	1
268	T	K	L	T	Y	D	E	A	V	1
275	A	V	Q	A	C	L	N	D	G	1
282	D	G	A	Q	I	A	K	V	G	1
289	V	G	Q	I	F	A	A	W	K	1
294	A	A	W	K	I	L	G	Y	D	1
304	C	D	A	G	W	L	A	D	G	1
306	A	G	W	L	A	D	G	S	V	1
315	R	Y	P	I	S	R	P	R	R	1
323	R	R	C	S	P	T	E	A	A	1
344	L	Y	G	V	Y	C	F	R	A	1
346	G	V	Y	C	F	R	A	Y	N	1
151P3D4 v.2
HLA Peptide
Scoring Results A1 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
188	R	K	E	K	A	E	I	H	Y	29	Portion of
123	N	T	N	P	S	R	R	P	Y	26	SEQ ID
367	P	A	D	L	A	G	S	G	Y	26	NO: 5;
106	S	F	C	R	N	K	L	K	Y	25	each start
59	F	V	G	S	Y	K	L	A	Y	23	position
302	S	T	Y	D	S	L	S	P	Y	23	is
169	A	P	H	E	V	G	W	K	Y	21	specified,
220	Y	T	E	S	P	G	G	G	S	20	the length
83	R	K	D	K	V	L	L	G	R	18	of peptide
97	S	C	E	G	I	N	I	S	G	18	is 9
157	A	S	E	A	Y	K	K	V	C	17	amino
212	N	M	K	K	K	I	D	K	Y	17	acids, the
296	S	C	P	T	S	S	S	T	Y	17	end
55	G	H	V	Q	F	V	G	S	Y	16	position
69	N	D	G	E	H	W	T	V	Y	16	for each
323	P	S	G	G	G	G	L	K	K	16	peptide is
353	P	K	S	E	N	N	S	W	Y	16	the start
153	P	Q	G	H	A	S	E	A	Y	15	position
361	Y	V	E	N	G	R	P	A	D	15	plus
385	S	L	E	E	G	L	G	G	K	15	eight.
77	Y	Q	D	E	K	Q	R	K	D	14
354	K	S	E	N	N	S	W	Y	V	14
386	L	E	E	G	L	G	G	K	Q	14
400	K	A	E	N	G	P	H	L	L	14
7	K	T	F	P	L	R	A	L	H	13
21	I	R	D	H	S	G	Q	K	M	13
30	K	Q	D	K	K	V	D	L	L	13
51	A	K	D	F	G	H	V	Q	F	13
68	S	N	D	G	E	H	W	T	V	13
78	Q	D	E	K	Q	R	K	D	K	13
145	K	A	D	G	G	S	C	C	P	13
5	T	T	K	T	F	P	L	R	A	12
17	V	V	E	S	I	R	D	H	S	12
170	P	H	E	V	G	W	K	Y	Q	12
183	T	L	E	E	K	R	K	E	K	12
184	L	E	E	K	R	K	E	K	A	12
191	K	A	E	I	H	Y	R	K	N	12
208	Q	A	E	K	N	M	K	K	K	12
244	A	T	R	A	T	R	I	G	H	12
264	A	H	R	P	P	A	L	S	A	12
301	S	S	T	Y	D	S	L	S	P	12
1	M	L	E	H	T	T	K	T	F	11
4	H	T	T	K	T	F	P	L	R	11
34	K	V	D	L	L	V	P	T	K	11
40	P	T	K	V	T	G	I	I	T	11
216	K	I	D	K	Y	T	E	S	P	11
226	G	G	S	P	R	G	L	G	F	11
279	A	S	P	A	A	W	L	P	L	11
382	A	I	E	S	L	E	E	G	L	11
384	E	S	L	E	E	G	L	G	G	11
394	Q	K	D	K	E	R	K	A	E	11
31	Q	D	K	K	V	D	L	L	V	10
70	D	G	E	H	W	T	V	Y	Q	10
74	W	T	V	Y	Q	D	E	K	Q	10
133	F	Q	V	P	S	R	I	F	W	10
142	R	Q	E	K	A	D	G	G	S	10
291	W	T	R	P	S	S	C	P	T	10
295	S	S	C	P	T	S	S	S	T	10
303	T	Y	D	S	L	S	P	Y	G	10
364	N	G	R	P	A	D	L	A	G	10
373	S	G	Y	C	G	A	L	W	K	10
396	D	K	E	R	K	A	E	N	G	10
82	Q	R	K	D	K	V	L	L	G	9
112	L	K	Y	L	A	F	L	H	K	9
150	S	C	C	P	Q	G	H	A	S	9
160	A	Y	K	K	V	C	L	S	G	9
180	V	T	A	T	L	E	E	K	R	9
182	A	T	L	E	E	K	R	K	E	9
196	Y	R	K	N	K	Q	L	M	R	9
229	P	R	G	L	G	F	I	F	K	9
247	A	T	R	I	G	H	P	G	G	9
300	S	S	S	T	Y	D	S	L	S	9
306	S	L	S	P	Y	G	P	R	N	9
67	Y	S	N	D	G	E	H	W	T	8
222	E	S	P	G	G	G	S	P	R	8
310	Y	G	P	R	N	P	L	P	N	8
322	S	P	S	G	G	G	G	L	K	8
32	D	K	K	V	D	L	L	V	P	7
43	V	T	G	I	I	T	Q	G	A	7
47	I	T	Q	G	A	K	D	F	G	7
96	V	S	C	E	G	I	N	I	S	7
105	G	S	F	C	R	N	K	L	K	7
127	S	R	R	P	Y	H	F	Q	V	7
199	N	K	Q	L	M	R	L	Q	K	7
221	T	E	S	P	G	G	G	S	P	7
236	F	K	T	I	A	P	L	A	A	7
237	K	T	I	A	P	L	A	A	T	7
250	I	G	H	P	G	G	R	T	P	7
256	R	T	P	R	A	G	S	S	A	7
272	A	R	A	P	V	P	A	A	S	7
278	A	A	S	P	A	A	W	L	P	7
288	R	T	P	W	T	R	P	S	S	7
309	P	Y	G	P	R	N	P	L	P	7
321	H	S	P	S	G	G	G	G	L	7
324	S	G	G	G	G	L	K	K	P	7
338	G	Q	K	H	N	V	L	A	R	7
346	R	G	K	P	Q	R	K	P	K	7
372	G	S	G	Y	C	G	A	L	W	7
8	T	F	P	L	R	A	L	H	I	6
10	P	L	R	A	L	H	I	V	V	6
41	T	K	V	T	G	I	I	T	Q	6
54	F	G	H	V	Q	F	V	G	S	6
95	V	V	S	C	E	G	I	N	I	6
109	R	N	K	L	K	Y	L	A	F	6
166	L	S	G	A	P	H	E	V	G	6
167	S	G	A	P	H	E	V	G	W	6
178	Q	A	V	T	A	T	L	E	E	6
227	G	S	P	R	G	L	G	F	I	6
262	S	S	A	H	R	P	P	A	L	6
281	P	A	A	W	L	P	L	R	T	6
283	A	W	L	P	L	R	T	P	W	6
298	P	T	S	S	S	T	Y	D	S	6
307	L	S	P	Y	G	P	R	N	P	6
333	A	R	H	C	Q	G	Q	K	H	6
358	N	S	W	Y	V	E	N	G	R	6
380	W	K	A	I	E	S	L	E	E	6
13	A	L	H	I	V	V	E	S	I	5
23	D	H	S	G	Q	K	M	K	Q	5
35	V	D	L	L	V	P	T	K	V	5
37	L	L	V	P	T	K	V	T	G	5
45	G	I	I	T	Q	G	A	K	D	5
57	V	Q	F	V	G	S	Y	K	L	5
104	S	G	S	F	C	R	N	K	L	5
126	P	S	R	R	P	Y	H	F	Q	5
149	G	S	C	C	P	Q	G	H	A	5
204	R	L	Q	K	Q	A	E	K	N	5
223	S	P	G	G	G	S	P	R	G	5
261	G	S	S	A	H	R	P	P	A	5
263	S	A	H	R	P	P	A	L	S	5
274	A	P	V	P	A	A	S	P	A	5
294	P	S	S	C	P	T	S	S	S	5
305	D	S	L	S	P	Y	G	P	R	5
308	S	P	Y	G	P	R	N	P	L	5
320	R	H	S	P	S	G	G	G	G	5
329	L	K	K	P	A	R	H	C	Q	5
388	E	G	L	G	G	K	Q	K	D	5
15	H	I	V	V	E	S	I	R	D	4
19	E	S	I	R	D	H	S	G	Q	4
24	H	S	G	Q	K	M	K	Q	D	4
27	Q	K	M	K	Q	D	K	K	V	4
61	G	S	Y	K	L	A	Y	S	N	4
87	V	L	L	G	R	K	A	V	V	4
102	N	I	S	G	S	F	C	R	N	4
103	I	S	G	S	F	C	R	N	K	4
128	R	R	P	Y	H	F	Q	V	P	4
131	Y	H	F	Q	V	P	S	R	I	4
135	V	P	S	R	I	F	W	R	Q	4
136	P	S	R	I	F	W	R	Q	E	4
177	Y	Q	A	V	T	A	T	L	E	4
211	K	N	M	K	K	K	I	D	K	4
225	G	G	G	S	P	R	G	L	G	4
228	S	P	R	G	L	G	F	I	F	4
231	G	L	G	F	I	F	K	T	I	4
233	G	F	I	F	K	T	I	A	P	4
238	T	I	A	P	L	A	A	T	R	4
251	G	H	P	G	G	R	T	P	R	4
255	G	R	T	P	R	A	G	S	S	4
265	H	R	P	P	A	L	S	A	R	4
270	L	S	A	R	A	P	V	P	A	4
271	S	A	R	A	P	V	P	A	A	4
280	S	P	A	A	W	L	P	L	R	4
287	L	R	T	P	W	T	R	P	S	4
299	T	S	S	S	T	Y	D	S	L	4
312	P	R	N	P	L	P	N	P	R	4
314	N	P	L	P	N	P	R	H	S	4
316	L	P	N	P	R	H	S	P	S	4
343	V	L	A	R	G	K	P	Q	R	4
345	A	R	G	K	P	Q	R	K	P	4
350	Q	R	K	P	K	S	E	N	N	4
377	G	A	L	W	K	A	I	E	S	4
390	L	G	G	K	Q	K	D	K	E	4
22	R	D	H	S	G	Q	K	M	K	3
36	D	L	L	V	P	T	K	V	T	3
39	V	P	T	K	V	T	G	I	I	3
49	Q	G	A	K	D	F	G	H	V	3
53	D	F	G	H	V	Q	F	V	G	3
56	H	V	Q	F	V	G	S	Y	K	3
58	Q	F	V	G	S	Y	K	L	A	3
63	Y	K	L	A	Y	S	N	D	G	3
85	D	K	V	L	L	G	R	K	A	3
86	K	V	L	L	G	R	K	A	V	3
90	G	R	K	A	V	V	V	S	C	3
91	R	K	A	V	V	V	S	C	E	3
111	K	L	K	Y	L	A	F	L	H	3
114	Y	L	A	F	L	H	K	R	M	3
130	P	Y	H	F	Q	V	P	S	R	3
137	S	R	I	F	W	R	Q	E	K	3
144	E	K	A	D	G	G	S	C	C	3
159	E	A	Y	K	K	V	C	L	S	3
164	V	C	L	S	G	A	P	H	E	3
173	V	G	W	K	Y	Q	A	V	T	3
192	A	E	I	H	Y	R	K	N	K	3
207	K	Q	A	E	K	N	M	K	K	3
209	A	E	K	N	M	K	K	K	I	3
230	R	G	L	G	F	I	F	K	T	3
269	A	L	S	A	R	A	P	V	P	3
315	P	L	P	N	P	R	H	S	P	3
335	H	C	Q	G	Q	K	H	N	V	3
337	Q	G	Q	K	H	N	V	L	A	3
341	H	N	V	L	A	R	G	K	P	3
355	S	E	N	N	S	W	Y	V	E	3
359	S	W	Y	V	E	N	G	R	P	3
363	E	N	G	R	P	A	D	L	A	3
368	A	D	L	A	G	S	G	Y	C	3
369	D	L	A	G	S	G	Y	C	G	3
371	A	G	S	G	Y	C	G	A	L	3
374	G	Y	C	G	A	L	W	K	A	3
387	E	E	G	L	G	G	K	Q	K	3
14	L	H	I	V	V	E	S	I	R	2
20	S	I	R	D	H	S	G	Q	K	2
25	S	G	Q	K	M	K	Q	D	K	2
26	G	Q	K	M	K	Q	D	K	K	2
46	I	I	T	Q	G	A	K	D	F	2
50	G	A	K	D	F	G	H	V	Q	2
52	K	D	F	G	H	V	Q	F	V	2
62	S	Y	K	L	A	Y	S	N	D	2
64	K	L	A	Y	S	N	D	G	E	2
66	A	Y	S	N	D	G	E	H	W	2
72	E	H	W	T	V	Y	Q	D	E	2
79	D	E	K	Q	R	K	D	K	V	2
81	K	Q	R	K	D	K	V	L	L	2
88	L	L	G	R	K	A	V	V	V	2
89	L	G	R	K	A	V	V	V	S	2
92	K	A	V	V	V	S	C	E	G	2
101	I	N	I	S	G	S	F	C	R	2
108	C	R	N	K	L	K	Y	L	A	2
113	K	Y	L	A	F	L	H	K	R	2
116	A	F	L	H	K	R	M	N	T	2
117	F	L	H	K	R	M	N	T	N	2
138	R	I	F	W	R	Q	E	K	A	2
139	I	F	W	R	Q	E	K	A	D	2
146	A	D	G	G	S	C	C	P	Q	2
151	C	C	P	Q	G	H	A	S	E	2
155	G	H	A	S	E	A	Y	K	K	2
156	H	A	S	E	A	Y	K	K	V	2
158	S	E	A	Y	K	K	V	C	L	2
161	Y	K	K	V	C	L	S	G	A	2
165	C	L	S	G	A	P	H	E	V	2
174	G	W	K	Y	Q	A	V	T	A	2
176	K	Y	Q	A	V	T	A	T	L	2
193	E	I	H	Y	R	K	N	K	Q	2
195	H	Y	R	K	N	K	Q	L	M	2
197	R	K	N	K	Q	L	M	R	L	2
198	K	N	K	Q	L	M	R	L	Q	2
200	K	Q	L	M	R	L	Q	K	Q	2
202	L	M	R	L	Q	K	Q	A	E	2
235	I	F	K	T	I	A	P	L	A	2
241	P	L	A	A	T	R	A	T	R	2
249	R	I	G	H	P	G	G	R	T	2
254	G	G	R	T	P	R	A	G	S	2
257	T	P	R	A	G	S	S	A	H	2
282	A	A	W	L	P	L	R	T	P	2
286	P	L	R	T	P	W	T	R	P	2
304	Y	D	S	L	S	P	Y	G	P	2
313	R	N	P	L	P	N	P	R	H	2
328	G	L	K	K	P	A	R	H	C	2
334	R	H	C	Q	G	Q	K	H	N	2
339	Q	K	H	N	V	L	A	R	G	2
347	G	K	P	Q	R	K	P	K	S	2
357	N	N	S	W	Y	V	E	N	G	2
362	V	E	N	G	R	P	A	D	L	2
370	L	A	G	S	G	Y	C	G	A	2
375	Y	C	G	A	L	W	K	A	I	2
378	A	L	W	K	A	I	E	S	L	2
379	L	W	K	A	I	E	S	L	E	2
383	I	E	S	L	E	E	G	L	G	2
389	G	L	G	G	K	Q	K	D	K	2
393	K	Q	K	D	K	E	R	K	A	2
6	T	K	T	F	P	L	R	A	L	1
9	F	P	L	R	A	L	H	I	V	1
11	L	R	A	L	H	I	V	V	E	1
12	R	A	L	H	I	V	V	E	S	1
18	V	E	S	I	R	D	H	S	G	1
28	K	M	K	Q	D	K	K	V	D	1
38	L	V	P	T	K	V	T	G	I	1
42	K	V	T	G	I	I	T	Q	G	1
60	V	G	S	Y	K	L	A	Y	S	1
71	G	E	H	W	T	V	Y	Q	D	1
73	H	W	T	V	Y	Q	D	E	K	1
76	V	Y	Q	D	E	K	Q	R	K	1
80	E	K	Q	R	K	D	K	V	L	1
93	A	V	V	V	S	C	E	G	I	1
94	V	V	V	S	C	E	G	I	N	1
100	G	I	N	I	S	G	S	F	C	1
107	F	C	R	N	K	L	K	Y	L	1
110	N	K	L	K	Y	L	A	F	L	1
115	L	A	F	L	H	K	R	M	N	1
118	L	H	K	R	M	N	T	N	P	1
120	K	R	M	N	T	N	P	S	R	1
122	M	N	T	N	P	S	R	R	P	1
124	T	N	P	S	R	R	P	Y	H	1
132	H	F	Q	V	P	S	R	I	F	1
140	F	W	R	Q	E	K	A	D	G	1
143	Q	E	K	A	D	G	G	S	C	1
152	C	P	Q	G	H	A	S	E	A	1
163	K	V	C	L	S	G	A	P	H	1
168	G	A	P	H	E	V	G	W	K	1
171	H	E	V	G	W	K	Y	Q	A	1
175	W	K	Y	Q	A	V	T	A	T	1
179	A	V	T	A	T	L	E	E	K	1
194	I	H	Y	R	K	N	K	Q	L	1
201	Q	L	M	R	L	Q	K	Q	A	1
206	Q	K	Q	A	E	K	N	M	K	1
224	P	G	G	G	S	P	R	G	L	1
234	F	I	F	K	T	I	A	P	L	1
240	A	P	L	A	A	T	R	A	T	1
243	A	A	T	R	A	T	R	I	G	1
246	R	A	T	R	I	G	H	P	G	1
248	T	R	I	G	H	P	G	G	R	1
252	H	P	G	G	R	T	P	R	A	1
258	P	R	A	G	S	S	A	H	R	1
260	A	G	S	S	A	H	R	P	P	1
268	P	A	L	S	A	R	A	P	V	1
273	R	A	P	V	P	A	A	S	P	1
276	V	P	A	A	S	P	A	A	W	1
277	P	A	A	S	P	A	A	W	L	1
284	W	L	P	L	R	T	P	W	T	1
290	P	W	T	R	P	S	S	C	P	1
311	G	P	R	N	P	L	P	N	P	1
319	P	R	H	S	P	S	G	G	G	1
325	G	G	G	G	L	K	K	P	A	1
336	C	Q	G	Q	K	H	N	V	L	1
342	N	V	L	A	R	G	K	P	Q	1
344	L	A	R	G	K	P	Q	R	K	1
349	P	Q	R	K	P	K	S	E	N	1
352	K	P	K	S	E	N	N	S	W	1
360	W	Y	V	E	N	G	R	P	A	1
398	E	R	K	A	E	N	G	P	H	1
399	R	K	A	E	N	G	P	H	L	1

TABLE XXIII
151P3D4 v.1
HLA Peptide
Scoring Results A*0201 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
4	L	L	L	L	V	L	I	S	I	28	Portion
88	Y	L	K	E	V	D	V	F	V	25	of SEQ
123	S	L	V	I	T	D	L	T	L	25	ID NO:
144	G	L	E	D	D	T	V	V	V	25	3; each
84	L	T	S	D	Y	L	K	E	V	23	start
76	K	I	R	I	K	W	T	K	L	22	position
151	V	V	A	L	D	L	Q	G	V	22	is
3	S	L	L	L	L	V	L	I	S	20	specified,
51	S	H	R	G	G	N	V	T	L	20	the length
159	V	V	F	P	Y	F	P	R	L	20	of
263	Y	L	I	H	P	T	K	L	T	20	peptide is
5	L	L	L	V	L	I	S	I	C	19	9 amino
41	L	V	E	A	E	Q	A	K	V	19	acids, the
69	A	F	G	S	G	I	H	K	I	19	end
137	Y	K	C	E	V	I	E	G	L	19	position
152	V	A	L	D	L	Q	G	V	V	19	for each
2	K	S	L	L	L	L	V	L	I	18	peptide is
22	Y	T	L	D	H	D	R	A	I	18	the start
186	A	V	I	A	S	F	D	Q	L	18	position
279	C	L	N	D	G	A	Q	I	A	18	plus
281	N	D	G	A	Q	I	A	K	V	18	eight.
291	Q	I	F	A	A	W	K	I	L	18
32	I	Q	A	E	N	G	P	H	L	17
34	A	E	N	G	P	H	L	L	V	17
121	D	A	S	L	V	I	T	D	L	17
227	G	G	Q	N	T	V	P	G	V	17
284	A	Q	I	A	K	V	G	Q	I	17
308	W	L	A	D	G	S	V	R	Y	17
1	M	K	S	L	L	L	L	V	L	16
7	L	V	L	I	S	I	C	W	A	16
33	Q	A	E	N	G	P	H	L	L	16
39	H	L	L	V	E	A	E	Q	A	16
86	S	D	Y	L	K	E	V	D	V	16
106	G	G	Y	Q	G	R	V	F	L	16
113	F	L	K	G	G	S	D	S	D	16
116	G	G	S	D	S	D	A	S	L	16
181	C	L	D	Q	D	A	V	I	A	16
262	Y	Y	L	I	H	P	T	K	L	16
336	G	F	P	D	K	K	H	K	L	16
40	L	L	V	E	A	E	Q	A	K	15
125	V	I	T	D	L	T	L	E	D	15
141	V	I	E	G	L	E	D	D	T	15
155	D	L	Q	G	V	V	F	P	Y	15
179	Q	A	C	L	D	Q	D	A	V	15
180	A	C	L	D	Q	D	A	V	I	15
207	A	G	W	L	S	D	G	S	V	15
209	W	L	S	D	G	S	V	Q	Y	15
264	L	I	H	P	T	K	L	T	Y	15
298	I	L	G	Y	D	R	C	D	A	15
306	A	G	W	L	A	D	G	S	V	15
324	R	C	S	P	T	E	A	A	V	15
339	D	K	K	H	K	L	Y	G	V	15
8	V	L	I	S	I	C	W	A	D	14
10	I	S	I	C	W	A	D	H	L	14
16	D	H	L	S	D	N	Y	T	L	14
142	I	E	G	L	E	D	D	T	V	14
146	E	D	D	T	V	V	V	A	L	14
148	D	T	V	V	V	A	L	D	L	14
153	A	L	D	L	Q	G	V	V	F	14
164	F	P	R	L	G	R	Y	N	L	14
201	G	L	D	W	C	N	A	G	W	14
224	E	P	C	G	G	Q	N	T	V	14
256	N	F	N	G	R	F	Y	Y	L	14
268	T	K	L	T	Y	D	E	A	V	14
270	L	T	Y	D	E	A	V	Q	A	14
278	A	C	L	N	D	G	A	Q	I	14
293	F	A	A	W	K	I	L	G	Y	14
297	K	I	L	G	Y	D	R	C	D	14
327	P	T	E	A	A	V	R	F	V	14
343	K	L	Y	G	V	Y	C	F	R	14
36	N	G	P	H	L	L	V	E	A	13
81	W	T	K	L	T	S	D	Y	L	13
83	K	L	T	S	D	Y	L	K	E	13
104	T	Y	G	G	Y	Q	G	R	V	13
145	L	E	D	D	T	V	V	V	A	13
189	A	S	F	D	Q	L	Y	D	A	13
193	Q	L	Y	D	A	W	R	G	G	13
194	L	Y	D	A	W	R	G	G	L	13
202	L	D	W	C	N	A	G	W	L	13
272	Y	D	E	A	V	Q	A	C	L	13
287	A	K	V	G	Q	I	F	A	A	13
6	L	L	V	L	I	S	I	C	W	12
9	L	I	S	I	C	W	A	D	H	12
23	T	L	D	H	D	R	A	I	H	12
58	T	L	P	C	K	F	Y	R	D	12
118	S	D	S	D	A	S	L	V	I	12
124	L	V	I	T	D	L	T	L	E	12
133	D	Y	G	R	Y	K	C	E	V	12
154	L	D	L	Q	G	V	V	F	P	12
166	R	L	G	R	Y	N	L	N	F	12
171	N	L	N	F	H	E	A	Q	Q	12
174	F	H	E	A	Q	Q	A	C	L	12
187	V	I	A	S	F	D	Q	L	Y	12
214	S	V	Q	Y	P	I	T	K	P	12
230	N	T	V	P	G	V	R	N	Y	12
290	G	Q	I	F	A	A	W	K	I	12
301	Y	D	R	C	D	A	G	W	L	12
309	L	A	D	G	S	V	R	Y	P	12
11	S	I	C	W	A	D	H	L	S	11
17	H	L	S	D	N	Y	T	L	D	11
24	L	D	H	D	R	A	I	H	I	11
49	V	F	S	H	R	G	G	N	V	11
73	G	I	H	K	I	R	I	K	W	11
103	K	T	Y	G	G	Y	Q	G	R	11
117	G	S	D	S	D	A	S	L	V	11
120	S	D	A	S	L	V	I	T	D	11
130	T	L	E	D	Y	G	R	Y	K	11
140	E	V	I	E	G	L	E	D	D	11
143	E	G	L	E	D	D	T	V	V	11
211	S	D	G	S	V	Q	Y	P	I	11
257	F	N	G	R	F	Y	Y	L	I	11
269	K	L	T	Y	D	E	A	V	Q	11
275	A	V	Q	A	C	L	N	D	G	11
286	I	A	K	V	G	Q	I	F	A	11
294	A	A	W	K	I	L	G	Y	D	11
310	A	D	G	S	V	R	Y	P	I	11
330	A	A	V	R	F	V	G	F	P	11
28	R	A	I	H	I	Q	A	E	N	10
29	A	I	H	I	Q	A	E	N	G	10
78	R	I	K	W	T	K	L	T	S	10
79	I	K	W	T	K	L	T	S	D	10
90	K	E	V	D	V	F	V	S	M	10
95	F	V	S	M	G	Y	H	K	K	10
96	V	S	M	G	Y	H	K	K	T	10
97	S	M	G	Y	H	K	K	T	Y	10
122	A	S	L	V	I	T	D	L	T	10
126	I	T	D	L	T	L	E	D	Y	10
128	D	L	T	L	E	D	Y	G	R	10
129	L	T	L	E	D	Y	G	R	Y	10
134	Y	G	R	Y	K	C	E	V	I	10
197	A	W	R	G	G	L	D	W	C	10
242	D	K	D	K	S	R	Y	D	V	10
260	R	F	Y	Y	L	I	H	P	T	10
285	Q	I	A	K	V	G	Q	I	F	10
304	C	D	A	G	W	L	A	D	G	10
313	S	V	R	Y	P	I	S	R	P	10
44	A	E	Q	A	K	V	F	S	H	9
57	V	T	L	P	C	K	F	Y	R	9
71	G	S	G	I	H	K	I	R	I	9
72	S	G	I	H	K	I	R	I	K	9
77	I	R	I	K	W	T	K	L	T	9
119	D	S	D	A	S	L	V	I	T	9
276	V	Q	A	C	L	N	D	G	A	9
346	G	V	Y	C	F	R	A	Y	N	9
31	H	I	Q	A	E	N	G	P	H	8
50	F	S	H	R	G	G	N	V	T	8
66	D	P	T	A	F	G	S	G	I	8
74	I	H	K	I	R	I	K	W	T	8
111	R	V	F	L	K	G	G	S	D	8
114	L	K	G	G	S	D	S	D	A	8
149	T	V	V	V	A	L	D	L	Q	8
169	R	Y	N	L	N	F	H	E	A	8
182	L	D	Q	D	A	V	I	A	S	8
205	C	N	A	G	W	L	S	D	G	8
210	L	S	D	G	S	V	Q	Y	P	8
219	I	T	K	P	R	E	P	C	G	8
246	S	R	Y	D	V	F	C	F	T	8
283	G	A	Q	I	A	K	V	G	Q	8
288	K	V	G	Q	I	F	A	A	W	8
323	R	R	C	S	P	T	E	A	A	8
342	H	K	L	Y	G	V	Y	C	F	8
13	C	W	A	D	H	L	S	D	N	7
15	A	D	H	L	S	D	N	Y	T	7
37	G	P	H	L	L	V	E	A	E	7
48	K	V	F	S	H	R	G	G	N	7
54	G	G	N	V	T	L	P	C	K	7
61	C	K	F	Y	R	D	P	T	A	7
63	F	Y	R	D	P	T	A	F	G	7
68	T	A	F	G	S	G	I	H	K	7
107	G	Y	Q	G	R	V	F	L	K	7
150	V	V	V	A	L	D	L	Q	G	7
172	L	N	F	H	E	A	Q	Q	A	7
178	Q	Q	A	C	L	D	Q	D	A	7
183	D	Q	D	A	V	I	A	S	F	7
196	D	A	W	R	G	G	L	D	W	7
217	Y	P	I	T	K	P	R	E	P	7
231	T	V	P	G	V	R	N	Y	G	7
249	D	V	F	C	F	T	S	N	F	7
265	I	H	P	T	K	L	T	Y	D	7
271	T	Y	D	E	A	V	Q	A	C	7
344	L	Y	G	V	Y	C	F	R	A	7
12	I	C	W	A	D	H	L	S	D	6
18	L	S	D	N	Y	T	L	D	H	6
19	S	D	N	Y	T	L	D	H	D	6
27	D	R	A	I	H	I	Q	A	E	6
30	I	H	I	Q	A	E	N	G	P	6
52	H	R	G	G	N	V	T	L	P	6
91	E	V	D	V	F	V	S	M	G	6
99	G	Y	H	K	K	T	Y	G	G	6
131	L	E	D	Y	G	R	Y	K	C	6
167	L	G	R	Y	N	L	N	F	H	6
170	Y	N	L	N	F	H	E	A	Q	6
177	A	Q	Q	A	C	L	D	Q	D	6
188	I	A	S	F	D	Q	L	Y	D	6
200	G	G	L	D	W	C	N	A	G	6
204	W	C	N	A	G	W	L	S	D	6
206	N	A	G	W	L	S	D	G	S	6
223	R	E	P	C	G	G	Q	N	T	6
234	G	V	R	N	Y	G	F	W	D	6
236	R	N	Y	G	F	W	D	K	D	6
253	F	T	S	N	F	N	G	R	F	6
259	G	R	F	Y	Y	L	I	H	P	6
267	P	T	K	L	T	Y	D	E	A	6
317	P	I	S	R	P	R	R	R	C	6
322	R	R	R	C	S	P	T	E	A	6
329	E	A	A	V	R	F	V	G	F	6
334	F	V	G	F	P	D	K	K	H	6
14	W	A	D	H	L	S	D	N	Y	5
46	Q	A	K	V	F	S	H	R	G	5
64	Y	R	D	P	T	A	F	G	S	5
87	D	Y	L	K	E	V	D	V	F	5
89	L	K	E	V	D	V	F	V	S	5
108	Y	Q	G	R	V	F	L	K	G	5
109	Q	G	R	V	F	L	K	G	G	5
112	V	F	L	K	G	G	S	D	S	5
136	R	Y	K	C	E	V	I	E	G	5
158	G	V	V	F	P	Y	F	P	R	5
215	V	Q	Y	P	I	T	K	P	R	5
218	P	I	T	K	P	R	E	P	C	5
221	K	P	R	E	P	C	G	G	Q	5
238	Y	G	F	W	D	K	D	K	S	5
239	G	F	W	D	K	D	K	S	R	5
255	S	N	F	N	G	R	F	Y	Y	5
261	F	Y	Y	L	I	H	P	T	K	5
277	Q	A	C	L	N	D	G	A	Q	5
280	L	N	D	G	A	Q	I	A	K	5
299	L	G	Y	D	R	C	D	A	G	5
305	D	A	G	W	L	A	D	G	S	5
326	S	P	T	E	A	A	V	R	F	5
331	A	V	R	F	V	G	F	P	D	5
332	V	R	F	V	G	F	P	D	K	5
333	R	F	V	G	F	P	D	K	K	5
25	D	H	D	R	A	I	H	I	Q	4
26	H	D	R	A	I	H	I	Q	A	4
35	E	N	G	P	H	L	L	V	E	4
42	V	E	A	E	Q	A	K	V	F	4
55	G	N	V	T	L	P	C	K	F	4
67	P	T	A	F	G	S	G	I	H	4
75	H	K	I	R	I	K	W	T	K	4
93	D	V	F	V	S	M	G	Y	H	4
135	G	R	Y	K	C	E	V	I	E	4
147	D	D	T	V	V	V	A	L	D	4
161	F	P	Y	F	P	R	L	G	R	4
162	P	Y	F	P	R	L	G	R	Y	4
190	S	F	D	Q	L	Y	D	A	W	4
191	F	D	Q	L	Y	D	A	W	R	4
195	Y	D	A	W	R	G	G	L	D	4
199	R	G	G	L	D	W	C	N	A	4
212	D	G	S	V	Q	Y	P	I	T	4
213	G	S	V	Q	Y	P	I	T	K	4
226	C	G	G	Q	N	T	V	P	G	4
245	K	S	R	Y	D	V	F	C	F	4
289	V	G	Q	I	F	A	A	W	K	4
292	I	F	A	A	W	K	I	L	G	4
296	W	K	I	L	G	Y	D	R	C	4
300	G	Y	D	R	C	D	A	G	W	4
302	D	R	C	D	A	G	W	L	A	4
303	R	C	D	A	G	W	L	A	D	4
312	G	S	V	R	Y	P	I	S	R	4
314	V	R	Y	P	I	S	R	P	R	4
316	Y	P	I	S	R	P	R	R	R	4
318	I	S	R	P	R	R	R	C	S	4
319	S	R	P	R	R	R	C	S	P	4
320	R	P	R	R	R	C	S	P	T	4
21	N	Y	T	L	D	H	D	R	A	3
38	P	H	L	L	V	E	A	E	Q	3
53	R	G	G	N	V	T	L	P	C	3
56	N	V	T	L	P	C	K	F	Y	3
59	L	P	C	K	F	Y	R	D	P	3
62	K	F	Y	R	D	P	T	A	F	3
80	K	W	T	K	L	T	S	D	Y	3
82	T	K	L	T	S	D	Y	L	K	3
127	T	D	L	T	L	E	D	Y	G	3
139	C	E	V	I	E	G	L	E	D	3
156	L	Q	G	V	V	F	P	Y	F	3
163	Y	F	P	R	L	G	R	Y	N	3
168	G	R	Y	N	L	N	F	H	E	3
173	N	F	H	E	A	Q	Q	A	C	3
185	D	A	V	I	A	S	F	D	Q	3
198	W	R	G	G	L	D	W	C	N	3
208	G	W	L	S	D	G	S	V	Q	3
232	V	P	G	V	R	N	Y	G	F	3
235	V	R	N	Y	G	F	W	D	K	3
247	R	Y	D	V	F	C	F	T	S	3
248	Y	D	V	F	C	F	T	S	N	3
266	H	P	T	K	L	T	Y	D	E	3
295	A	W	K	I	L	G	Y	D	R	3
307	G	W	L	A	D	G	S	V	R	3
335	V	G	F	P	D	K	K	H	K	3
341	K	H	K	L	Y	G	V	Y	C	3
20	D	N	Y	T	L	D	H	D	R	2
43	E	A	E	Q	A	K	V	F	S	2
47	A	K	V	F	S	H	R	G	G	2
65	R	D	P	T	A	F	G	S	G	2
70	F	G	S	G	I	H	K	I	R	2
94	V	F	V	S	M	G	Y	H	K	2
98	M	G	Y	H	K	K	T	Y	G	2
100	Y	H	K	K	T	Y	G	G	Y	2
102	K	K	T	Y	G	G	Y	Q	G	2
110	G	R	V	F	L	K	G	G	S	2
115	K	G	G	S	D	S	D	A	S	2
157	Q	G	V	V	F	P	Y	F	P	2
165	P	R	L	G	R	Y	N	L	N	2
175	H	E	A	Q	Q	A	C	L	D	2
176	E	A	Q	Q	A	C	L	D	Q	2
184	Q	D	A	V	I	A	S	F	D	2
228	G	Q	N	T	V	P	G	V	R	2
229	Q	N	T	V	P	G	V	R	N	2
244	D	K	S	R	Y	D	V	F	C	2
251	F	C	F	T	S	N	F	N	G	2
274	E	A	V	Q	A	C	L	N	D	2
325	C	S	P	T	E	A	A	V	R	2
328	T	E	A	A	V	R	F	V	G	2
340	K	K	H	K	L	Y	G	V	Y	2
345	Y	G	V	Y	C	F	R	A	Y	2
92	V	D	V	F	V	S	M	G	Y	1
105	Y	G	G	Y	Q	G	R	V	F	1
160	V	F	P	Y	F	P	R	L	G	1
216	Q	Y	P	I	T	K	P	R	E	1
220	T	K	P	R	E	P	C	G	G	1
240	F	W	D	K	D	K	S	R	Y	1
241	W	D	K	D	K	S	R	Y	D	1
250	V	F	C	F	T	S	N	F	N	1
252	C	F	T	S	N	F	N	G	R	1
258	N	G	R	F	Y	Y	L	I	H	1
273	D	E	A	V	Q	A	C	L	N	1
315	R	Y	P	I	S	R	P	R	R	1
337	F	P	D	K	K	H	K	L	Y	1
45	E	Q	A	K	V	F	S	H	R	−1
132	E	D	Y	G	R	Y	K	C	E	−1
203	D	W	C	N	A	G	W	L	S	−1
225	P	C	G	G	Q	N	T	V	P	−1
222	P	R	E	P	C	G	G	Q	N	−2
237	N	Y	G	F	W	D	K	D	K	−2
233	P	G	V	R	N	Y	G	F	W	−3
338	P	D	K	K	H	K	L	Y	G	−3
151P3D4 v.2
HLA Peptide
Scoring Results A*0201 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
378	A	L	W	K	A	I	E	S	L	29	Portion of
87	V	L	L	G	R	K	A	V	V	27	SEQ ID
13	A	L	H	I	V	V	E	S	I	26	NO: 5;
234	F	I	F	K	T	I	A	P	L	26	each start
88	L	L	G	R	K	A	V	V	V	25	position
165	C	L	S	G	A	P	H	E	V	25	is
382	A	I	E	S	L	E	E	G	L	21	specified,
38	L	V	P	T	K	V	T	G	I	20	the length
385	S	L	E	E	G	L	G	G	K	20	of peptide
86	K	V	L	L	G	R	K	A	V	19	is 9
110	N	K	L	K	Y	L	A	F	L	19	amino
231	G	L	G	F	I	F	K	T	I	19	acids, the
237	K	T	I	A	P	L	A	A	T	19	end
9	F	P	L	R	A	L	H	I	V	18	position
10	P	L	R	A	L	H	I	V	V	18	for each
37	L	L	V	P	T	K	V	T	G	18	peptide is
52	K	D	F	G	H	V	Q	F	V	18	the start
36	D	L	L	V	P	T	K	V	T	17	position
57	V	Q	F	V	G	S	Y	K	L	17	plus
114	Y	L	A	F	L	H	K	R	M	17	eight.
156	H	A	S	E	A	Y	K	K	V	17
176	K	Y	Q	A	V	T	A	T	L	17
238	T	I	A	P	L	A	A	T	R	17
271	S	A	R	A	P	V	P	A	A	17
284	W	L	P	L	R	T	P	W	T	17
308	S	P	Y	G	P	R	N	P	L	17
400	K	A	E	N	G	P	H	L	L	17
30	K	Q	D	K	K	V	D	L	L	16
68	S	N	D	G	E	H	W	T	V	16
158	S	E	A	Y	K	K	V	C	L	16
242	L	A	A	T	R	A	T	R	I	16
262	S	S	A	H	R	P	P	A	L	16
277	P	A	A	S	P	A	A	W	L	16
306	S	L	S	P	Y	G	P	R	N	16
343	V	L	A	R	G	K	P	Q	R	16
362	V	E	N	G	R	P	A	D	L	16
371	A	G	S	G	Y	C	G	A	L	16
35	V	D	L	L	V	P	T	K	V	15
45	G	I	I	T	Q	G	A	K	D	15
93	A	V	V	V	S	C	E	G	I	15
107	F	C	R	N	K	L	K	Y	L	15
127	S	R	R	P	Y	H	F	Q	V	15
138	R	I	F	W	R	Q	E	K	A	15
197	R	K	N	K	Q	L	M	R	L	15
201	Q	L	M	R	L	Q	K	Q	A	15
227	G	S	P	R	G	L	G	F	I	15
230	R	G	L	G	F	I	F	K	T	15
268	P	A	L	S	A	R	A	P	V	15
381	K	A	I	E	S	L	E	E	G	15
399	R	K	A	E	N	G	P	H	L	15
6	T	K	T	F	P	L	R	A	L	14
12	R	A	L	H	I	V	V	E	S	14
29	M	K	Q	D	K	K	V	D	L	14
104	S	G	S	F	C	R	N	K	L	14
117	F	L	H	K	R	M	N	T	N	14
212	N	M	K	K	K	I	D	K	Y	14
216	K	I	D	K	Y	T	E	S	P	14
282	A	A	W	L	P	L	R	T	P	14
369	D	L	A	G	S	G	Y	C	G	14
33	K	K	V	D	L	L	V	P	T	13
34	K	V	D	L	L	V	P	T	K	13
64	K	L	A	Y	S	N	D	G	E	13
81	K	Q	R	K	D	K	V	L	L	13
95	V	V	S	C	E	G	I	N	I	13
172	E	V	G	W	K	Y	Q	A	V	13
183	T	L	E	E	K	R	K	E	K	13
194	I	H	Y	R	K	N	K	Q	L	13
241	P	L	A	A	T	R	A	T	R	13
249	R	I	G	H	P	G	G	R	T	13
269	A	L	S	A	R	A	P	V	P	13
279	A	S	P	A	A	W	L	P	L	13
321	H	S	P	S	G	G	G	G	L	13
335	H	C	Q	G	Q	K	H	N	V	13
370	L	A	G	S	G	Y	C	G	A	13
374	G	Y	C	G	A	L	W	K	A	13
389	G	L	G	G	K	Q	K	D	K	13
1	M	L	E	H	T	T	K	T	F	12
16	I	V	V	E	S	I	R	D	H	12
27	Q	K	M	K	Q	D	K	K	V	12
43	V	T	G	I	I	T	Q	G	A	12
49	Q	G	A	K	D	F	G	H	V	12
182	A	T	L	E	E	K	R	K	E	12
204	R	L	Q	K	Q	A	E	K	N	12
264	A	H	R	P	P	A	L	S	A	12
299	T	S	S	S	T	Y	D	S	L	12
302	S	T	Y	D	S	L	S	P	Y	12
336	C	Q	G	Q	K	H	N	V	L	12
7	K	T	F	P	L	R	A	L	H	11
20	S	I	R	D	H	S	G	Q	K	11
67	Y	S	N	D	G	E	H	W	T	11
113	K	Y	L	A	F	L	H	K	R	11
131	Y	H	F	Q	V	P	S	R	I	11
179	A	V	T	A	T	L	E	E	K	11
202	L	M	R	L	Q	K	Q	A	E	11
240	A	P	L	A	A	T	R	A	T	11
315	P	L	P	N	P	R	H	S	P	11
324	S	G	G	G	G	L	K	K	P	11
328	G	L	K	K	P	A	R	H	C	11
375	Y	C	G	A	L	W	K	A	I	11
11	L	R	A	L	H	I	V	V	E	10
31	Q	D	K	K	V	D	L	L	V	10
39	V	P	T	K	V	T	G	I	I	10
42	K	V	T	G	I	I	T	Q	G	10
46	I	I	T	Q	G	A	K	D	F	10
79	D	E	K	Q	R	K	D	K	V	10
96	V	S	C	E	G	I	N	I	S	10
100	G	I	N	I	S	G	S	F	C	10
102	N	I	S	G	S	F	C	R	N	10
111	K	L	K	Y	L	A	F	L	H	10
161	Y	K	K	V	C	L	S	G	A	10
175	W	K	Y	Q	A	V	T	A	T	10
180	V	T	A	T	L	E	E	K	R	10
209	A	E	K	N	M	K	K	K	I	10
224	P	G	G	G	S	P	R	G	L	10
239	I	A	P	L	A	A	T	R	A	10
247	A	T	R	I	G	H	P	G	G	10
256	R	T	P	R	A	G	S	S	A	10
270	L	S	A	R	A	P	V	P	A	10
291	W	T	R	P	S	S	C	P	T	10
295	S	S	C	P	T	S	S	S	T	10
354	K	S	E	N	N	S	W	Y	V	10
377	G	A	L	W	K	A	I	E	S	10
3	E	H	T	T	K	T	F	P	L	9
5	T	T	K	T	F	P	L	R	A	9
8	T	F	P	L	R	A	L	H	I	9
65	L	A	Y	S	N	D	G	E	H	9
116	A	F	L	H	K	R	M	N	T	9
121	R	M	N	T	N	P	S	R	R	9
145	K	A	D	G	G	S	C	C	P	9
167	S	G	A	P	H	E	V	G	W	9
168	G	A	P	H	E	V	G	W	K	9
173	V	G	W	K	Y	Q	A	V	T	9
178	Q	A	V	T	A	T	L	E	E	9
186	E	K	R	K	E	K	A	E	I	9
200	K	Q	L	M	R	L	Q	K	Q	9
252	H	P	G	G	R	T	P	R	A	9
263	S	A	H	R	P	P	A	L	S	9
272	A	R	A	P	V	P	A	A	S	9
273	R	A	P	V	P	A	A	S	P	9
280	S	P	A	A	W	L	P	L	R	9
281	P	A	A	W	L	P	L	R	T	9
344	L	A	R	G	K	P	Q	R	K	9
361	Y	V	E	N	G	R	P	A	D	9
15	H	I	V	V	E	S	I	R	D	8
21	I	R	D	H	S	G	Q	K	M	8
41	T	K	V	T	G	I	I	T	Q	8
47	I	T	Q	G	A	K	D	F	G	8
55	G	H	V	Q	F	V	G	S	Y	8
59	F	V	G	S	Y	K	L	A	Y	8
89	L	G	R	K	A	V	V	V	S	8
90	G	R	K	A	V	V	V	S	C	8
134	Q	V	P	S	R	I	F	W	R	8
152	C	P	Q	G	H	A	S	E	A	8
207	K	Q	A	E	K	N	M	K	K	8
232	L	G	F	I	F	K	T	I	A	8
250	I	G	H	P	G	G	R	T	P	8
274	A	P	V	P	A	A	S	P	A	8
278	A	A	S	P	A	A	W	L	P	8
286	P	L	R	T	P	W	T	R	P	8
365	G	R	P	A	D	L	A	G	S	8
393	K	Q	K	D	K	E	R	K	A	8
28	K	M	K	Q	D	K	K	V	D	7
50	G	A	K	D	F	G	H	V	Q	7
60	V	G	S	Y	K	L	A	Y	S	7
77	Y	Q	D	E	K	Q	R	K	D	7
80	E	K	Q	R	K	D	K	V	L	7
92	K	A	V	V	V	S	C	E	G	7
108	C	R	N	K	L	K	Y	L	A	7
115	L	A	F	L	H	K	R	M	N	7
123	N	T	N	P	S	R	R	P	Y	7
159	E	A	Y	K	K	V	C	L	S	7
163	K	V	C	L	S	G	A	P	H	7
171	H	E	V	G	W	K	Y	Q	A	7
174	G	W	K	Y	Q	A	V	T	A	7
184	L	E	E	K	R	K	E	K	A	7
193	E	I	H	Y	R	K	N	K	Q	7
203	M	R	L	Q	K	Q	A	E	K	7
215	K	K	I	D	K	Y	T	E	S	7
220	Y	T	E	S	P	G	G	G	S	7
223	S	P	G	G	G	S	P	R	G	7
243	A	A	T	R	A	T	R	I	G	7
244	A	T	R	A	T	R	I	G	H	7
265	H	R	P	P	A	L	S	A	R	7
266	R	P	P	A	L	S	A	R	A	7
275	P	V	P	A	A	S	P	A	A	7
283	A	W	L	P	L	R	T	P	W	7
288	R	T	P	W	T	R	P	S	S	7
311	G	P	R	N	P	L	P	N	P	7
325	G	G	G	G	L	K	K	P	A	7
61	G	S	Y	K	L	A	Y	S	N	6
63	Y	K	L	A	Y	S	N	D	G	6
71	G	E	H	W	T	V	Y	Q	D	6
82	Q	R	K	D	K	V	L	L	G	6
83	R	K	D	K	V	L	L	G	R	6
85	D	K	V	L	L	G	R	K	A	6
91	R	K	A	V	V	V	S	C	E	6
101	I	N	I	S	G	S	F	C	R	6
149	G	S	C	C	P	Q	G	H	A	6
150	S	C	C	P	Q	G	H	A	S	6
151	C	C	P	Q	G	H	A	S	E	6
155	G	H	A	S	E	A	Y	K	K	6
164	V	C	L	S	G	A	P	H	E	6
169	A	P	H	E	V	G	W	K	Y	6
191	K	A	E	I	H	Y	R	K	N	6
221	T	E	S	P	G	G	G	S	P	6
233	G	F	I	F	K	T	I	A	P	6
235	I	F	K	T	I	A	P	L	A	6
236	F	K	T	I	A	P	L	A	A	6
245	T	R	A	T	R	I	G	H	P	6
261	G	S	S	A	H	R	P	P	A	6
276	V	P	A	A	S	P	A	A	W	6
285	L	P	L	R	T	P	W	T	R	6
322	S	P	S	G	G	G	G	L	K	6
327	G	G	L	K	K	P	A	R	H	6
337	Q	G	Q	K	H	N	V	L	A	6
338	G	Q	K	H	N	V	L	A	R	6
339	Q	K	H	N	V	L	A	R	G	6
360	W	Y	V	E	N	G	R	P	A	6
366	R	P	A	D	L	A	G	S	G	6
368	A	D	L	A	G	S	G	Y	C	6
373	S	G	Y	C	G	A	L	W	K	6
386	L	E	E	G	L	G	G	K	Q	6
395	K	D	K	E	R	K	A	E	N	6
51	A	K	D	F	G	H	V	Q	F	5
58	Q	F	V	G	S	Y	K	L	A	5
74	W	T	V	Y	Q	D	E	K	Q	5
84	K	D	K	V	L	L	G	R	K	5
94	V	V	V	S	C	E	G	I	N	5
97	S	C	E	G	I	N	I	S	G	5
98	C	E	G	I	N	I	S	G	S	5
106	S	F	C	R	N	K	L	K	Y	5
120	K	R	M	N	T	N	P	S	R	5
137	S	R	I	F	W	R	Q	E	K	5
189	K	E	K	A	E	I	H	Y	R	5
226	G	G	S	P	R	G	L	G	F	5
228	S	P	R	G	L	G	F	I	F	5
248	T	R	I	G	H	P	G	G	R	5
251	G	H	P	G	G	R	T	P	R	5
254	G	G	R	T	P	R	A	G	S	5
259	R	A	G	S	S	A	H	R	P	5
287	L	R	T	P	W	T	R	P	S	5
316	L	P	N	P	R	H	S	P	S	5
342	N	V	L	A	R	G	K	P	Q	5
345	A	R	G	K	P	Q	R	K	P	5
357	N	N	S	W	Y	V	E	N	G	5
380	W	K	A	I	E	S	L	E	E	5
388	E	G	L	G	G	K	Q	K	D	5
4	H	T	T	K	T	F	P	L	R	4
14	L	H	I	V	V	E	S	I	R	4
17	V	V	E	S	I	R	D	H	S	4
18	V	E	S	I	R	D	H	S	G	4
40	P	T	K	V	T	G	I	I	T	4
54	F	G	H	V	Q	F	V	G	S	4
75	T	V	Y	Q	D	E	K	Q	R	4
112	L	K	Y	L	A	F	L	H	K	4
129	R	P	Y	H	F	Q	V	P	S	4
141	W	R	Q	E	K	A	D	G	G	4
146	A	D	G	G	S	C	C	P	Q	4
160	A	Y	K	K	V	C	L	S	G	4
177	Y	Q	A	V	T	A	T	L	E	4
192	A	E	I	H	Y	R	K	N	K	4
195	H	Y	R	K	N	K	Q	L	M	4
205	L	Q	K	Q	A	E	K	N	M	4
208	Q	A	E	K	N	M	K	K	K	4
246	R	A	T	R	I	G	H	P	G	4
255	G	R	T	P	R	A	G	S	S	4
296	S	C	P	T	S	S	S	T	Y	4
298	P	T	S	S	S	T	Y	D	S	4
304	Y	D	S	L	S	P	Y	G	P	4
314	N	P	L	P	N	P	R	H	S	4
323	P	S	G	G	G	G	L	K	K	4
326	G	G	G	L	K	K	P	A	R	4
329	L	K	K	P	A	R	H	C	Q	4
331	K	P	A	R	H	C	Q	G	Q	4
333	A	R	H	C	Q	G	Q	K	H	4
340	K	H	N	V	L	A	R	G	K	4
347	G	K	P	Q	R	K	P	K	S	4
355	S	E	N	N	S	W	Y	V	E	4
364	N	G	R	P	A	D	L	A	G	4
376	C	G	A	L	W	K	A	I	E	4
390	L	G	G	K	Q	K	D	K	E	4
23	D	H	S	G	Q	K	M	K	Q	3
26	G	Q	K	M	K	Q	D	K	K	3
32	D	K	K	V	D	L	L	V	P	3
44	T	G	I	I	T	Q	G	A	K	3
56	H	V	Q	F	V	G	S	Y	K	3
103	I	S	G	S	F	C	R	N	K	3
119	H	K	R	M	N	T	N	P	S	3
130	P	Y	H	F	Q	V	P	S	R	3
133	F	Q	V	P	S	R	I	F	W	3
139	I	F	W	R	Q	E	K	A	D	3
140	F	W	R	Q	E	K	A	D	G	3
162	K	K	V	C	L	S	G	A	P	3
166	L	S	G	A	P	H	E	V	G	3
187	K	R	K	E	K	A	E	I	H	3
196	Y	R	K	N	K	Q	L	M	R	3
211	K	N	M	K	K	K	I	D	K	3
214	K	K	K	I	D	K	Y	T	E	3
219	K	Y	T	E	S	P	G	G	G	3
257	T	P	R	A	G	S	S	A	H	3
258	P	R	A	G	S	S	A	H	R	3
289	T	P	W	T	R	P	S	S	C	3
292	T	R	P	S	S	C	P	T	S	3
300	S	S	S	T	Y	D	S	L	S	3
301	S	S	T	Y	D	S	L	S	P	3
307	L	S	P	Y	G	P	R	N	P	3
310	Y	G	P	R	N	P	L	P	N	3
320	R	H	S	P	S	G	G	G	G	3
348	K	P	Q	R	K	P	K	S	E	3
352	K	P	K	S	E	N	N	S	W	3
359	S	W	Y	V	E	N	G	R	P	3
384	E	S	L	E	E	G	L	G	G	3
397	K	E	R	K	A	E	N	G	P	3
2	L	E	H	T	T	K	T	F	P	2
25	S	G	Q	K	M	K	Q	D	K	2
48	T	Q	G	A	K	D	F	G	H	2
66	A	Y	S	N	D	G	E	H	W	2
69	N	D	G	E	H	W	T	V	Y	2
70	D	G	E	H	W	T	V	Y	Q	2
73	H	W	T	V	Y	Q	D	E	K	2
76	V	Y	Q	D	E	K	Q	R	K	2
109	R	N	K	L	K	Y	L	A	F	2
144	E	K	A	D	G	G	S	C	C	2
148	G	G	S	C	C	P	Q	G	H	2
154	Q	G	H	A	S	E	A	Y	K	2
181	T	A	T	L	E	E	K	R	K	2
190	E	K	A	E	I	H	Y	R	K	2
213	M	K	K	K	I	D	K	Y	T	2
218	D	K	Y	T	E	S	P	G	G	2
225	G	G	G	S	P	R	G	L	G	2
260	A	G	S	S	A	H	R	P	P	2
293	R	P	S	S	C	P	T	S	S	2
294	P	S	S	C	P	T	S	S	S	2
303	T	Y	D	S	L	S	P	Y	G	2
305	D	S	L	S	P	Y	G	P	R	2
312	P	R	N	P	L	P	N	P	R	2
313	R	N	P	L	P	N	P	R	H	2
341	H	N	V	L	A	R	G	K	P	2
350	Q	R	K	P	K	S	E	N	N	2
356	E	N	N	S	W	Y	V	E	N	2
358	N	S	W	Y	V	E	N	G	R	2
363	E	N	G	R	P	A	D	L	A	2
367	P	A	D	L	A	G	S	G	Y	2
372	G	S	G	Y	C	G	A	L	W	2
383	I	E	S	L	E	E	G	L	G	2
391	G	G	K	Q	K	D	K	E	R	2
22	R	D	H	S	G	Q	K	M	K	1
62	S	Y	K	L	A	Y	S	N	D	1
99	E	G	I	N	I	S	G	S	F	1
105	G	S	F	C	R	N	K	L	K	1
118	L	H	K	R	M	N	T	N	P	1
124	T	N	P	S	R	R	P	Y	H	1
125	N	P	S	R	R	P	Y	H	F	1
132	H	F	Q	V	P	S	R	I	F	1
135	V	P	S	R	I	F	W	R	Q	1
143	Q	E	K	A	D	G	G	S	C	1
157	A	S	E	A	Y	K	K	V	C	1
198	K	N	K	Q	L	M	R	L	Q	1
199	N	K	Q	L	M	R	L	Q	K	1
206	Q	K	Q	A	E	K	N	M	K	1
222	E	S	P	G	G	G	S	P	R	1
318	N	P	R	H	S	P	S	G	G	1
330	K	K	P	A	R	H	C	Q	G	1
332	P	A	R	H	C	Q	G	Q	K	1
334	R	H	C	Q	G	Q	K	H	N	1
351	R	K	P	K	S	E	N	N	S	1
379	L	W	K	A	I	E	S	L	E	1
392	G	K	Q	K	D	K	E	R	K	1
53	D	F	G	H	V	Q	F	V	G	−1
126	P	S	R	R	P	Y	H	F	Q	−1
128	R	R	P	Y	H	F	Q	V	P	−1
188	R	K	E	K	A	E	I	H	Y	−1
229	P	R	G	L	G	F	I	F	K	−1
297	C	P	T	S	S	S	T	Y	D	−1
319	P	R	H	S	P	S	G	G	G	−1
353	P	K	S	E	N	N	S	W	Y	−1
396	D	K	E	R	K	A	E	N	G	−1
72	E	H	W	T	V	Y	Q	D	E	−2
78	Q	D	E	K	Q	R	K	D	K	−2
136	P	S	R	I	F	W	R	Q	E	−2
153	P	Q	G	H	A	S	E	A	Y	−2
210	E	K	N	M	K	K	K	I	D	−2
253	P	G	G	R	T	P	R	A	G	−2
387	E	E	G	L	G	G	K	Q	K	−2
170	P	H	E	V	G	W	K	Y	Q	−3
185	E	E	K	R	K	E	K	A	E	−3
290	P	W	T	R	P	S	S	C	P	−3
398	E	R	K	A	E	N	G	P	H	−4

TABLE XXIV
151P3D4
HLA Peptide Scoring
Results A*0202 9-mers SYFPEITHI
											SEQ.
Pos	1	2	3	4	5	6	7	8	9	score	ID NO.
	NO DATA

TABLE XXV
151P3D4
HLA Peptide Scoring
Results A*0203 9-mers SYFPEITHI
											SEQ.
Pos	1	2	3	4	5	6	7	8	9	score	ID NO.
	NO DATA

TABLE XXVI
151P3D4 v.1
HLA Peptide
Scoring Results A3 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
153	A	L	D	L	Q	G	V	V	F	29	Portion
209	W	L	S	D	G	S	V	Q	Y	26	of SEQ
130	T	L	E	D	Y	G	R	Y	K	24	ID NO:
166	R	L	G	R	Y	N	L	N	F	24	3; each
264	L	I	H	P	T	K	L	T	Y	24	start
308	W	L	A	D	G	S	V	R	Y	24	position
343	K	L	Y	G	V	Y	C	F	R	24	is
40	L	L	V	E	A	E	Q	A	K	22	specified,
95	F	V	S	M	G	Y	H	K	K	22	the length
111	R	V	F	L	K	G	G	S	D	22	of
186	A	V	I	A	S	F	D	Q	L	21	peptide is
75	H	K	I	R	I	K	W	T	K	20	9 amino
78	R	I	K	W	T	K	L	T	S	20	acids, the
269	K	L	T	Y	D	E	A	V	Q	20	end
331	A	V	R	F	V	G	F	P	D	20	position
123	S	L	V	I	T	D	L	T	L	19	for each
144	G	L	E	D	D	T	V	V	V	19	peptide is
155	D	L	Q	G	V	V	F	P	Y	19	the start
261	F	Y	Y	L	I	H	P	T	K	19	position
285	Q	I	A	K	V	G	Q	I	F	19	plus
23	T	L	D	H	D	R	A	I	H	18	eight.
39	H	L	L	V	E	A	E	Q	A	18
150	V	V	V	A	L	D	L	Q	G	18
234	G	V	R	N	Y	G	F	W	D	18
289	V	G	Q	I	F	A	A	W	K	18
307	G	W	L	A	D	G	S	V	R	18
346	G	V	Y	C	F	R	A	Y	N	18
3	S	L	L	L	L	V	L	I	S	17
56	N	V	T	L	P	C	K	F	Y	17
62	K	F	Y	R	D	P	T	A	F	17
76	K	I	R	I	K	W	T	K	L	17
88	Y	L	K	E	V	D	V	F	V	17
113	F	L	K	G	G	S	D	S	D	17
181	C	L	D	Q	D	A	V	I	A	17
193	Q	L	Y	D	A	W	R	G	G	17
249	D	V	F	C	F	T	S	N	F	17
288	K	V	G	Q	I	F	A	A	W	17
313	S	V	R	Y	P	I	S	R	P	17
333	R	F	V	G	F	P	D	K	K	17
4	L	L	L	L	V	L	I	S	I	16
9	L	I	S	I	C	W	A	D	H	16
51	S	H	R	G	G	N	V	T	L	16
83	K	L	T	S	D	Y	L	K	E	16
140	E	V	I	E	G	L	E	D	D	16
171	N	L	N	F	H	E	A	Q	Q	16
279	C	L	N	D	G	A	Q	I	A	16
5	L	L	L	V	L	I	S	I	C	15
29	A	I	H	I	Q	A	E	N	G	15
31	H	I	Q	A	E	N	G	P	H	15
41	L	V	E	A	E	Q	A	K	V	15
48	K	V	F	S	H	R	G	G	N	15
68	T	A	F	G	S	G	I	H	K	15
72	S	G	I	H	K	I	R	I	K	15
93	D	V	F	V	S	M	G	Y	H	15
103	K	T	Y	G	G	Y	Q	G	R	15
128	D	L	T	L	E	D	Y	G	R	15
187	V	I	A	S	F	D	Q	L	Y	15
213	G	S	V	Q	Y	P	I	T	K	15
270	L	T	Y	D	E	A	V	Q	A	15
275	A	V	Q	A	C	L	N	D	G	15
278	A	C	L	N	D	G	A	Q	I	15
297	K	I	L	G	Y	D	R	C	D	15
320	R	P	R	R	R	C	S	P	T	15
7	L	V	L	I	S	I	C	W	A	14
8	V	L	I	S	I	C	W	A	D	14
91	E	V	D	V	F	V	S	M	G	14
107	G	Y	Q	G	R	V	F	L	K	14
124	L	V	I	T	D	L	T	L	E	14
158	G	V	V	F	P	Y	F	P	R	14
231	T	V	P	G	V	R	N	Y	G	14
243	K	D	K	S	R	Y	D	V	F	14
325	C	S	P	T	E	A	A	V	R	14
334	F	V	G	F	P	D	K	K	H	14
340	K	K	H	K	L	Y	G	V	Y	14
42	V	E	A	E	Q	A	K	V	F	13
94	V	F	V	S	M	G	Y	H	K	13
159	V	V	F	P	Y	F	P	R	L	13
180	A	C	L	D	Q	D	A	V	I	13
201	G	L	D	W	C	N	A	G	W	13
263	Y	L	I	H	P	T	K	L	T	13
280	L	N	D	G	A	Q	I	A	K	13
284	A	Q	I	A	K	V	G	Q	I	13
298	I	L	G	Y	D	R	C	D	A	13
326	S	P	T	E	A	A	V	R	F	13
335	V	G	F	P	D	K	K	H	K	13
17	H	L	S	D	N	Y	T	L	D	12
44	A	E	Q	A	K	V	F	S	H	12
50	F	S	H	R	G	G	N	V	T	12
80	K	W	T	K	L	T	S	D	Y	12
82	T	K	L	T	S	D	Y	L	K	12
125	V	I	T	D	L	T	L	E	D	12
151	V	V	A	L	D	L	Q	G	V	12
161	F	P	Y	F	P	R	L	G	R	12
162	P	Y	F	P	R	L	G	R	Y	12
183	D	Q	D	A	V	I	A	S	F	12
208	G	W	L	S	D	G	S	V	Q	12
214	S	V	Q	Y	P	I	T	K	P	12
235	V	R	N	Y	G	F	W	D	K	12
291	Q	I	F	A	A	W	K	I	L	12
295	A	W	K	I	L	G	Y	D	R	12
303	R	C	D	A	G	W	L	A	D	12
317	P	I	S	R	P	R	R	R	C	12
332	V	R	F	V	G	F	P	D	K	12
341	K	H	K	L	Y	G	V	Y	C	12
6	L	L	V	L	I	S	I	C	W	11
58	T	L	P	C	K	F	Y	R	D	11
86	S	D	Y	L	K	E	V	D	V	11
90	K	E	V	D	V	F	V	S	M	11
97	S	M	G	Y	H	K	K	T	Y	11
102	K	K	T	Y	G	G	Y	Q	G	11
105	Y	G	G	Y	Q	G	R	V	F	11
106	G	G	Y	Q	G	R	V	F	L	11
196	D	A	W	R	G	G	L	D	W	11
197	A	W	R	G	G	L	D	W	C	11
215	V	Q	Y	P	I	T	K	P	R	11
228	G	Q	N	T	V	P	G	V	R	11
230	N	T	V	P	G	V	R	N	Y	11
255	S	N	F	N	G	R	F	Y	Y	11
293	F	A	A	W	K	I	L	G	Y	11
314	V	R	Y	P	I	S	R	P	R	11
318	I	S	R	P	R	R	R	C	S	11
324	R	C	S	P	T	E	A	A	V	11
329	E	A	A	V	R	F	V	G	F	11
2	K	S	L	L	L	L	V	L	I	10
28	R	A	I	H	I	Q	A	E	N	10
35	E	N	G	P	H	L	L	V	E	10
54	G	G	N	V	T	L	P	C	K	10
87	D	Y	L	K	E	V	D	V	F	10
112	V	F	L	K	G	G	S	D	S	10
129	L	T	L	E	D	Y	G	R	Y	10
141	V	I	E	G	L	E	D	D	T	10
149	T	V	V	V	A	L	D	L	Q	10
222	P	R	E	P	C	G	G	Q	N	10
236	R	N	Y	G	F	W	D	K	D	10
237	N	Y	G	F	W	D	K	D	K	10
245	K	S	R	Y	D	V	F	C	F	10
258	N	G	R	F	Y	Y	L	I	H	10
312	G	S	V	R	Y	P	I	S	R	10
315	R	Y	P	I	S	R	P	R	R	10
316	Y	P	I	S	R	P	R	R	R	10
321	P	R	R	R	C	S	P	T	E	10
11	S	I	C	W	A	D	H	L	S	9
12	I	C	W	A	D	H	L	S	D	9
45	E	Q	A	K	V	F	S	H	R	9
53	R	G	G	N	V	T	L	P	C	9
57	V	T	L	P	C	K	F	Y	R	9
73	G	I	H	K	I	R	I	K	W	9
118	S	D	S	D	A	S	L	V	I	9
126	I	T	D	L	T	L	E	D	Y	9
145	L	E	D	D	T	V	V	V	A	9
184	Q	D	A	V	I	A	S	F	D	9
191	F	D	Q	L	Y	D	A	W	R	9
204	W	C	N	A	G	W	L	S	D	9
218	P	I	T	K	P	R	E	P	C	9
223	R	E	P	C	G	G	Q	N	T	9
229	Q	N	T	V	P	G	V	R	N	9
240	F	W	D	K	D	K	S	R	Y	9
254	T	S	N	F	N	G	R	F	Y	9
319	S	R	P	R	R	R	C	S	P	9
322	R	R	R	C	S	P	T	E	A	9
328	T	E	A	A	V	R	F	V	G	9
1	M	K	S	L	L	L	L	V	L	8
10	I	S	I	C	W	A	D	H	L	8
18	L	S	D	N	Y	T	L	D	H	8
20	D	N	Y	T	L	D	H	D	R	8
26	H	D	R	A	I	H	I	Q	A	8
34	A	E	N	G	P	H	L	L	V	8
66	D	P	T	A	F	G	S	G	I	8
67	P	T	A	F	G	S	G	I	H	8
92	V	D	V	F	V	S	M	G	Y	8
100	Y	H	K	K	T	Y	G	G	Y	8
132	E	D	Y	G	R	Y	K	C	E	8
134	Y	G	R	Y	K	C	E	V	I	8
135	G	R	Y	K	C	E	V	I	E	8
143	E	G	L	E	D	D	T	V	V	8
152	V	A	L	D	L	Q	G	V	V	8
154	L	D	L	Q	G	V	V	F	P	8
177	A	Q	Q	A	C	L	D	Q	D	8
219	I	T	K	P	R	E	P	C	G	8
221	K	P	R	E	P	C	G	G	Q	8
224	E	P	C	G	G	Q	N	T	V	8
239	G	F	W	D	K	D	K	S	R	8
247	R	Y	D	V	F	C	F	T	S	8
260	R	F	Y	Y	L	I	H	P	T	8
282	D	G	A	Q	I	A	K	V	G	8
299	L	G	Y	D	R	C	D	A	G	8
301	Y	D	R	C	D	A	G	W	L	8
342	H	K	L	Y	G	V	Y	C	F	8
32	I	Q	A	E	N	G	P	H	L	7
38	P	H	L	L	V	E	A	E	Q	7
63	F	Y	R	D	P	T	A	F	G	7
65	R	D	P	T	A	F	G	S	G	7
74	I	H	K	I	R	I	K	W	T	7
108	Y	Q	G	R	V	F	L	K	G	7
139	C	E	V	I	E	G	L	E	D	7
142	I	E	G	L	E	D	D	T	V	7
148	D	T	V	V	V	A	L	D	L	7
164	F	P	R	L	G	R	Y	N	L	7
167	L	G	R	Y	N	L	N	F	H	7
195	Y	D	A	W	R	G	G	L	D	7
207	A	G	W	L	S	D	G	S	V	7
225	P	C	G	G	Q	N	T	V	P	7
244	D	K	S	R	Y	D	V	F	C	7
246	S	R	Y	D	V	F	C	F	T	7
306	A	G	W	L	A	D	G	S	V	7
330	A	A	V	R	F	V	G	F	P	7
337	F	P	D	K	K	H	K	L	Y	7
345	Y	G	V	Y	C	F	R	A	Y	7
14	W	A	D	H	L	S	D	N	Y	6
16	D	H	L	S	D	N	Y	T	L	6
24	L	D	H	D	R	A	I	H	I	6
33	Q	A	E	N	G	P	H	L	L	6
49	V	F	S	H	R	G	G	N	V	6
61	C	K	F	Y	R	D	P	T	A	6
64	Y	R	D	P	T	A	F	G	S	6
70	F	G	S	G	I	H	K	I	R	6
79	I	K	W	T	K	L	T	S	D	6
98	M	G	Y	H	K	K	T	Y	G	6
116	G	G	S	D	S	D	A	S	L	6
117	G	S	D	S	D	A	S	L	V	6
119	D	S	D	A	S	L	V	I	T	6
120	S	D	A	S	L	V	I	T	D	6
146	E	D	D	T	V	V	V	A	L	6
163	Y	F	P	R	L	G	R	Y	N	6
165	P	R	L	G	R	Y	N	L	N	6
172	L	N	F	H	E	A	Q	Q	A	6
205	C	N	A	G	W	L	S	D	G	6
232	V	P	G	V	R	N	Y	G	F	6
253	F	T	S	N	F	N	G	R	F	6
272	Y	D	E	A	V	Q	A	C	L	6
287	A	K	V	G	Q	I	F	A	A	6
290	G	Q	I	F	A	A	W	K	I	6
296	W	K	I	L	G	Y	D	R	C	6
300	G	Y	D	R	C	D	A	G	W	6
304	C	D	A	G	W	L	A	D	G	6
13	C	W	A	D	H	L	S	D	N	5
30	I	H	I	Q	A	E	N	G	P	5
55	G	N	V	T	L	P	C	K	F	5
69	A	F	G	S	G	I	H	K	I	5
77	I	R	I	K	W	T	K	L	T	5
101	H	K	K	T	Y	G	G	Y	Q	5
109	Q	G	R	V	F	L	K	G	G	5
114	L	K	G	G	S	D	S	D	A	5
122	A	S	L	V	I	T	D	L	T	5
136	R	Y	K	C	E	V	I	E	G	5
156	L	Q	G	V	V	F	P	Y	F	5
168	G	R	Y	N	L	N	F	H	E	5
169	R	Y	N	L	N	F	H	E	A	5
174	F	H	E	A	Q	Q	A	C	L	5
188	I	A	S	F	D	Q	L	Y	D	5
192	D	Q	L	Y	D	A	W	R	G	5
199	R	G	G	L	D	W	C	N	A	5
202	L	D	W	C	N	A	G	W	L	5
217	Y	P	I	T	K	P	R	E	P	5
262	Y	Y	L	I	H	P	T	K	L	5
277	Q	A	C	L	N	D	G	A	Q	5
281	N	D	G	A	Q	I	A	K	V	5
283	G	A	Q	I	A	K	V	G	Q	5
286	I	A	K	V	G	Q	I	F	A	5
292	I	F	A	A	W	K	I	L	G	5
310	A	D	G	S	V	R	Y	P	I	5
323	R	R	C	S	P	T	E	A	A	5
15	A	D	H	L	S	D	N	Y	T	4
22	Y	T	L	D	H	D	R	A	I	4
36	N	G	P	H	L	L	V	E	A	4
43	E	A	E	Q	A	K	V	F	S	4
85	T	S	D	Y	L	K	E	V	D	4
89	L	K	E	V	D	V	F	V	S	4
115	K	G	G	S	D	S	D	A	S	4
138	K	C	E	V	I	E	G	L	E	4
147	D	D	T	V	V	V	A	L	D	4
170	Y	N	L	N	F	H	E	A	Q	4
175	H	E	A	Q	Q	A	C	L	D	4
179	Q	A	C	L	D	Q	D	A	V	4
189	A	S	F	D	Q	L	Y	D	A	4
194	L	Y	D	A	W	R	G	G	L	4
200	G	G	L	D	W	C	N	A	G	4
203	D	W	C	N	A	G	W	L	S	4
220	T	K	P	R	E	P	C	G	G	4
226	C	G	G	Q	N	T	V	P	G	4
233	P	G	V	R	N	Y	G	F	W	4
252	C	F	T	S	N	F	N	G	R	4
256	N	F	N	G	R	F	Y	Y	L	4
265	I	H	P	T	K	L	T	Y	D	4
273	D	E	A	V	Q	A	C	L	N	4
294	A	A	W	K	I	L	G	Y	D	4
302	D	R	C	D	A	G	W	L	A	4
338	P	D	K	K	H	K	L	Y	G	4
25	D	H	D	R	A	I	H	I	Q	3
27	D	R	A	I	H	I	Q	A	E	3
46	Q	A	K	V	F	S	H	R	G	3
47	A	K	V	F	S	H	R	G	G	3
52	H	R	G	G	N	V	T	L	P	3
104	T	Y	G	G	Y	Q	G	R	V	3
121	D	A	S	L	V	I	T	D	L	3
131	L	E	D	Y	G	R	Y	K	C	3
133	D	Y	G	R	Y	K	C	E	V	3
157	Q	G	V	V	F	P	Y	F	P	3
176	E	A	Q	Q	A	C	L	D	Q	3
178	Q	Q	A	C	L	D	Q	D	A	3
216	Q	Y	P	I	T	K	P	R	E	3
241	W	D	K	D	K	S	R	Y	D	3
248	Y	D	V	F	C	F	T	S	N	3
257	F	N	G	R	F	Y	Y	L	I	3
268	T	K	L	T	Y	D	E	A	V	3
274	E	A	V	Q	A	C	L	N	D	3
305	D	A	G	W	L	A	D	G	S	3
37	G	P	H	L	L	V	E	A	E	2
60	P	C	K	F	Y	R	D	P	T	2
81	W	T	K	L	T	S	D	Y	L	2
96	V	S	M	G	Y	H	K	K	T	2
127	T	D	L	T	L	E	D	Y	G	2
137	Y	K	C	E	V	I	E	G	L	2
173	N	F	H	E	A	Q	Q	A	C	2
182	L	D	Q	D	A	V	I	A	S	2
190	S	F	D	Q	L	Y	D	A	W	2
198	W	R	G	G	L	D	W	C	N	2
210	L	S	D	G	S	V	Q	Y	P	2
211	S	D	G	S	V	Q	Y	P	I	2
267	P	T	K	L	T	Y	D	E	A	2
271	T	Y	D	E	A	V	Q	A	C	2
309	L	A	D	G	S	V	R	Y	P	2
311	D	G	S	V	R	Y	P	I	S	2
327	P	T	E	A	A	V	R	F	V	2
336	G	F	P	D	K	K	H	K	L	2
339	D	K	K	H	K	L	Y	G	V	2
19	S	D	N	Y	T	L	D	H	D	1
21	N	Y	T	L	D	H	D	R	A	1
71	G	S	G	I	H	K	I	R	I	1
84	L	T	S	D	Y	L	K	E	V	1
99	G	Y	H	K	K	T	Y	G	G	1
110	G	R	V	F	L	K	G	G	S	1
160	V	F	P	Y	F	P	R	L	G	1
185	D	A	V	I	A	S	F	D	Q	1
227	G	G	Q	N	T	V	P	G	V	1
242	D	K	D	K	S	R	Y	D	V	1
276	V	Q	A	C	L	N	D	G	A	1
151P3D4 v.2
HLA Peptide
Scoring Results A3 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
34	K	V	D	L	L	V	P	T	K	28	Portion of
20	S	I	R	D	H	S	G	Q	K	27	SEQ ID
56	H	V	Q	F	V	G	S	Y	K	27	NO: 5;
238	T	I	A	P	L	A	A	T	R	26	each start
88	L	L	G	R	K	A	V	V	V	25	position
179	A	V	T	A	T	L	E	E	K	25	is
241	P	L	A	A	T	R	A	T	R	25	specified,
385	S	L	E	E	G	L	G	G	K	25	the length
163	K	V	C	L	S	G	A	P	H	24	of peptide
269	A	L	S	A	R	A	P	V	P	24	is 9
373	S	G	Y	C	G	A	L	W	K	24	amino
87	V	L	L	G	R	K	A	V	V	23	acids, the
183	T	L	E	E	K	R	K	E	K	23	end
343	V	L	A	R	G	K	P	Q	R	23	position
389	G	L	G	G	K	Q	K	D	K	23	for each
37	L	L	V	P	T	K	V	T	G	21	peptide is
75	T	V	Y	Q	D	E	K	Q	R	21	the start
111	K	L	K	Y	L	A	F	L	H	21	position
59	F	V	G	S	Y	K	L	A	Y	20	plus eight
86	K	V	L	L	G	R	K	A	V	20
323	P	S	G	G	G	G	L	K	K	20
10	P	L	R	A	L	H	I	V	V	19
42	K	V	T	G	I	I	T	Q	G	19
46	I	I	T	Q	G	A	K	D	F	19
134	Q	V	P	S	R	I	F	W	R	19
322	S	P	S	G	G	G	G	L	K	19
342	N	V	L	A	R	G	K	P	Q	19
346	R	G	K	P	Q	R	K	P	K	19
387	E	E	G	L	G	G	K	Q	K	19
1	M	L	E	H	T	T	K	T	F	18
112	L	K	Y	L	A	F	L	H	K	18
199	N	K	Q	L	M	R	L	Q	K	18
201	Q	L	M	R	L	Q	K	Q	A	18
13	A	L	H	I	V	V	E	S	I	17
16	I	V	V	E	S	I	R	D	H	17
22	R	D	H	S	G	Q	K	M	K	17
45	G	I	I	T	Q	G	A	K	D	17
154	Q	G	H	A	S	E	A	Y	K	17
192	A	E	I	H	Y	R	K	N	K	17
204	R	L	Q	K	Q	A	E	K	N	17
207	K	Q	A	E	K	N	M	K	K	17
264	A	H	R	P	P	A	L	S	A	17
306	S	L	S	P	Y	G	P	R	N	17
332	P	A	R	H	C	Q	G	Q	K	17
344	L	A	R	G	K	P	Q	R	K	17
36	D	L	L	V	P	T	K	V	T	16
44	T	G	I	I	T	Q	G	A	K	16
51	A	K	D	F	G	H	V	Q	F	16
117	F	L	H	K	R	M	N	T	N	16
203	M	R	L	Q	K	Q	A	E	K	16
249	R	I	G	H	P	G	G	R	T	16
340	K	H	N	V	L	A	R	G	K	16
369	D	L	A	G	S	G	Y	C	G	16
84	K	D	K	V	L	L	G	R	K	15
100	G	I	N	I	S	G	S	F	C	15
109	R	N	K	L	K	Y	L	A	F	15
137	S	R	I	F	W	R	Q	E	K	15
206	Q	K	Q	A	E	K	N	M	K	15
226	G	G	S	P	R	G	L	G	F	15
256	R	T	P	R	A	G	S	S	A	15
257	T	P	R	A	G	S	S	A	H	15
302	S	T	Y	D	S	L	S	P	Y	15
361	Y	V	E	N	G	R	P	A	D	15
378	A	L	W	K	A	I	E	S	L	15
7	K	T	F	P	L	R	A	L	H	14
64	K	L	A	Y	S	N	D	G	E	14
138	R	I	F	W	R	Q	E	K	A	14
155	G	H	A	S	E	A	Y	K	K	14
169	A	P	H	E	V	G	W	K	Y	14
211	K	N	M	K	K	K	I	D	K	14
222	E	S	P	G	G	G	S	P	R	14
231	G	L	G	F	I	F	K	T	I	14
250	I	G	H	P	G	G	R	T	P	14
284	W	L	P	L	R	T	P	W	T	14
285	L	P	L	R	T	P	W	T	R	14
286	P	L	R	T	P	W	T	R	P	14
296	S	C	P	T	S	S	S	T	Y	14
315	P	L	P	N	P	R	H	S	P	14
328	G	L	K	K	P	A	R	H	C	14
78	Q	D	E	K	Q	R	K	D	K	13
93	A	V	V	V	S	C	E	G	I	13
95	V	V	S	C	E	G	I	N	I	13
106	S	F	C	R	N	K	L	K	Y	13
165	C	L	S	G	A	P	H	E	V	13
176	K	Y	Q	A	V	T	A	T	L	13
187	K	R	K	E	K	A	E	I	H	13
194	I	H	Y	R	K	N	K	Q	L	13
216	K	I	D	K	Y	T	E	S	P	13
228	S	P	R	G	L	G	F	I	F	13
229	P	R	G	L	G	F	I	F	K	13
244	A	T	R	A	T	R	I	G	H	13
272	A	R	A	P	V	P	A	A	S	13
275	P	V	P	A	A	S	P	A	A	13
367	P	A	D	L	A	G	S	G	Y	13
26	G	Q	K	M	K	Q	D	K	K	12
38	L	V	P	T	K	V	T	G	I	12
69	N	D	G	E	H	W	T	V	Y	12
83	R	K	D	K	V	L	L	G	R	12
103	I	S	G	S	F	C	R	N	K	12
105	G	S	F	C	R	N	K	L	K	12
121	R	M	N	T	N	P	S	R	R	12
129	R	P	Y	H	F	Q	V	P	S	12
168	G	A	P	H	E	V	G	W	K	12
172	E	V	G	W	K	Y	Q	A	V	12
174	G	W	K	Y	Q	A	V	T	A	12
190	E	K	A	E	I	H	Y	R	K	12
208	Q	A	E	K	N	M	K	K	K	12
237	K	T	I	A	P	L	A	A	T	12
273	R	A	P	V	P	A	A	S	P	12
274	A	P	V	P	A	A	S	P	A	12
366	R	P	A	D	L	A	G	S	G	12
14	L	H	I	V	V	E	S	I	R	11
17	V	V	E	S	I	R	D	H	S	11
25	S	G	Q	K	M	K	Q	D	K	11
76	V	Y	Q	D	E	K	Q	R	K	11
89	L	G	R	K	A	V	V	V	S	11
94	V	V	V	S	C	E	G	I	N	11
99	E	G	I	N	I	S	G	S	F	11
101	I	N	I	S	G	S	F	C	R	11
113	K	Y	L	A	F	L	H	K	R	11
114	Y	L	A	F	L	H	K	R	M	11
143	Q	E	K	A	D	G	G	S	C	11
181	T	A	T	L	E	E	K	R	K	11
196	Y	R	K	N	K	Q	L	M	R	11
221	T	E	S	P	G	G	G	S	P	11
234	F	I	F	K	T	I	A	P	L	11
248	T	R	I	G	H	P	G	G	R	11
255	G	R	T	P	R	A	G	S	S	11
265	H	R	P	P	A	L	S	A	R	11
320	R	H	S	P	S	G	G	G	G	11
327	G	G	L	K	K	P	A	R	H	11
353	P	K	S	E	N	N	S	W	Y	11
382	A	I	E	S	L	E	E	G	L	11
11	L	R	A	L	H	I	V	V	E	10
12	R	A	L	H	I	V	V	E	S	10
73	H	W	T	V	Y	Q	D	E	K	10
81	K	Q	R	K	D	K	V	L	L	10
90	G	R	K	A	V	V	V	S	C	10
102	N	I	S	G	S	F	C	R	N	10
120	K	R	M	N	T	N	P	S	R	10
123	N	T	N	P	S	R	R	P	Y	10
125	N	P	S	R	R	P	Y	H	F	10
127	S	R	R	P	Y	H	F	Q	V	10
144	E	K	A	D	G	G	S	C	C	10
160	A	Y	K	K	V	C	L	S	G	10
188	R	K	E	K	A	E	I	H	Y	10
189	K	E	K	A	E	I	H	Y	R	10
193	E	I	H	Y	R	K	N	K	Q	10
246	R	A	T	R	I	G	H	P	G	10
251	G	H	P	G	G	R	T	P	R	10
258	P	R	A	G	S	S	A	H	R	10
283	A	W	L	P	L	R	T	P	W	10
330	K	K	P	A	R	H	C	Q	G	10
333	A	R	H	C	Q	G	Q	K	H	10
348	K	P	Q	R	K	P	K	S	E	10
364	N	G	R	P	A	D	L	A	G	10
368	A	D	L	A	G	S	G	Y	C	10
392	G	K	Q	K	D	K	E	R	K	10
395	K	D	K	E	R	K	A	E	N	10
8	T	F	P	L	R	A	L	H	I	9
19	E	S	I	R	D	H	S	G	Q	9
50	G	A	K	D	F	G	H	V	Q	9
55	G	H	V	Q	F	V	G	S	Y	9
61	G	S	Y	K	L	A	Y	S	N	9
65	L	A	Y	S	N	D	G	E	H	9
91	R	K	A	V	V	V	S	C	E	9
157	A	S	E	A	Y	K	K	V	C	9
167	S	G	A	P	H	E	V	G	W	9
214	K	K	K	I	D	K	Y	T	E	9
215	K	K	I	D	K	Y	T	E	S	9
247	A	T	R	I	G	H	P	G	G	9
266	R	P	P	A	L	S	A	R	A	9
270	L	S	A	R	A	P	V	P	A	9
278	A	A	S	P	A	A	W	L	P	9
295	S	S	C	P	T	S	S	S	T	9
313	R	N	P	L	P	N	P	R	H	9
338	G	Q	K	H	N	V	L	A	R	9
384	E	S	L	E	E	G	L	G	G	9
399	R	K	A	E	N	G	P	H	L	9
15	H	I	V	V	E	S	I	R	D	8
28	K	M	K	Q	D	K	K	V	D	8
32	D	K	K	V	D	L	L	V	P	8
33	K	K	V	D	L	L	V	P	T	8
80	E	K	Q	R	K	D	K	V	L	8
82	Q	R	K	D	K	V	L	L	G	8
116	A	F	L	H	K	R	M	N	T	8
128	R	R	P	Y	H	F	Q	V	P	8
150	S	C	C	P	Q	G	H	A	S	8
152	C	P	Q	G	H	A	S	E	A	8
212	N	M	K	K	K	I	D	K	Y	8
230	R	G	L	G	F	I	F	K	T	8
240	A	P	L	A	A	T	R	A	T	8
263	S	A	H	R	P	P	A	L	S	8
276	V	P	A	A	S	P	A	A	W	8
277	P	A	A	S	P	A	A	W	L	8
279	A	S	P	A	A	W	L	P	L	8
280	S	P	A	A	W	L	P	L	R	8
282	A	A	W	L	P	L	R	T	P	8
289	T	P	W	T	R	P	S	S	C	8
293	R	P	S	S	C	P	T	S	S	8
308	S	P	Y	G	P	R	N	P	L	8
312	P	R	N	P	L	P	N	P	R	8
316	L	P	N	P	R	H	S	P	S	8
362	V	E	N	G	R	P	A	D	L	8
398	E	R	K	A	E	N	G	P	H	8
31	Q	D	K	K	V	D	L	L	V	7
48	T	Q	G	A	K	D	F	G	H	7
66	A	Y	S	N	D	G	E	H	W	7
68	S	N	D	G	E	H	W	T	V	7
124	T	N	P	S	R	R	P	Y	H	7
136	P	S	R	I	F	W	R	Q	E	7
145	K	A	D	G	G	S	C	C	P	7
151	C	C	P	Q	G	H	A	S	E	7
153	P	Q	G	H	A	S	E	A	Y	7
158	S	E	A	Y	K	K	V	C	L	7
164	V	C	L	S	G	A	P	H	E	7
173	V	G	W	K	Y	Q	A	V	T	7
200	K	Q	L	M	R	L	Q	K	Q	7
239	I	A	P	L	A	A	T	R	A	7
242	L	A	A	T	R	A	T	R	I	7
254	G	G	R	T	P	R	A	G	S	7
259	R	A	G	S	S	A	H	R	P	7
271	S	A	R	A	P	V	P	A	A	7
288	R	T	P	W	T	R	P	S	S	7
305	D	S	L	S	P	Y	G	P	R	7
310	Y	G	P	R	N	P	L	P	N	7
318	N	P	R	H	S	P	S	G	G	7
326	G	G	G	L	K	K	P	A	R	7
331	K	P	A	R	H	C	Q	G	Q	7
339	Q	K	H	N	V	L	A	R	G	7
350	Q	R	K	P	K	S	E	N	N	7
371	A	G	S	G	Y	C	G	A	L	7
381	K	A	I	E	S	L	E	E	G	7
396	D	K	E	R	K	A	E	N	G	7
400	K	A	E	N	G	P	H	L	L	7
29	M	K	Q	D	K	K	V	D	L	6
35	V	D	L	L	V	P	T	K	V	6
41	T	K	V	T	G	I	I	T	Q	6
62	S	Y	K	L	A	Y	S	N	D	6
126	P	S	R	R	P	Y	H	F	Q	6
130	P	Y	H	F	Q	V	P	S	R	6
139	I	F	W	R	Q	E	K	A	D	6
140	F	W	R	Q	E	K	A	D	G	6
166	L	S	G	A	P	H	E	V	G	6
175	W	K	Y	Q	A	V	T	A	T	6
182	A	T	L	E	E	K	R	K	E	6
185	E	E	K	R	K	E	K	A	E	6
186	E	K	R	K	E	K	A	E	I	6
217	I	D	K	Y	T	E	S	P	G	6
219	K	Y	T	E	S	P	G	G	G	6
227	G	S	P	R	G	L	G	F	I	6
235	I	F	K	T	I	A	P	L	A	6
236	F	K	T	I	A	P	L	A	A	6
243	A	A	T	R	A	T	R	I	G	6
262	S	S	A	H	R	P	P	A	L	6
267	P	P	A	L	S	A	R	A	P	6
268	P	A	L	S	A	R	A	P	V	6
290	P	W	T	R	P	S	S	C	P	6
291	W	T	R	P	S	S	C	P	T	6
301	S	S	T	Y	D	S	L	S	P	6
314	N	P	L	P	N	P	R	H	S	6
321	H	S	P	S	G	G	G	G	L	6
334	R	H	C	Q	G	Q	K	H	N	6
337	Q	G	Q	K	H	N	V	L	A	6
349	P	Q	R	K	P	K	S	E	N	6
352	K	P	K	S	E	N	N	S	W	6
355	S	E	N	N	S	W	Y	V	E	6
359	S	W	Y	V	E	N	G	R	P	6
363	E	N	G	R	P	A	D	L	A	6
372	G	S	G	Y	C	G	A	L	W	6
377	G	A	L	W	K	A	I	E	S	6
379	L	W	K	A	I	E	S	L	E	6
386	L	E	E	G	L	G	G	K	Q	6
388	E	G	L	G	G	K	Q	K	D	6
391	G	G	K	Q	K	D	K	E	R	6
393	K	Q	K	D	K	E	R	K	A	6
397	K	E	R	K	A	E	N	G	P	6
5	T	T	K	T	F	P	L	R	A	5
9	F	P	L	R	A	L	H	I	V	5
18	V	E	S	I	R	D	H	S	G	5
21	I	R	D	H	S	G	Q	K	M	5
52	K	D	F	G	H	V	Q	F	V	5
53	D	F	G	H	V	Q	F	V	G	5
97	S	C	E	G	I	N	I	S	G	5
107	F	C	R	N	K	L	K	Y	L	5
110	N	K	L	K	Y	L	A	F	L	5
118	L	H	K	R	M	N	T	N	P	5
131	Y	H	F	Q	V	P	S	R	I	5
141	W	R	Q	E	K	A	D	G	G	5
142	R	Q	E	K	A	D	G	G	S	5
146	A	D	G	G	S	C	C	P	Q	5
148	G	G	S	C	C	P	Q	G	H	5
159	E	A	Y	K	K	V	C	L	S	5
162	K	K	V	C	L	S	G	A	P	5
171	H	E	V	G	W	K	Y	Q	A	5
177	Y	Q	A	V	T	A	T	L	E	5
178	Q	A	V	T	A	T	L	E	E	5
180	V	T	A	T	L	E	E	K	R	5
197	R	K	N	K	Q	L	M	R	L	5
202	L	M	R	L	Q	K	Q	A	E	5
209	A	E	K	N	M	K	K	K	I	5
223	S	P	G	G	G	S	P	R	G	5
233	G	F	I	F	K	T	I	A	P	5
253	P	G	G	R	T	P	R	A	G	5
281	P	A	A	W	L	P	L	R	T	5
294	P	S	S	C	P	T	S	S	S	5
309	P	Y	G	P	R	N	P	L	P	5
317	P	N	P	R	H	S	P	S	G	5
324	S	G	G	G	G	L	K	K	P	5
329	L	K	K	P	A	R	H	C	Q	5
336	C	Q	G	Q	K	H	N	V	L	5
358	N	S	W	Y	V	E	N	G	R	5
365	G	R	P	A	D	L	A	G	S	5
376	C	G	A	L	W	K	A	I	E	5
380	W	K	A	I	E	S	L	E	E	5
4	H	T	T	K	T	F	P	L	R	4
24	H	S	G	Q	K	M	K	Q	D	4
30	K	Q	D	K	K	V	D	L	L	4
40	P	T	K	V	T	G	I	I	T	4
47	I	T	Q	G	A	K	D	F	G	4
49	Q	G	A	K	D	F	G	H	V	4
54	F	G	H	V	Q	F	V	G	S	4
58	Q	F	V	G	S	Y	K	L	A	4
60	V	G	S	Y	K	L	A	Y	S	4
63	Y	K	L	A	Y	S	N	D	G	4
67	Y	S	N	D	G	E	H	W	T	4
70	D	G	E	H	W	T	V	Y	Q	4
85	D	K	V	L	L	G	R	K	A	4
92	K	A	V	V	V	S	C	E	G	4
98	C	E	G	I	N	I	S	G	S	4
132	H	F	Q	V	P	S	R	I	F	4
133	F	Q	V	P	S	R	I	F	W	4
161	Y	K	K	V	C	L	S	G	A	4
191	K	A	E	I	H	Y	R	K	N	4
198	K	N	K	Q	L	M	R	L	Q	4
218	D	K	Y	T	E	S	P	G	G	4
220	Y	T	E	S	P	G	G	G	S	4
245	T	R	A	T	R	I	G	H	P	4
252	H	P	G	G	R	T	P	R	A	4
292	T	R	P	S	S	C	P	T	S	4
300	S	S	S	T	Y	D	S	L	S	4
311	G	P	R	N	P	L	P	N	P	4
351	R	K	P	K	S	E	N	N	S	4
354	K	S	E	N	N	S	W	Y	V	4
356	E	N	N	S	W	Y	V	E	N	4
360	W	Y	V	E	N	G	R	P	A	4
383	I	E	S	L	E	E	G	L	G	4
394	Q	K	D	K	E	R	K	A	E	4
23	D	H	S	G	Q	K	M	K	Q	3
71	G	E	H	W	T	V	Y	Q	D	3
79	D	E	K	Q	R	K	D	K	V	3
96	V	S	C	E	G	I	N	I	S	3
119	H	K	R	M	N	T	N	P	S	3
135	V	P	S	R	I	F	W	R	Q	3
147	D	G	G	S	C	C	P	Q	G	3
195	H	Y	R	K	N	K	Q	L	M	3
224	P	G	G	G	S	P	R	G	L	3
260	A	G	S	S	A	H	R	P	P	3
261	G	S	S	A	H	R	P	P	A	3
287	L	R	T	P	W	T	R	P	S	3
307	L	S	P	Y	G	P	R	N	P	3
341	H	N	V	L	A	R	G	K	P	3
345	A	R	G	K	P	Q	R	K	P	3
375	Y	C	G	A	L	W	K	A	I	3
27	Q	K	M	K	Q	D	K	K	V	2
39	V	P	T	K	V	T	G	I	I	2
57	V	Q	F	V	G	S	Y	K	L	2
77	Y	Q	D	E	K	Q	R	K	D	2
104	S	G	S	F	C	R	N	K	L	2
115	L	A	F	L	H	K	R	M	N	2
170	P	H	E	V	G	W	K	Y	Q	2
184	L	E	E	K	R	K	E	K	A	2
225	G	G	G	S	P	R	G	L	G	2
232	L	G	F	I	F	K	T	I	A	2
299	T	S	S	S	T	Y	D	S	L	2
304	Y	D	S	L	S	P	Y	G	P	2
325	G	G	G	G	L	K	K	P	A	2
335	H	C	Q	G	Q	K	H	N	V	2
347	G	K	P	Q	R	K	P	K	S	2
370	L	A	G	S	G	Y	C	G	A	2
374	G	Y	C	G	A	L	W	K	A	2
2	L	E	H	T	T	K	T	F	P	1
3	E	H	T	T	K	T	F	P	L	1
6	T	K	T	F	P	L	R	A	L	1
43	V	T	G	I	I	T	Q	G	A	1
72	E	H	W	T	V	Y	Q	D	E	1
122	M	N	T	N	P	S	R	R	P	1
149	G	S	C	C	P	Q	G	H	A	1
156	H	A	S	E	A	Y	K	K	V	1
205	L	Q	K	Q	A	E	K	N	M	1
210	E	K	N	M	K	K	K	I	D	1
213	M	K	K	K	I	D	K	Y	T	1
297	C	P	T	S	S	S	T	Y	D	1
319	P	R	H	S	P	S	G	G	G	1

TABLE XXVII
151P3D4 v.1
HLA Peptide
Scoring Results A26 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
155	D	L	Q	G	V	V	F	P	Y	30	Portion of
249	D	V	F	C	F	T	S	N	F	30	SEQ ID
159	V	V	F	P	Y	F	P	R	L	28	NO: 3;
129	L	T	L	E	D	Y	G	R	Y	27	each start
230	N	T	V	P	G	V	R	N	Y	27	position is
186	A	V	I	A	S	F	D	Q	L	26	specified,
126	I	T	D	L	T	L	E	D	Y	25	the length
140	E	V	I	E	G	L	E	D	D	24	of peptide
148	D	T	V	V	V	A	L	D	L	24	is 9 amino
91	E	V	D	V	F	V	S	M	G	23	acids, the
93	D	V	F	V	S	M	G	Y	H	23	end
183	D	Q	D	A	V	I	A	S	F	23	position
187	V	I	A	S	F	D	Q	L	Y	23	for each
285	Q	I	A	K	V	G	Q	I	F	23	peptide is
329	E	A	A	V	R	F	V	G	F	23	the start
264	L	I	H	P	T	K	L	T	Y	22	position
308	W	L	A	D	G	S	V	R	Y	22	plus eight
87	D	Y	L	K	E	V	D	V	F	21
146	E	D	D	T	V	V	V	A	L	21
153	A	L	D	L	Q	G	V	V	F	21
209	W	L	S	D	G	S	V	Q	Y	21
253	F	T	S	N	F	N	G	R	F	21
56	N	V	T	L	P	C	K	F	Y	20
76	K	I	R	I	K	W	T	K	L	20
256	N	F	N	G	R	F	Y	Y	L	20
291	Q	I	F	A	A	W	K	I	L	20
81	W	T	K	L	T	S	D	Y	L	19
162	P	Y	F	P	R	L	G	R	Y	19
166	R	L	G	R	Y	N	L	N	F	19
103	K	T	Y	G	G	Y	Q	G	R	18
121	D	A	S	L	V	I	T	D	L	18
336	G	F	P	D	K	K	H	K	L	18
62	K	F	Y	R	D	P	T	A	F	17
100	Y	H	K	K	T	Y	G	G	Y	17
151	V	V	A	L	D	L	Q	G	V	17
288	K	V	G	Q	I	F	A	A	W	17
293	F	A	A	W	K	I	L	G	Y	17
84	L	T	S	D	Y	L	K	E	V	16
123	S	L	V	I	T	D	L	T	L	16
124	L	V	I	T	D	L	T	L	E	16
243	K	D	K	S	R	Y	D	V	F	16
267	P	T	K	L	T	Y	D	E	A	16
313	S	V	R	Y	P	I	S	R	P	16
340	K	K	H	K	L	Y	G	V	Y	16
7	L	V	L	I	S	I	C	W	A	15
16	D	H	L	S	D	N	Y	T	L	15
58	T	L	P	C	K	F	Y	R	D	15
90	K	E	V	D	V	F	V	S	M	15
95	F	V	S	M	G	Y	H	K	K	15
128	D	L	T	L	E	D	Y	G	R	15
137	Y	K	C	E	V	I	E	G	L	15
156	L	Q	G	V	V	F	P	Y	F	15
214	S	V	Q	Y	P	I	T	K	P	15
345	Y	G	V	Y	C	F	R	A	Y	15
5	L	L	L	V	L	I	S	I	C	14
42	V	E	A	E	Q	A	K	V	F	14
45	E	Q	A	K	V	F	S	H	R	14
48	K	V	F	S	H	R	G	G	N	14
83	K	L	T	S	D	Y	L	K	E	14
111	R	V	F	L	K	G	G	S	D	14
149	T	V	V	V	A	L	D	L	Q	14
158	G	V	V	F	P	Y	F	P	R	14
190	S	F	D	Q	L	Y	D	A	W	14
219	I	T	K	P	R	E	P	C	G	14
240	F	W	D	K	D	K	S	R	Y	14
245	K	S	R	Y	D	V	F	C	F	14
275	A	V	Q	A	C	L	N	D	G	14
326	S	P	T	E	A	A	V	R	F	14
327	P	T	E	A	A	V	R	F	V	14
342	H	K	L	Y	G	V	Y	C	F	14
343	K	L	Y	G	V	Y	C	F	R	14
1	M	K	S	L	L	L	L	V	L	13
3	S	L	L	L	L	V	L	I	S	13
4	L	L	L	L	V	L	I	S	I	13
14	W	A	D	H	L	S	D	N	Y	13
17	H	L	S	D	N	Y	T	L	D	13
27	D	R	A	I	H	I	Q	A	E	13
32	I	Q	A	E	N	G	P	H	L	13
80	K	W	T	K	L	T	S	D	Y	13
119	D	S	D	A	S	L	V	I	T	13
125	V	I	T	D	L	T	L	E	D	13
141	V	I	E	G	L	E	D	D	T	13
231	T	V	P	G	V	R	N	Y	G	13
270	L	T	Y	D	E	A	V	Q	A	13
337	F	P	D	K	K	H	K	L	Y	13
339	D	K	K	H	K	L	Y	G	V	13
8	V	L	I	S	I	C	W	A	D	12
22	Y	T	L	D	H	D	R	A	I	12
29	A	I	H	I	Q	A	E	N	G	12
35	E	N	G	P	H	L	L	V	E	12
40	L	L	V	E	A	E	Q	A	K	12
41	L	V	E	A	E	Q	A	K	V	12
55	G	N	V	T	L	P	C	K	F	12
57	V	T	L	P	C	K	F	Y	R	12
69	A	F	G	S	G	I	H	K	I	12
73	G	I	H	K	I	R	I	K	W	12
88	Y	L	K	E	V	D	V	F	V	12
92	V	D	V	F	V	S	M	G	Y	12
113	F	L	K	G	G	S	D	S	D	12
116	G	G	S	D	S	D	A	S	L	12
132	E	D	Y	G	R	Y	K	C	E	12
150	V	V	V	A	L	D	L	Q	G	12
212	D	G	S	V	Q	Y	P	I	T	12
252	C	F	T	S	N	F	N	G	R	12
255	S	N	F	N	G	R	F	Y	Y	12
297	K	I	L	G	Y	D	R	C	D	12
9	L	I	S	I	C	W	A	D	H	11
10	I	S	I	C	W	A	D	H	L	11
25	D	H	D	R	A	I	H	I	Q	11
51	S	H	R	G	G	N	V	T	L	11
67	P	T	A	F	G	S	G	I	H	11
78	R	I	K	W	T	K	L	T	S	11
105	Y	G	G	Y	Q	G	R	V	F	11
147	D	D	T	V	V	V	A	L	D	11
181	C	L	D	Q	D	A	V	I	A	11
201	G	L	D	W	C	N	A	G	W	11
218	P	I	T	K	P	R	E	P	C	11
232	V	P	G	V	R	N	Y	G	F	11
260	R	F	Y	Y	L	I	H	P	T	11
311	D	G	S	V	R	Y	P	I	S	11
317	P	I	S	R	P	R	R	R	C	11
334	F	V	G	F	P	D	K	K	H	11
346	G	V	Y	C	F	R	A	Y	N	11
11	S	I	C	W	A	D	H	L	S	10
23	T	L	D	H	D	R	A	I	H	10
31	H	I	Q	A	E	N	G	P	H	10
97	S	M	G	Y	H	K	K	T	Y	10
106	G	G	Y	Q	G	R	V	F	L	10
144	G	L	E	D	D	T	V	V	V	10
171	N	L	N	F	H	E	A	Q	Q	10
173	N	F	H	E	A	Q	Q	A	C	10
174	F	H	E	A	Q	Q	A	C	L	10
193	Q	L	Y	D	A	W	R	G	G	10
194	L	Y	D	A	W	R	G	G	L	10
234	G	V	R	N	Y	G	F	W	D	10
254	T	S	N	F	N	G	R	F	Y	10
263	Y	L	I	H	P	T	K	L	T	10
279	C	L	N	D	G	A	Q	I	A	10
331	A	V	R	F	V	G	F	P	D	10
39	H	L	L	V	E	A	E	Q	A	9
130	T	L	E	D	Y	G	R	Y	K	9
164	F	P	R	L	G	R	Y	N	L	9
210	L	S	D	G	S	V	Q	Y	P	9
239	G	F	W	D	K	D	K	S	R	9
242	D	K	D	K	S	R	Y	D	V	9
262	Y	Y	L	I	H	P	T	K	L	9
269	K	L	T	Y	D	E	A	V	Q	9
271	T	Y	D	E	A	V	Q	A	C	9
272	Y	D	E	A	V	Q	A	C	L	9
333	R	F	V	G	F	P	D	K	K	9
6	L	L	V	L	I	S	I	C	W	8
33	Q	A	E	N	G	P	H	L	L	8
36	N	G	P	H	L	L	V	E	A	8
43	E	A	E	Q	A	K	V	F	S	8
66	D	P	T	A	F	G	S	G	I	8
94	V	F	V	S	M	G	Y	H	K	8
112	V	F	L	K	G	G	S	D	S	8
143	E	G	L	E	D	D	T	V	V	8
163	Y	F	P	R	L	G	R	Y	N	8
189	A	S	F	D	Q	L	Y	D	A	8
202	L	D	W	C	N	A	G	W	L	8
205	C	N	A	G	W	L	S	D	G	8
224	E	P	C	G	G	Q	N	T	V	8
273	D	E	A	V	Q	A	C	L	N	8
274	E	A	V	Q	A	C	L	N	D	8
282	D	G	A	Q	I	A	K	V	G	8
284	A	Q	I	A	K	V	G	Q	I	8
287	A	K	V	G	Q	I	F	A	A	8
298	I	L	G	Y	D	R	C	D	A	8
301	Y	D	R	C	D	A	G	W	L	8
304	C	D	A	G	W	L	A	D	G	8
305	D	A	G	W	L	A	D	G	S	8
309	L	A	D	G	S	V	R	Y	P	8
13	C	W	A	D	H	L	S	D	N	7
20	D	N	Y	T	L	D	H	D	R	7
49	V	F	S	H	R	G	G	N	V	7
72	S	G	I	H	K	I	R	I	K	7
120	S	D	A	S	L	V	I	T	D	7
133	D	Y	G	R	Y	K	C	E	V	7
145	L	E	D	D	T	V	V	V	A	7
160	V	F	P	Y	F	P	R	L	G	7
176	E	A	Q	Q	A	C	L	D	Q	7
192	D	Q	L	Y	D	A	W	R	G	7
244	D	K	S	R	Y	D	V	F	C	7
259	G	R	F	Y	Y	L	I	H	P	7
281	N	D	G	A	Q	I	A	K	V	7
292	I	F	A	A	W	K	I	L	G	7
296	W	K	I	L	G	Y	D	R	C	7
302	D	R	C	D	A	G	W	L	A	7
332	V	R	F	V	G	F	P	D	K	7
2	K	S	L	L	L	L	V	L	I	6
37	G	P	H	L	L	V	E	A	E	6
44	A	E	Q	A	K	V	F	S	H	6
52	H	R	G	G	N	V	T	L	P	6
65	R	D	P	T	A	F	G	S	G	6
68	T	A	F	G	S	G	I	H	K	6
79	I	K	W	T	K	L	T	S	D	6
107	G	Y	Q	G	R	V	F	L	K	6
136	R	Y	K	C	E	V	I	E	G	6
154	L	D	L	Q	G	V	V	F	P	6
165	P	R	L	G	R	Y	N	L	N	6
182	L	D	Q	D	A	V	I	A	S	6
185	D	A	V	I	A	S	F	D	Q	6
196	D	A	W	R	G	G	L	D	W	6
197	A	W	R	G	G	L	D	W	C	6
203	D	W	C	N	A	G	W	L	S	6
227	G	G	Q	N	T	V	P	G	V	6
250	V	F	C	F	T	S	N	F	N	6
265	I	H	P	T	K	L	T	Y	D	6
19	S	D	N	Y	T	L	D	H	D	5
54	G	G	N	V	T	L	P	C	K	5
59	L	P	C	K	F	Y	R	D	P	5
74	I	H	K	I	R	I	K	W	T	5
108	Y	Q	G	R	V	F	L	K	G	5
109	Q	G	R	V	F	L	K	G	G	5
169	R	Y	N	L	N	F	H	E	A	5
177	A	Q	Q	A	C	L	D	Q	D	5
246	S	R	Y	D	V	F	C	F	T	5
248	Y	D	V	F	C	F	T	S	N	5
294	A	A	W	K	I	L	G	Y	D	5
335	V	G	F	P	D	K	K	H	K	5
28	R	A	I	H	I	Q	A	E	N	4
30	I	H	I	Q	A	E	N	G	P	4
64	Y	R	D	P	T	A	F	G	S	4
89	L	K	E	V	D	V	F	V	S	4
114	L	K	G	G	S	D	S	D	A	4
167	L	G	R	Y	N	L	N	F	H	4
172	L	N	F	H	E	A	Q	Q	A	4
217	Y	P	I	T	K	P	R	E	P	4
233	P	G	V	R	N	Y	G	F	W	4
235	V	R	N	Y	G	F	W	D	K	4
251	F	C	F	T	S	N	F	N	G	4
257	F	N	G	R	F	Y	Y	L	I	4
258	N	G	R	F	Y	Y	L	I	H	4
280	L	N	D	G	A	Q	I	A	K	4
315	R	Y	P	I	S	R	P	R	R	4
316	Y	P	I	S	R	P	R	R	R	4
324	R	C	S	P	T	E	A	A	V	4
330	A	A	V	R	F	V	G	F	P	4
61	C	K	F	Y	R	D	P	T	A	3
77	I	R	I	K	W	T	K	L	T	3
96	V	S	M	G	Y	H	K	K	T	3
99	G	Y	H	K	K	T	Y	G	G	3
104	T	Y	G	G	Y	Q	G	R	V	3
117	G	S	D	S	D	A	S	L	V	3
175	H	E	A	Q	Q	A	C	L	D	3
178	Q	Q	A	C	L	D	Q	D	A	3
180	A	C	L	D	Q	D	A	V	I	3
198	W	R	G	G	L	D	W	C	N	3
216	Q	Y	P	I	T	K	P	R	E	3
221	K	P	R	E	P	C	G	G	Q	3
222	P	R	E	P	C	G	G	Q	N	3
223	R	E	P	C	G	G	Q	N	T	3
225	P	C	G	G	Q	N	T	V	P	3
236	R	N	Y	G	F	W	D	K	D	3
238	Y	G	F	W	D	K	D	K	S	3
241	W	D	K	D	K	S	R	Y	D	3
276	V	Q	A	C	L	N	D	G	A	3
290	G	Q	I	F	A	A	W	K	I	3
300	G	Y	D	R	C	D	A	G	W	3
24	L	D	H	D	R	A	I	H	I	2
34	A	E	N	G	P	H	L	L	V	2
38	P	H	L	L	V	E	A	E	Q	2
46	Q	A	K	V	F	S	H	R	G	2
47	A	K	V	F	S	H	R	G	G	2
63	F	Y	R	D	P	T	A	F	G	2
70	F	G	S	G	I	H	K	I	R	2
75	H	K	I	R	I	K	W	T	K	2
85	T	S	D	Y	L	K	E	V	D	2
86	S	D	Y	L	K	E	V	D	V	2
110	G	R	V	F	L	K	G	G	S	2
115	K	G	G	S	D	S	D	A	S	2
131	L	E	D	Y	G	R	Y	K	C	2
135	G	R	Y	K	C	E	V	I	E	2
152	V	A	L	D	L	Q	G	V	V	2
168	G	R	Y	N	L	N	F	H	E	2
184	Q	D	A	V	I	A	S	F	D	2
200	G	G	L	D	W	C	N	A	G	2
206	N	A	G	W	L	S	D	G	S	2
207	A	G	W	L	S	D	G	S	V	2
208	G	W	L	S	D	G	S	V	Q	2
215	V	Q	Y	P	I	T	K	P	R	2
220	T	K	P	R	E	P	C	G	G	2
226	C	G	G	Q	N	T	V	P	G	2
229	Q	N	T	V	P	G	V	R	N	2
266	H	P	T	K	L	T	Y	D	E	2
278	A	C	L	N	D	G	A	Q	I	2
283	G	A	Q	I	A	K	V	G	Q	2
295	A	W	K	I	L	G	Y	D	R	2
299	L	G	Y	D	R	C	D	A	G	2
303	R	C	D	A	G	W	L	A	D	2
314	V	R	Y	P	I	S	R	P	R	2
318	I	S	R	P	R	R	R	C	S	2
319	S	R	P	R	R	R	C	S	P	2
322	R	R	R	C	S	P	T	E	A	2
323	R	R	C	S	P	T	E	A	A	2
325	C	S	P	T	E	A	A	V	R	2
338	P	D	K	K	H	K	L	Y	G	2
341	K	H	K	L	Y	G	V	Y	C	2
12	I	C	W	A	D	H	L	S	D	1
15	A	D	H	L	S	D	N	Y	T	1
18	L	S	D	N	Y	T	L	D	H	1
21	N	Y	T	L	D	H	D	R	A	1
26	H	D	R	A	I	H	I	Q	A	1
60	P	C	K	F	Y	R	D	P	T	1
71	G	S	G	I	H	K	I	R	I	1
82	T	K	L	T	S	D	Y	L	K	1
98	M	G	Y	H	K	K	T	Y	G	1
101	H	K	K	T	Y	G	G	Y	Q	1
102	K	K	T	Y	G	G	Y	Q	G	1
118	S	D	S	D	A	S	L	V	I	1
127	T	D	L	T	L	E	D	Y	G	1
134	Y	G	R	Y	K	C	E	V	I	1
139	C	E	V	I	E	G	L	E	D	1
161	F	P	Y	F	P	R	L	G	R	1
170	Y	N	L	N	F	H	E	A	Q	1
179	Q	A	C	L	D	Q	D	A	V	1
191	F	D	Q	L	Y	D	A	W	R	1
195	Y	D	A	W	R	G	G	L	D	1
199	R	G	G	L	D	W	C	N	A	1
204	W	C	N	A	G	W	L	S	D	1
211	S	D	G	S	V	Q	Y	P	I	1
213	G	S	V	Q	Y	P	I	T	K	1
247	R	Y	D	V	F	C	F	T	S	1
261	F	Y	Y	L	I	H	P	T	K	1
268	T	K	L	T	Y	D	E	A	V	1
277	Q	A	C	L	N	D	G	A	Q	1
286	I	A	K	V	G	Q	I	F	A	1
289	V	G	Q	I	F	A	A	W	K	1
306	A	G	W	L	A	D	G	S	V	1
307	G	W	L	A	D	G	S	V	R	1
310	A	D	G	S	V	R	Y	P	I	1
312	G	S	V	R	Y	P	I	S	R	1
320	R	P	R	R	R	C	S	P	T	1
321	P	R	R	R	C	S	P	T	E	1
328	T	E	A	A	V	R	F	V	G	1
344	L	Y	G	V	Y	C	F	R	A	1
151P3D4 v.2
HLA Peptide
Scoring Results A26 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
302	S	T	Y	D	S	L	S	P	Y	27	Portion of
234	F	I	F	K	T	I	A	P	L	26	SEQ ID
123	N	T	N	P	S	R	R	P	Y	23	NO: 5;
172	E	V	G	W	K	Y	Q	A	V	23	each start
59	F	V	G	S	Y	K	L	A	Y	22	position
378	A	L	W	K	A	I	E	S	L	22	is
46	I	I	T	Q	G	A	K	D	F	21	specified,
382	A	I	E	S	L	E	E	G	L	21	the length
99	E	G	I	N	I	S	G	S	F	19	of peptide
114	Y	L	A	F	L	H	K	R	M	19	is 9
1	M	L	E	H	T	T	K	T	F	18	amino
102	N	I	S	G	S	F	C	R	N	18	acids, the
212	N	M	K	K	K	I	D	K	Y	18	end
237	K	T	I	A	P	L	A	A	T	18	position
369	D	L	A	G	S	G	Y	C	G	18	for each
16	I	V	V	E	S	I	R	D	H	17	peptide is
34	K	V	D	L	L	V	P	T	K	17	the start
38	L	V	P	T	K	V	T	G	I	17	position
42	K	V	T	G	I	I	T	Q	G	17	plus eight
106	S	F	C	R	N	K	L	K	Y	17
109	R	N	K	L	K	Y	L	A	F	17
193	E	I	H	Y	R	K	N	K	Q	17
4	H	T	T	K	T	F	P	L	R	16
7	K	T	F	P	L	R	A	L	H	16
55	G	H	V	Q	F	V	G	S	Y	16
132	H	F	Q	V	P	S	R	I	F	16
134	Q	V	P	S	R	I	F	W	R	16
197	R	K	N	K	Q	L	M	R	L	16
3	E	H	T	T	K	T	F	P	L	15
30	K	Q	D	K	K	V	D	L	L	15
45	G	I	I	T	Q	G	A	K	D	15
80	E	K	Q	R	K	D	K	V	L	15
179	A	V	T	A	T	L	E	E	K	15
238	T	I	A	P	L	A	A	T	R	15
385	S	L	E	E	G	L	G	G	K	15
36	D	L	L	V	P	T	K	V	T	14
110	N	K	L	K	Y	L	A	F	L	14
299	T	S	S	S	T	Y	D	S	L	14
6	T	K	T	F	P	L	R	A	L	13
13	A	L	H	I	V	V	E	S	I	13
51	A	K	D	F	G	H	V	Q	F	13
58	Q	F	V	G	S	Y	K	L	A	13
107	F	C	R	N	K	L	K	Y	L	13
117	F	L	H	K	R	M	N	T	N	13
138	R	I	F	W	R	Q	E	K	A	13
169	A	P	H	E	V	G	W	K	Y	13
180	V	T	A	T	L	E	E	K	R	13
182	A	T	L	E	E	K	R	K	E	13
216	K	I	D	K	Y	T	E	S	P	13
226	G	G	S	P	R	G	L	G	F	13
228	S	P	R	G	L	G	F	I	F	13
256	R	T	P	R	A	G	S	S	A	13
275	P	V	P	A	A	S	P	A	A	13
288	R	T	P	W	T	R	P	S	S	13
291	W	T	R	P	S	S	C	P	T	13
296	S	C	P	T	S	S	S	T	Y	13
353	P	K	S	E	N	N	S	W	Y	13
356	E	N	N	S	W	Y	V	E	N	13
367	P	A	D	L	A	G	S	G	Y	13
399	R	K	A	E	N	G	P	H	L	13
5	T	T	K	T	F	P	L	R	A	12
17	V	V	E	S	I	R	D	H	S	12
20	S	I	R	D	H	S	G	Q	K	12
21	I	R	D	H	S	G	Q	K	M	12
43	V	T	G	I	I	T	Q	G	A	12
47	I	T	Q	G	A	K	D	F	G	12
53	D	F	G	H	V	Q	F	V	G	12
69	N	D	G	E	H	W	T	V	Y	12
74	W	T	V	Y	Q	D	E	K	Q	12
75	T	V	Y	Q	D	E	K	Q	R	12
93	A	V	V	V	S	C	E	G	I	12
100	G	I	N	I	S	G	S	F	C	12
159	E	A	Y	K	K	V	C	L	S	12
163	K	V	C	L	S	G	A	P	H	12
183	T	L	E	E	K	R	K	E	K	12
188	R	K	E	K	A	E	I	H	Y	12
220	Y	T	E	S	P	G	G	G	S	12
224	P	G	G	G	S	P	R	G	L	12
231	G	L	G	F	I	F	K	T	I	12
247	A	T	R	I	G	H	P	G	G	12
298	P	T	S	S	S	T	Y	D	S	12
306	S	L	S	P	Y	G	P	R	N	12
361	Y	V	E	N	G	R	P	A	D	12
15	H	I	V	V	E	S	I	R	D	11
23	D	H	S	G	Q	K	M	K	Q	11
29	M	K	Q	D	K	K	V	D	L	11
32	D	K	K	V	D	L	L	V	P	11
37	L	L	V	P	T	K	V	T	G	11
40	P	T	K	V	T	G	I	I	T	11
56	H	V	Q	F	V	G	S	Y	K	11
57	V	Q	F	V	G	S	Y	K	L	11
64	K	L	A	Y	S	N	D	G	E	11
72	E	H	W	T	V	Y	Q	D	E	11
86	K	V	L	L	G	R	K	A	V	11
87	V	L	L	G	R	K	A	V	V	11
94	V	V	V	S	C	E	G	I	N	11
95	V	V	S	C	E	G	I	N	I	11
125	N	P	S	R	R	P	Y	H	F	11
153	P	Q	G	H	A	S	E	A	Y	11
158	S	E	A	Y	K	K	V	C	L	11
165	C	L	S	G	A	P	H	E	V	11
204	R	L	Q	K	Q	A	E	K	N	11
205	L	Q	K	Q	A	E	K	N	M	11
244	A	T	R	A	T	R	I	G	H	11
249	R	I	G	H	P	G	G	R	T	11
262	S	S	A	H	R	P	P	A	L	11
277	P	A	A	S	P	A	A	W	L	11
305	D	S	L	S	P	Y	G	P	R	11
321	H	S	P	S	G	G	G	G	L	11
328	G	L	K	K	P	A	R	H	C	11
343	V	L	A	R	G	K	P	Q	R	11
362	V	E	N	G	R	P	A	D	L	11
371	A	G	S	G	Y	C	G	A	L	11
389	G	L	G	G	K	Q	K	D	K	11
19	E	S	I	R	D	H	S	G	Q	10
81	K	Q	R	K	D	K	V	L	L	10
88	L	L	G	R	K	A	V	V	V	10
111	K	L	K	Y	L	A	F	L	H	10
190	E	K	A	E	I	H	Y	R	K	10
194	I	H	Y	R	K	N	K	Q	L	10
195	H	Y	R	K	N	K	Q	L	M	10
201	Q	L	M	R	L	Q	K	Q	A	10
222	E	S	P	G	G	G	S	P	R	10
233	G	F	I	F	K	T	I	A	P	10
241	P	L	A	A	T	R	A	T	R	10
284	W	L	P	L	R	T	P	W	T	10
308	S	P	Y	G	P	R	N	P	L	10
315	P	L	P	N	P	R	H	S	P	10
336	C	Q	G	Q	K	H	N	V	L	10
342	N	V	L	A	R	G	K	P	Q	10
381	K	A	I	E	S	L	E	E	G	10
388	E	G	L	G	G	K	Q	K	D	10
10	P	L	R	A	L	H	I	V	V	9
52	K	D	F	G	H	V	Q	F	V	9
79	D	E	K	Q	R	K	D	K	V	9
104	S	G	S	F	C	R	N	K	L	9
116	A	F	L	H	K	R	M	N	T	9
144	E	K	A	D	G	G	S	C	C	9
147	D	G	G	S	C	C	P	Q	G	9
176	K	Y	Q	A	V	T	A	T	L	9
185	E	E	K	R	K	E	K	A	E	9
186	E	K	R	K	E	K	A	E	I	9
215	K	K	I	D	K	Y	T	E	S	9
265	H	R	P	P	A	L	S	A	R	9
269	A	L	S	A	R	A	P	V	P	9
279	A	S	P	A	A	W	L	P	L	9
286	P	L	R	T	P	W	T	R	P	9
384	E	S	L	E	E	G	L	G	G	9
8	T	F	P	L	R	A	L	H	I	8
85	D	K	V	L	L	G	R	K	A	8
139	I	F	W	R	Q	E	K	A	D	8
218	D	K	Y	T	E	S	P	G	G	8
235	I	F	K	T	I	A	P	L	A	8
396	D	K	E	R	K	A	E	N	G	8
400	K	A	E	N	G	P	H	L	L	8
24	H	S	G	Q	K	M	K	Q	D	7
33	K	K	V	D	L	L	V	P	T	7
49	Q	G	A	K	D	F	G	H	V	7
54	F	G	H	V	Q	F	V	G	S	7
62	S	Y	K	L	A	Y	S	N	D	7
70	D	G	E	H	W	T	V	Y	Q	7
82	Q	R	K	D	K	V	L	L	G	7
83	R	K	D	K	V	L	L	G	R	7
84	K	D	K	V	L	L	G	R	K	7
90	G	R	K	A	V	V	V	S	C	7
130	P	Y	H	F	Q	V	P	S	R	7
156	H	A	S	E	A	Y	K	K	V	7
161	Y	K	K	V	C	L	S	G	A	7
198	K	N	K	Q	L	M	R	L	Q	7
210	E	K	N	M	K	K	K	I	D	7
230	R	G	L	G	F	I	F	K	T	7
324	S	G	G	G	G	L	K	K	P	7
365	G	R	P	A	D	L	A	G	S	7
374	G	Y	C	G	A	L	W	K	A	7
387	E	E	G	L	G	G	K	Q	K	7
398	E	R	K	A	E	N	G	P	H	7
11	L	R	A	L	H	I	V	V	E	6
12	R	A	L	H	I	V	V	E	S	6
60	V	G	S	Y	K	L	A	Y	S	6
89	L	G	R	K	A	V	V	V	S	6
91	R	K	A	V	V	V	S	C	E	6
96	V	S	C	E	G	I	N	I	S	6
98	C	E	G	I	N	I	S	G	S	6
128	R	R	P	Y	H	F	Q	V	P	6
175	W	K	Y	Q	A	V	T	A	T	6
200	K	Q	L	M	R	L	Q	K	Q	6
207	K	Q	A	E	K	N	M	K	K	6
208	Q	A	E	K	N	M	K	K	K	6
245	T	R	A	T	R	I	G	H	P	6
258	P	R	A	G	S	S	A	H	R	6
271	S	A	R	A	P	V	P	A	A	6
280	S	P	A	A	W	L	P	L	R	6
311	G	P	R	N	P	L	P	N	P	6
338	G	Q	K	H	N	V	L	A	R	6
339	Q	K	H	N	V	L	A	R	G	6
363	E	N	G	R	P	A	D	L	A	6
370	L	A	G	S	G	Y	C	G	A	6
71	G	E	H	W	T	V	Y	Q	D	5
77	Y	Q	D	E	K	Q	R	K	D	5
112	L	K	Y	L	A	F	L	H	K	5
113	K	Y	L	A	F	L	H	K	R	5
131	Y	H	F	Q	V	P	S	R	I	5
135	V	P	S	R	I	F	W	R	Q	5
167	S	G	A	P	H	E	V	G	W	5
168	G	A	P	H	E	V	G	W	K	5
189	K	E	K	A	E	I	H	Y	R	5
191	K	A	E	I	H	Y	R	K	N	5
227	G	S	P	R	G	L	G	F	I	5
248	T	R	I	G	H	P	G	G	R	5
272	A	R	A	P	V	P	A	A	S	5
344	L	A	R	G	K	P	Q	R	K	5
350	Q	R	K	P	K	S	E	N	N	5
357	N	N	S	W	Y	V	E	N	G	5
395	K	D	K	E	R	K	A	E	N	5
9	F	P	L	R	A	L	H	I	V	4
41	T	K	V	T	G	I	I	T	Q	4
126	P	S	R	R	P	Y	H	F	Q	4
137	S	R	I	F	W	R	Q	E	K	4
141	W	R	Q	E	K	A	D	G	G	4
150	S	C	C	P	Q	G	H	A	S	4
151	C	C	P	Q	G	H	A	S	E	4
152	C	P	Q	G	H	A	S	E	A	4
187	K	R	K	E	K	A	E	I	H	4
203	M	R	L	Q	K	Q	A	E	K	4
219	K	Y	T	E	S	P	G	G	G	4
223	S	P	G	G	G	S	P	R	G	4
229	P	R	G	L	G	F	I	F	K	4
252	H	P	G	G	R	T	P	R	A	4
266	R	P	P	A	L	S	A	R	A	4
276	V	P	A	A	S	P	A	A	W	4
282	A	A	W	L	P	L	R	T	P	4
292	T	R	P	S	S	C	P	T	S	4
295	S	S	C	P	T	S	S	S	T	4
303	T	Y	D	S	L	S	P	Y	G	4
320	R	H	S	P	S	G	G	G	G	4
327	G	G	L	K	K	P	A	R	H	4
335	H	C	Q	G	Q	K	H	N	V	4
346	R	G	K	P	Q	R	K	P	K	4
347	G	K	P	Q	R	K	P	K	S	4
351	R	K	P	K	S	E	N	N	S	4
366	R	P	A	D	L	A	G	S	G	4
386	L	E	E	G	L	G	G	K	Q	4
391	G	G	K	Q	K	D	K	E	R	4
393	K	Q	K	D	K	E	R	K	A	4
14	L	H	I	V	V	E	S	I	R	3
26	G	Q	K	M	K	Q	D	K	K	3
27	Q	K	M	K	Q	D	K	K	V	3
44	T	G	I	I	T	Q	G	A	K	3
61	G	S	Y	K	L	A	Y	S	N	3
68	S	N	D	G	E	H	W	T	V	3
76	V	Y	Q	D	E	K	Q	R	K	3
97	S	C	E	G	I	N	I	S	G	3
101	I	N	I	S	G	S	F	C	R	3
115	L	A	F	L	H	K	R	M	N	3
124	T	N	P	S	R	R	P	Y	H	3
127	S	R	R	P	Y	H	F	Q	V	3
133	F	Q	V	P	S	R	I	F	W	3
145	K	A	D	G	G	S	C	C	P	3
146	A	D	G	G	S	C	C	P	Q	3
155	G	H	A	S	E	A	Y	K	K	3
160	A	Y	K	K	V	C	L	S	G	3
164	V	C	L	S	G	A	P	H	E	3
171	H	E	V	G	W	K	Y	Q	A	3
174	G	W	K	Y	Q	A	V	T	A	3
192	A	E	I	H	Y	R	K	N	K	3
196	Y	R	K	N	K	Q	L	M	R	3
202	L	M	R	L	Q	K	Q	A	E	3
221	T	E	S	P	G	G	G	S	P	3
251	G	H	P	G	G	R	T	P	R	3
255	G	R	T	P	R	A	G	S	S	3
259	R	A	G	S	S	A	H	R	P	3
264	A	H	R	P	P	A	L	S	A	3
267	P	P	A	L	S	A	R	A	P	3
273	R	A	P	V	P	A	A	S	P	3
274	A	P	V	P	A	A	S	P	A	3
281	P	A	A	W	L	P	L	R	T	3
283	A	W	L	P	L	R	T	P	W	3
309	P	Y	G	P	R	N	P	L	P	3
312	P	R	N	P	L	P	N	P	R	3
313	R	N	P	L	P	N	P	R	H	3
314	N	P	L	P	N	P	R	H	S	3
316	L	P	N	P	R	H	S	P	S	3
317	P	N	P	R	H	S	P	S	G	3
318	N	P	R	H	S	P	S	G	G	3
323	P	S	G	G	G	G	L	K	K	3
325	G	G	G	G	L	K	K	P	A	3
326	G	G	G	L	K	K	P	A	R	3
329	L	K	K	P	A	R	H	C	Q	3
331	K	P	A	R	H	C	Q	G	Q	3
333	A	R	H	C	Q	G	Q	K	H	3
349	P	Q	R	K	P	K	S	E	N	3
352	K	P	K	S	E	N	N	S	W	3
364	N	G	R	P	A	D	L	A	G	3
390	L	G	G	K	Q	K	D	K	E	3
394	Q	K	D	K	E	R	K	A	E	3
22	R	D	H	S	G	Q	K	M	K	2
25	S	G	Q	K	M	K	Q	D	K	2
28	K	M	K	Q	D	K	K	V	D	2
31	Q	D	K	K	V	D	L	L	V	2
48	T	Q	G	A	K	D	F	G	H	2
50	G	A	K	D	F	G	H	V	Q	2
65	L	A	Y	S	N	D	G	E	H	2
78	Q	D	E	K	Q	R	K	D	K	2
103	I	S	G	S	F	C	R	N	K	2
105	G	S	F	C	R	N	K	L	K	2
108	C	R	N	K	L	K	Y	L	A	2
118	L	H	K	R	M	N	T	N	P	2
120	K	R	M	N	T	N	P	S	R	2
121	R	M	N	T	N	P	S	R	R	2
140	F	W	R	Q	E	K	A	D	G	2
142	R	Q	E	K	A	D	G	G	S	2
143	Q	E	K	A	D	G	G	S	C	2
148	G	G	S	C	C	P	Q	G	H	2
154	Q	G	H	A	S	E	A	Y	K	2
162	K	K	V	C	L	S	G	A	P	2
173	V	G	W	K	Y	Q	A	V	T	2
184	L	E	E	K	R	K	E	K	A	2
209	A	E	K	N	M	K	K	K	I	2
211	K	N	M	K	K	K	I	D	K	2
213	M	K	K	K	I	D	K	Y	T	2
217	I	D	K	Y	T	E	S	P	G	2
232	L	G	F	I	F	K	T	I	A	2
239	I	A	P	L	A	A	T	R	A	2
242	L	A	A	T	R	A	T	R	I	2
250	I	G	H	P	G	G	R	T	P	2
254	G	G	R	T	P	R	A	G	S	2
257	T	P	R	A	G	S	S	A	H	2
268	P	A	L	S	A	R	A	P	V	2
270	L	S	A	R	A	P	V	P	A	2
278	A	A	S	P	A	A	W	L	P	2
287	L	R	T	P	W	T	R	P	S	2
289	T	P	W	T	R	P	S	S	C	2
293	R	P	S	S	C	P	T	S	S	2
294	P	S	S	C	P	T	S	S	S	2
297	C	P	T	S	S	S	T	Y	D	2
304	Y	D	S	L	S	P	Y	G	P	2
307	L	S	P	Y	G	P	R	N	P	2
319	P	R	H	S	P	S	G	G	G	2
322	S	P	S	G	G	G	G	L	K	2
330	K	K	P	A	R	H	C	Q	G	2
334	R	H	C	Q	G	Q	K	H	N	2
337	Q	G	Q	K	H	N	V	L	A	2
340	K	H	N	V	L	A	R	G	K	2
345	A	R	G	K	P	Q	R	K	P	2
348	K	P	Q	R	K	P	K	S	E	2
360	W	Y	V	E	N	G	R	P	A	2
375	Y	C	G	A	L	W	K	A	I	2
376	C	G	A	L	W	K	A	I	E	2
377	G	A	L	W	K	A	I	E	S	2
379	L	W	K	A	I	E	S	L	E	2
380	W	K	A	I	E	S	L	E	E	2
392	G	K	Q	K	D	K	E	R	K	2
397	K	E	R	K	A	E	N	G	P	2
18	V	E	S	I	R	D	H	S	G	1
35	V	D	L	L	V	P	T	K	V	1
39	V	P	T	K	V	T	G	I	I	1
66	A	Y	S	N	D	G	E	H	W	1
67	Y	S	N	D	G	E	H	W	T	1
73	H	W	T	V	Y	Q	D	E	K	1
92	K	A	V	V	V	S	C	E	G	1
122	M	N	T	N	P	S	R	R	P	1
129	R	P	Y	H	F	Q	V	P	S	1
136	P	S	R	I	F	W	R	Q	E	1
149	G	S	C	C	P	Q	G	H	A	1
177	Y	Q	A	V	T	A	T	L	E	1
178	Q	A	V	T	A	T	L	E	E	1
181	T	A	T	L	E	E	K	R	K	1
199	N	K	Q	L	M	R	L	Q	K	1
206	Q	K	Q	A	E	K	N	M	K	1
214	K	K	K	I	D	K	Y	T	E	1
225	G	G	G	S	P	R	G	L	G	1
236	F	K	T	I	A	P	L	A	A	1
240	A	P	L	A	A	T	R	A	T	1
253	P	G	G	R	T	P	R	A	G	1
260	A	G	S	S	A	H	R	P	P	1
261	G	S	S	A	H	R	P	P	A	1
263	S	A	H	R	P	P	A	L	S	1
290	P	W	T	R	P	S	S	C	P	1
300	S	S	S	T	Y	D	S	L	S	1
301	S	S	T	Y	D	S	L	S	P	1
310	Y	G	P	R	N	P	L	P	N	1
332	P	A	R	H	C	Q	G	Q	K	1
341	H	N	V	L	A	R	G	K	P	1
355	S	E	N	N	S	W	Y	V	E	1
358	N	S	W	Y	V	E	N	G	R	1
359	S	W	Y	V	E	N	G	R	P	1
372	G	S	G	Y	C	G	A	L	W	1

TABLE XXVIII
151P3D4 v.1
HLA Peptide
Scoring Results B*0702 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
164	F	P	R	L	G	R	Y	N	L	23	Portion
320	R	P	R	R	R	C	S	P	T	20	of SEQ
224	E	P	C	G	G	Q	N	T	V	19	ID NO:
66	D	P	T	A	F	G	S	G	I	18	3; each
326	S	P	T	E	A	A	V	R	F	18	start
232	V	P	G	V	R	N	Y	G	F	17	position
51	S	H	R	G	G	N	V	T	L	16	is
146	E	D	D	T	V	V	V	A	L	16	specified,
161	F	P	Y	F	P	R	L	G	R	16	the length
221	K	P	R	E	P	C	G	G	Q	16	of
1	M	K	S	L	L	L	L	V	L	15	peptide is
34	A	E	N	G	P	H	L	L	V	15	9 amino
32	I	Q	A	E	N	G	P	H	L	14	acids, the
76	K	I	R	I	K	W	T	K	L	14	end
106	G	G	Y	Q	G	R	V	F	L	14	position
186	A	V	I	A	S	F	D	Q	L	14	for each
116	G	G	S	D	S	D	A	S	L	13	peptide is
121	D	A	S	L	V	I	T	D	L	13	the start
153	A	L	D	L	Q	G	V	V	F	13	position
159	V	V	F	P	Y	F	P	R	L	13	plus eight
194	L	Y	D	A	W	R	G	G	L	13
256	N	F	N	G	R	F	Y	Y	L	13
37	G	P	H	L	L	V	E	A	E	12
123	S	L	V	I	T	D	L	T	L	12
148	D	T	V	V	V	A	L	D	L	12
174	F	H	E	A	Q	Q	A	C	L	12
266	H	P	T	K	L	T	Y	D	E	12
272	Y	D	E	A	V	Q	A	C	L	12
301	Y	D	R	C	D	A	G	W	L	12
323	R	R	C	S	P	T	E	A	A	12
324	R	C	S	P	T	E	A	A	V	12
337	F	P	D	K	K	H	K	L	Y	12
10	I	S	I	C	W	A	D	H	L	11
59	L	P	C	K	F	Y	R	D	P	11
118	S	D	S	D	A	S	L	V	I	11
145	L	E	D	D	T	V	V	V	A	11
262	Y	Y	L	I	H	P	T	K	L	11
287	A	K	V	G	Q	I	F	A	A	11
291	Q	I	F	A	A	W	K	I	L	11
310	A	D	G	S	V	R	Y	P	I	11
329	E	A	A	V	R	F	V	G	F	11
16	D	H	L	S	D	N	Y	T	L	10
33	Q	A	E	N	G	P	H	L	L	10
81	W	T	K	L	T	S	D	Y	L	10
90	K	E	V	D	V	F	V	S	M	10
119	D	S	D	A	S	L	V	I	T	10
137	Y	K	C	E	V	I	E	G	L	10
144	G	L	E	D	D	T	V	V	V	10
166	R	L	G	R	Y	N	L	N	F	10
180	A	C	L	D	Q	D	A	V	I	10
202	L	D	W	C	N	A	G	W	L	10
217	Y	P	I	T	K	P	R	E	P	10
245	K	S	R	Y	D	V	F	C	F	10
263	Y	L	I	H	P	T	K	L	T	10
278	A	C	L	N	D	G	A	Q	I	10
284	A	Q	I	A	K	V	G	Q	I	10
316	Y	P	I	S	R	P	R	R	R	10
322	R	R	R	C	S	P	T	E	A	10
336	G	F	P	D	K	K	H	K	L	10
2	K	S	L	L	L	L	V	L	I	9
26	H	D	R	A	I	H	I	Q	A	9
49	V	F	S	H	R	G	G	N	V	9
62	K	F	Y	R	D	P	T	A	F	9
69	A	F	G	S	G	I	H	K	I	9
77	I	R	I	K	W	T	K	L	T	9
87	D	Y	L	K	E	V	D	V	F	9
88	Y	L	K	E	V	D	V	F	V	9
96	V	S	M	G	Y	H	K	K	T	9
104	T	Y	G	G	Y	Q	G	R	V	9
105	Y	G	G	Y	Q	G	R	V	F	9
114	L	K	G	G	S	D	S	D	A	9
122	A	S	L	V	I	T	D	L	T	9
134	Y	G	R	Y	K	C	E	V	I	9
143	E	G	L	E	D	D	T	V	V	9
156	L	Q	G	V	V	F	P	Y	F	9
181	C	L	D	Q	D	A	V	I	A	9
183	D	Q	D	A	V	I	A	S	F	9
212	D	G	S	V	Q	Y	P	I	T	9
242	D	K	D	K	S	R	Y	D	V	9
281	N	D	G	A	Q	I	A	K	V	9
285	Q	I	A	K	V	G	Q	I	F	9
298	I	L	G	Y	D	R	C	D	A	9
327	P	T	E	A	A	V	R	F	V	9
15	A	D	H	L	S	D	N	Y	T	8
36	N	G	P	H	L	L	V	E	A	8
41	L	V	E	A	E	Q	A	K	V	8
42	V	E	A	E	Q	A	K	V	F	8
50	F	S	H	R	G	G	N	V	T	8
60	P	C	K	F	Y	R	D	P	T	8
63	F	Y	R	D	P	T	A	F	G	8
84	L	T	S	D	Y	L	K	E	V	8
86	S	D	Y	L	K	E	V	D	V	8
141	V	I	E	G	L	E	D	D	T	8
142	I	E	G	L	E	D	D	T	V	8
169	R	Y	N	L	N	F	H	E	A	8
189	A	S	F	D	Q	L	Y	D	A	8
199	R	G	G	L	D	W	C	N	A	8
207	A	G	W	L	S	D	G	S	V	8
211	S	D	G	S	V	Q	Y	P	I	8
223	R	E	P	C	G	G	Q	N	T	8
227	G	G	Q	N	T	V	P	G	V	8
243	K	D	K	S	R	Y	D	V	F	8
246	S	R	Y	D	V	F	C	F	T	8
253	F	T	S	N	F	N	G	R	F	8
260	R	F	Y	Y	L	I	H	P	T	8
270	L	T	Y	D	E	A	V	Q	A	8
286	I	A	K	V	G	Q	I	F	A	8
306	A	G	W	L	A	D	G	S	V	8
22	Y	T	L	D	H	D	R	A	I	7
61	C	K	F	Y	R	D	P	T	A	7
71	G	S	G	I	H	K	I	R	I	7
74	I	H	K	I	R	I	K	W	T	7
117	G	S	D	S	D	A	S	L	V	7
133	D	Y	G	R	Y	K	C	E	V	7
151	V	V	A	L	D	L	Q	G	V	7
152	V	A	L	D	L	Q	G	V	V	7
178	Q	Q	A	C	L	D	Q	D	A	7
179	Q	A	C	L	D	Q	D	A	V	7
249	D	V	F	C	F	T	S	N	F	7
257	F	N	G	R	F	Y	Y	L	I	7
268	T	K	L	T	Y	D	E	A	V	7
276	V	Q	A	C	L	N	D	G	A	7
302	D	R	C	D	A	G	W	L	A	7
342	H	K	L	Y	G	V	Y	C	F	7
344	L	Y	G	V	Y	C	F	R	A	7
4	L	L	L	L	V	L	I	S	I	6
7	L	V	L	I	S	I	C	W	A	6
21	N	Y	T	L	D	H	D	R	A	6
24	L	D	H	D	R	A	I	H	I	6
35	E	N	G	P	H	L	L	V	E	6
39	H	L	L	V	E	A	E	Q	A	6
53	R	G	G	N	V	T	L	P	C	6
55	G	N	V	T	L	P	C	K	F	6
172	L	N	F	H	E	A	Q	Q	A	6
197	A	W	R	G	G	L	D	W	C	6
218	P	I	T	K	P	R	E	P	C	6
229	Q	N	T	V	P	G	V	R	N	6
267	P	T	K	L	T	Y	D	E	A	6
279	C	L	N	D	G	A	Q	I	A	6
290	G	Q	I	F	A	A	W	K	I	6
303	R	C	D	A	G	W	L	A	D	6
317	P	I	S	R	P	R	R	R	C	6
331	A	V	R	F	V	G	F	P	D	6
339	D	K	K	H	K	L	Y	G	V	6
52	H	R	G	G	N	V	T	L	P	5
188	I	A	S	F	D	Q	L	Y	D	5
225	P	C	G	G	Q	N	T	V	P	5
226	C	G	G	Q	N	T	V	P	G	5
244	D	K	S	R	Y	D	V	F	C	5
288	K	V	G	Q	I	F	A	A	W	5
313	S	V	R	Y	P	I	S	R	P	5
318	I	S	R	P	R	R	R	C	S	5
12	I	C	W	A	D	H	L	S	D	4
18	L	S	D	N	Y	T	L	D	H	4
43	E	A	E	Q	A	K	V	F	S	4
44	A	E	Q	A	K	V	F	S	H	4
45	E	Q	A	K	V	F	S	H	R	4
56	N	V	T	L	P	C	K	F	Y	4
70	F	G	S	G	I	H	K	I	R	4
108	Y	Q	G	R	V	F	L	K	G	4
154	L	D	L	Q	G	V	V	F	P	4
155	D	L	Q	G	V	V	F	P	Y	4
158	G	V	V	F	P	Y	F	P	R	4
209	W	L	S	D	G	S	V	Q	Y	4
210	L	S	D	G	S	V	Q	Y	P	4
214	S	V	Q	Y	P	I	T	K	P	4
258	N	G	R	F	Y	Y	L	I	H	4
280	L	N	D	G	A	Q	I	A	K	4
304	C	D	A	G	W	L	A	D	G	4
309	L	A	D	G	S	V	R	Y	P	4
328	T	E	A	A	V	R	F	V	G	4
330	A	A	V	R	F	V	G	F	P	4
334	F	V	G	F	P	D	K	K	H	4
341	K	H	K	L	Y	G	V	Y	C	4
343	K	L	Y	G	V	Y	C	F	R	4
3	S	L	L	L	L	V	L	I	S	3
9	L	I	S	I	C	W	A	D	H	3
17	H	L	S	D	N	Y	T	L	D	3
23	T	L	D	H	D	R	A	I	H	3
68	T	A	F	G	S	G	I	H	K	3
78	R	I	K	W	T	K	L	T	S	3
80	K	W	T	K	L	T	S	D	Y	3
83	K	L	T	S	D	Y	L	K	E	3
91	E	V	D	V	F	V	S	M	G	3
103	K	T	Y	G	G	Y	Q	G	R	3
107	G	Y	Q	G	R	V	F	L	K	3
115	K	G	G	S	D	S	D	A	S	3
125	V	I	T	D	L	T	L	E	D	3
132	E	D	Y	G	R	Y	K	C	E	3
135	G	R	Y	K	C	E	V	I	E	3
139	C	E	V	I	E	G	L	E	D	3
150	V	V	V	A	L	D	L	Q	G	3
167	L	G	R	Y	N	L	N	F	H	3
176	E	A	Q	Q	A	C	L	D	Q	3
177	A	Q	Q	A	C	L	D	Q	D	3
196	D	A	W	R	G	G	L	D	W	3
198	W	R	G	G	L	D	W	C	N	3
204	W	C	N	A	G	W	L	S	D	3
205	C	N	A	G	W	L	S	D	G	3
215	V	Q	Y	P	I	T	K	P	R	3
219	I	T	K	P	R	E	P	C	G	3
231	T	V	P	G	V	R	N	Y	G	3
234	G	V	R	N	Y	G	F	W	D	3
236	R	N	Y	G	F	W	D	K	D	3
264	L	I	H	P	T	K	L	T	Y	3
269	K	L	T	Y	D	E	A	V	Q	3
271	T	Y	D	E	A	V	Q	A	C	3
274	E	A	V	Q	A	C	L	N	D	3
275	A	V	Q	A	C	L	N	D	G	3
292	I	F	A	A	W	K	I	L	G	3
293	F	A	A	W	K	I	L	G	Y	3
294	A	A	W	K	I	L	G	Y	D	3
295	A	W	K	I	L	G	Y	D	R	3
297	K	I	L	G	Y	D	R	C	D	3
307	G	W	L	A	D	G	S	V	R	3
308	W	L	A	D	G	S	V	R	Y	3
311	D	G	S	V	R	Y	P	I	S	3
315	R	Y	P	I	S	R	P	R	R	3
321	P	R	R	R	C	S	P	T	E	3
333	R	F	V	G	F	P	D	K	K	3
338	P	D	K	K	H	K	L	Y	G	3
340	K	K	H	K	L	Y	G	V	Y	3
27	D	R	A	I	H	I	Q	A	E	2
28	R	A	I	H	I	Q	A	E	N	2
29	A	I	H	I	Q	A	E	N	G	2
31	H	I	Q	A	E	N	G	P	H	2
47	A	K	V	F	S	H	R	G	G	2
48	K	V	F	S	H	R	G	G	N	2
64	Y	R	D	P	T	A	F	G	S	2
65	R	D	P	T	A	F	G	S	G	2
73	G	I	H	K	I	R	I	K	W	2
79	I	K	W	T	K	L	T	S	D	2
85	T	S	D	Y	L	K	E	V	D	2
89	L	K	E	V	D	V	F	V	S	2
95	F	V	S	M	G	Y	H	K	K	2
99	G	Y	H	K	K	T	Y	G	G	2
102	K	K	T	Y	G	G	Y	Q	G	2
109	Q	G	R	V	F	L	K	G	G	2
111	R	V	F	L	K	G	G	S	D	2
112	V	F	L	K	G	G	S	D	S	2
113	F	L	K	G	G	S	D	S	D	2
120	S	D	A	S	L	V	I	T	D	2
126	I	T	D	L	T	L	E	D	Y	2
131	L	E	D	Y	G	R	Y	K	C	2
136	R	Y	K	C	E	V	I	E	G	2
147	D	D	T	V	V	V	A	L	D	2
165	P	R	L	G	R	Y	N	L	N	2
182	L	D	Q	D	A	V	I	A	S	2
184	Q	D	A	V	I	A	S	F	D	2
190	S	F	D	Q	L	Y	D	A	W	2
195	Y	D	A	W	R	G	G	L	D	2
201	G	L	D	W	C	N	A	G	W	2
208	G	W	L	S	D	G	S	V	Q	2
222	P	R	E	P	C	G	G	Q	N	2
230	N	T	V	P	G	V	R	N	Y	2
240	F	W	D	K	D	K	S	R	Y	2
247	R	Y	D	V	F	C	F	T	S	2
248	Y	D	V	F	C	F	T	S	N	2
254	T	S	N	F	N	G	R	F	Y	2
265	I	H	P	T	K	L	T	Y	D	2
282	D	G	A	Q	I	A	K	V	G	2
283	G	A	Q	I	A	K	V	G	Q	2
300	G	Y	D	R	C	D	A	G	W	2
314	V	R	Y	P	I	S	R	P	R	2
325	C	S	P	T	E	A	A	V	R	2
332	V	R	F	V	G	F	P	D	K	2
345	Y	G	V	Y	C	F	R	A	Y	2
346	G	V	Y	C	F	R	A	Y	N	2
8	V	L	I	S	I	C	W	A	D	1
13	C	W	A	D	H	L	S	D	N	1
14	W	A	D	H	L	S	D	N	Y	1
25	D	H	D	R	A	I	H	I	Q	1
30	I	H	I	Q	A	E	N	G	P	1
38	P	H	L	L	V	E	A	E	Q	1
40	L	L	V	E	A	E	Q	A	K	1
54	G	G	N	V	T	L	P	C	K	1
57	V	T	L	P	C	K	F	Y	R	1
58	T	L	P	C	K	F	Y	R	D	1
67	P	T	A	F	G	S	G	I	H	1
94	V	F	V	S	M	G	Y	H	K	1
97	S	M	G	Y	H	K	K	T	Y	1
98	M	G	Y	H	K	K	T	Y	G	1
100	Y	H	K	K	T	Y	G	G	Y	1
101	H	K	K	T	Y	G	G	Y	Q	1
124	L	V	I	T	D	L	T	L	E	1
130	T	L	E	D	Y	G	R	Y	K	1
138	K	C	E	V	I	E	G	L	E	1
140	E	V	I	E	G	L	E	D	D	1
157	Q	G	V	V	F	P	Y	F	P	1
162	P	Y	F	P	R	L	G	R	Y	1
163	Y	F	P	R	L	G	R	Y	N	1
170	Y	N	L	N	F	H	E	A	Q	1
171	N	L	N	F	H	E	A	Q	Q	1
173	N	F	H	E	A	Q	Q	A	C	1
175	H	E	A	Q	Q	A	C	L	D	1
187	V	I	A	S	F	D	Q	L	Y	1
191	F	D	Q	L	Y	D	A	W	R	1
200	G	G	L	D	W	C	N	A	G	1
203	D	W	C	N	A	G	W	L	S	1
206	N	A	G	W	L	S	D	G	S	1
216	Q	Y	P	I	T	K	P	R	E	1
228	G	Q	N	T	V	P	G	V	R	1
233	P	G	V	R	N	Y	G	F	W	1
235	V	R	N	Y	G	F	W	D	K	1
237	N	Y	G	F	W	D	K	D	K	1
250	V	F	C	F	T	S	N	F	N	1
252	C	F	T	S	N	F	N	G	R	1
255	S	N	F	N	G	R	F	Y	Y	1
261	F	Y	Y	L	I	H	P	T	K	1
273	D	E	A	V	Q	A	C	L	N	1
277	Q	A	C	L	N	D	G	A	Q	1
289	V	G	Q	I	F	A	A	W	K	1
299	L	G	Y	D	R	C	D	A	G	1
305	D	A	G	W	L	A	D	G	S	1
319	S	R	P	R	R	R	C	S	P	1
335	V	G	F	P	D	K	K	H	K	1
151P3D4 v.2
HLA Peptide
Scoring Results B*0702 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
308	S	P	Y	G	P	R	N	P	L	27	Portion of
228	S	P	R	G	L	G	F	I	F	21	SEQ ID
240	A	P	L	A	A	T	R	A	T	21	NO: 5;
252	H	P	G	G	R	T	P	R	A	21	each start
274	A	P	V	P	A	A	S	P	A	20	position
266	R	P	P	A	L	S	A	R	A	19	is
39	V	P	T	K	V	T	G	I	I	18	specified,
125	N	P	S	R	R	P	Y	H	F	18	the length
152	C	P	Q	G	H	A	S	E	A	18	of peptide
371	A	G	S	G	Y	C	G	A	L	17	is 9
9	F	P	L	R	A	L	H	I	V	16	amino
81	K	Q	R	K	D	K	V	L	L	16	acids, the
264	A	H	R	P	P	A	L	S	A	16	end
279	A	S	P	A	A	W	L	P	L	16	position
311	G	P	R	N	P	L	P	N	P	16	for each
271	S	A	R	A	P	V	P	A	A	15	peptide is
277	P	A	A	S	P	A	A	W	L	15	the start
322	S	P	S	G	G	G	G	L	K	15	position
6	T	K	T	F	P	L	R	A	L	14	plus eight
30	K	Q	D	K	K	V	D	L	L	14
129	R	P	Y	H	F	Q	V	P	S	14
176	K	Y	Q	A	V	T	A	T	L	14
223	S	P	G	G	G	S	P	R	G	14
257	T	P	R	A	G	S	S	A	H	14
276	V	P	A	A	S	P	A	A	W	14
293	R	P	S	S	C	P	T	S	S	14
399	R	K	A	E	N	G	P	H	L	14
3	E	H	T	T	K	T	F	P	L	13
104	S	G	S	F	C	R	N	K	L	13
110	N	K	L	K	Y	L	A	F	L	13
135	V	P	S	R	I	F	W	R	Q	13
158	S	E	A	Y	K	K	V	C	L	13
169	A	P	H	E	V	G	W	K	Y	13
224	P	G	G	G	S	P	R	G	L	13
234	F	I	F	K	T	I	A	P	L	13
237	K	T	I	A	P	L	A	A	T	13
262	S	S	A	H	R	P	P	A	L	13
280	S	P	A	A	W	L	P	L	R	13
362	V	E	N	G	R	P	A	D	L	13
378	A	L	W	K	A	I	E	S	L	13
29	M	K	Q	D	K	K	V	D	L	12
80	E	K	Q	R	K	D	K	V	L	12
107	F	C	R	N	K	L	K	Y	L	12
197	R	K	N	K	Q	L	M	R	L	12
226	G	G	S	P	R	G	L	G	F	12
249	R	I	G	H	P	G	G	R	T	12
261	G	S	S	A	H	R	P	P	A	12
267	P	P	A	L	S	A	R	A	P	12
299	T	S	S	S	T	Y	D	S	L	12
316	L	P	N	P	R	H	S	P	S	12
318	N	P	R	H	S	P	S	G	G	12
331	K	P	A	R	H	C	Q	G	Q	12
336	C	Q	G	Q	K	H	N	V	L	12
366	R	P	A	D	L	A	G	S	G	12
382	A	I	E	S	L	E	E	G	L	12
36	D	L	L	V	P	T	K	V	T	11
51	A	K	D	F	G	H	V	Q	F	11
52	K	D	F	G	H	V	Q	F	V	11
186	E	K	R	K	E	K	A	E	I	11
194	I	H	Y	R	K	N	K	Q	L	11
297	C	P	T	S	S	S	T	Y	D	11
314	N	P	L	P	N	P	R	H	S	11
321	H	S	P	S	G	G	G	G	L	11
348	K	P	Q	R	K	P	K	S	E	11
352	K	P	K	S	E	N	N	S	W	11
363	E	N	G	R	P	A	D	L	A	11
400	K	A	E	N	G	P	H	L	L	11
10	P	L	R	A	L	H	I	V	V	10
33	K	K	V	D	L	L	V	P	T	10
57	V	Q	F	V	G	S	Y	K	L	10
87	V	L	L	G	R	K	A	V	V	10
88	L	L	G	R	K	A	V	V	V	10
109	R	N	K	L	K	Y	L	A	F	10
165	C	L	S	G	A	P	H	E	V	10
270	L	S	A	R	A	P	V	P	A	10
285	L	P	L	R	T	P	W	T	R	10
289	T	P	W	T	R	P	S	S	C	10
291	W	T	R	P	S	S	C	P	T	10
325	G	G	G	G	L	K	K	P	A	10
13	A	L	H	I	V	V	E	S	I	9
21	I	R	D	H	S	G	Q	K	M	9
31	Q	D	K	K	V	D	L	L	V	9
49	Q	G	A	K	D	F	G	H	V	9
68	S	N	D	G	E	H	W	T	V	9
86	K	V	L	L	G	R	K	A	V	9
95	V	V	S	C	E	G	I	N	I	9
116	A	F	L	H	K	R	M	N	T	9
127	S	R	R	P	Y	H	F	Q	V	9
132	H	F	Q	V	P	S	R	I	F	9
149	G	S	C	C	P	Q	G	H	A	9
172	E	V	G	W	K	Y	Q	A	V	9
173	V	G	W	K	Y	Q	A	V	T	9
175	W	K	Y	Q	A	V	T	A	T	9
195	H	Y	R	K	N	K	Q	L	M	9
230	R	G	L	G	F	I	F	K	T	9
236	F	K	T	I	A	P	L	A	A	9
268	P	A	L	S	A	R	A	P	V	9
275	P	V	P	A	A	S	P	A	A	9
281	P	A	A	W	L	P	L	R	T	9
337	Q	G	Q	K	H	N	V	L	A	9
375	Y	C	G	A	L	W	K	A	I	9
5	T	T	K	T	F	P	L	R	A	8
8	T	F	P	L	R	A	L	H	I	8
27	Q	K	M	K	Q	D	K	K	V	8
38	L	V	P	T	K	V	T	G	I	8
43	V	T	G	I	I	T	Q	G	A	8
58	Q	F	V	G	S	Y	K	L	A	8
93	A	V	V	V	S	C	E	G	I	8
156	H	A	S	E	A	Y	K	K	V	8
171	H	E	V	G	W	K	Y	Q	A	8
174	G	W	K	Y	Q	A	V	T	A	8
209	A	E	K	N	M	K	K	K	I	8
231	G	L	G	F	I	F	K	T	I	8
235	I	F	K	T	I	A	P	L	A	8
239	I	A	P	L	A	A	T	R	A	8
242	L	A	A	T	R	A	T	R	I	8
256	R	T	P	R	A	G	S	S	A	8
284	W	L	P	L	R	T	P	W	T	8
335	H	C	Q	G	Q	K	H	N	V	8
360	W	Y	V	E	N	G	R	P	A	8
374	G	Y	C	G	A	L	W	K	A	8
1	M	L	E	H	T	T	K	T	F	7
35	V	D	L	L	V	P	T	K	V	7
40	P	T	K	V	T	G	I	I	T	7
46	I	I	T	Q	G	A	K	D	F	7
85	D	K	V	L	L	G	R	K	A	7
89	L	G	R	K	A	V	V	V	S	7
99	E	G	I	N	I	S	G	S	F	7
108	C	R	N	K	L	K	Y	L	A	7
114	Y	L	A	F	L	H	K	R	M	7
138	R	I	F	W	R	Q	E	K	A	7
184	L	E	E	K	R	K	E	K	A	7
201	Q	L	M	R	L	Q	K	Q	A	7
213	M	K	K	K	I	D	K	Y	T	7
227	G	S	P	R	G	L	G	F	I	7
232	L	G	F	I	F	K	T	I	A	7
254	G	G	R	T	P	R	A	G	S	7
269	A	L	S	A	R	A	P	V	P	7
295	S	S	C	P	T	S	S	S	T	7
345	A	R	G	K	P	Q	R	K	P	7
354	K	S	E	N	N	S	W	Y	V	7
370	L	A	G	S	G	Y	C	G	A	7
393	K	Q	K	D	K	E	R	K	A	7
67	Y	S	N	D	G	E	H	W	T	6
79	D	E	K	Q	R	K	D	K	V	6
126	P	S	R	R	P	Y	H	F	Q	6
131	Y	H	F	Q	V	P	S	R	I	6
146	A	D	G	G	S	C	C	P	Q	6
161	Y	K	K	V	C	L	S	G	A	6
166	L	S	G	A	P	H	E	V	G	6
205	L	Q	K	Q	A	E	K	N	M	6
244	A	T	R	A	T	R	I	G	H	6
272	A	R	A	P	V	P	A	A	S	6
283	A	W	L	P	L	R	T	P	W	6
286	P	L	R	T	P	W	T	R	P	6
294	P	S	S	C	P	T	S	S	S	6
323	P	S	G	G	G	G	L	K	K	6
349	P	Q	R	K	P	K	S	E	N	6
364	N	G	R	P	A	D	L	A	G	6
66	A	Y	S	N	D	G	E	H	W	5
83	R	K	D	K	V	L	L	G	R	5
102	N	I	S	G	S	F	C	R	N	5
160	A	Y	K	K	V	C	L	S	G	5
222	E	S	P	G	G	G	S	P	R	5
225	G	G	G	S	P	R	G	L	G	5
247	A	T	R	I	G	H	P	G	G	5
251	G	H	P	G	G	R	T	P	R	5
260	A	G	S	S	A	H	R	P	P	5
273	R	A	P	V	P	A	A	S	P	5
278	A	A	S	P	A	A	W	L	P	5
282	A	A	W	L	P	L	R	T	P	5
306	S	L	S	P	Y	G	P	R	N	5
313	R	N	P	L	P	N	P	R	H	5
320	R	H	S	P	S	G	G	G	G	5
7	K	T	F	P	L	R	A	L	H	4
11	L	R	A	L	H	I	V	V	E	4
12	R	A	L	H	I	V	V	E	S	4
23	D	H	S	G	Q	K	M	K	Q	4
34	K	V	D	L	L	V	P	T	K	4
42	K	V	T	G	I	I	T	Q	G	4
47	I	T	Q	G	A	K	D	F	G	4
59	F	V	G	S	Y	K	L	A	Y	4
90	G	R	K	A	V	V	V	S	C	4
119	H	K	R	M	N	T	N	P	S	4
145	K	A	D	G	G	S	C	C	P	4
157	A	S	E	A	Y	K	K	V	C	4
163	K	V	C	L	S	G	A	P	H	4
167	S	G	A	P	H	E	V	G	W	4
216	K	I	D	K	Y	T	E	S	P	4
220	Y	T	E	S	P	G	G	G	S	4
221	T	E	S	P	G	G	G	S	P	4
241	P	L	A	A	T	R	A	T	R	4
258	P	R	A	G	S	S	A	H	R	4
263	S	A	H	R	P	P	A	L	S	4
305	D	S	L	S	P	Y	G	P	R	4
315	P	L	P	N	P	R	H	S	P	4
328	G	L	K	K	P	A	R	H	C	4
338	G	Q	K	H	N	V	L	A	R	4
344	L	A	R	G	K	P	Q	R	K	4
346	R	G	K	P	Q	R	K	P	K	4
369	D	L	A	G	S	G	Y	C	G	4
384	E	S	L	E	E	G	L	G	G	4
394	Q	K	D	K	E	R	K	A	E	4
397	K	E	R	K	A	E	N	G	P	4
4	H	T	T	K	T	F	P	L	R	3
32	D	K	K	V	D	L	L	V	P	3
37	L	L	V	P	T	K	V	T	G	3
54	F	G	H	V	Q	F	V	G	S	3
60	V	G	S	Y	K	L	A	Y	S	3
69	N	D	G	E	H	W	T	V	Y	3
70	D	G	E	H	W	T	V	Y	Q	3
82	Q	R	K	D	K	V	L	L	G	3
91	R	K	A	V	V	V	S	C	E	3
112	L	K	Y	L	A	F	L	H	K	3
120	K	R	M	N	T	N	P	S	R	3
122	M	N	T	N	P	S	R	R	P	3
123	N	T	N	P	S	R	R	P	Y	3
128	R	R	P	Y	H	F	Q	V	P	3
133	F	Q	V	P	S	R	I	F	W	3
140	F	W	R	Q	E	K	A	D	G	3
144	E	K	A	D	G	G	S	C	C	3
150	S	C	C	P	Q	G	H	A	S	3
159	E	A	Y	K	K	V	C	L	S	3
178	Q	A	V	T	A	T	L	E	E	3
179	A	V	T	A	T	L	E	E	K	3
192	A	E	I	H	Y	R	K	N	K	3
199	N	K	Q	L	M	R	L	Q	K	3
202	L	M	R	L	Q	K	Q	A	E	3
211	K	N	M	K	K	K	I	D	K	3
229	P	R	G	L	G	F	I	F	K	3
238	T	I	A	P	L	A	A	T	R	3
243	A	A	T	R	A	T	R	I	G	3
246	R	A	T	R	I	G	H	P	G	3
250	I	G	H	P	G	G	R	T	P	3
287	L	R	T	P	W	T	R	P	S	3
288	R	T	P	W	T	R	P	S	S	3
290	P	W	T	R	P	S	S	C	P	3
298	P	T	S	S	S	T	Y	D	S	3
309	P	Y	G	P	R	N	P	L	P	3
310	Y	G	P	R	N	P	L	P	N	3
319	P	R	H	S	P	S	G	G	G	3
324	S	G	G	G	G	L	K	K	P	3
326	G	G	G	L	K	K	P	A	R	3
333	A	R	H	C	Q	G	Q	K	H	3
342	N	V	L	A	R	G	K	P	Q	3
356	E	N	N	S	W	Y	V	E	N	3
357	N	N	S	W	Y	V	E	N	G	3
361	Y	V	E	N	G	R	P	A	D	3
368	A	D	L	A	G	S	G	Y	C	3
372	G	S	G	Y	C	G	A	L	W	3
380	W	K	A	I	E	S	L	E	E	3
383	I	E	S	L	E	E	G	L	G	3
386	L	E	E	G	L	G	G	K	Q	3
387	E	E	G	L	G	G	K	Q	K	3
388	E	G	L	G	G	K	Q	K	D	3
389	G	L	G	G	K	Q	K	D	K	3
398	E	R	K	A	E	N	G	P	H	3
2	L	E	H	T	T	K	T	F	P	2
18	V	E	S	I	R	D	H	S	G	2
20	S	I	R	D	H	S	G	Q	K	2
28	K	M	K	Q	D	K	K	V	D	2
45	G	I	I	T	Q	G	A	K	D	2
48	T	Q	G	A	K	D	F	G	H	2
50	G	A	K	D	F	G	H	V	Q	2
53	D	F	G	H	V	Q	F	V	G	2
64	K	L	A	Y	S	N	D	G	E	2
78	Q	D	E	K	Q	R	K	D	K	2
97	S	C	E	G	I	N	I	S	G	2
100	G	I	N	I	S	G	S	F	C	2
103	I	S	G	S	F	C	R	N	K	2
106	S	F	C	R	N	K	L	K	Y	2
113	K	Y	L	A	F	L	H	K	R	2
124	T	N	P	S	R	R	P	Y	H	2
130	P	Y	H	F	Q	V	P	S	R	2
136	P	S	R	I	F	W	R	Q	E	2
139	I	F	W	R	Q	E	K	A	D	2
142	R	Q	E	K	A	D	G	G	S	2
143	Q	E	K	A	D	G	G	S	C	2
147	D	G	G	S	C	C	P	Q	G	2
148	G	G	S	C	C	P	Q	G	H	2
153	P	Q	G	H	A	S	E	A	Y	2
154	Q	G	H	A	S	E	A	Y	K	2
162	K	K	V	C	L	S	G	A	P	2
177	Y	Q	A	V	T	A	T	L	E	2
182	A	T	L	E	E	K	R	K	E	2
185	E	E	K	R	K	E	K	A	E	2
188	R	K	E	K	A	E	I	H	Y	2
189	K	E	K	A	E	I	H	Y	R	2
190	E	K	A	E	I	H	Y	R	K	2
196	Y	R	K	N	K	Q	L	M	R	2
204	R	L	Q	K	Q	A	E	K	N	2
207	K	Q	A	E	K	N	M	K	K	2
215	K	K	I	D	K	Y	T	E	S	2
217	I	D	K	Y	T	E	S	P	G	2
233	G	F	I	F	K	T	I	A	P	2
248	T	R	I	G	H	P	G	G	R	2
253	P	G	G	R	T	P	R	A	G	2
259	R	A	G	S	S	A	H	R	P	2
265	H	R	P	P	A	L	S	A	R	2
300	S	S	S	T	Y	D	S	L	S	2
301	S	S	T	Y	D	S	L	S	P	2
303	T	Y	D	S	L	S	P	Y	G	2
304	Y	D	S	L	S	P	Y	G	P	2
312	P	R	N	P	L	P	N	P	R	2
327	G	G	L	K	K	P	A	R	H	2
329	L	K	K	P	A	R	H	C	Q	2
330	K	K	P	A	R	H	C	Q	G	2
332	P	A	R	H	C	Q	G	Q	K	2
343	V	L	A	R	G	K	P	Q	R	2
351	R	K	P	K	S	E	N	N	S	2
353	P	K	S	E	N	N	S	W	Y	2
365	G	R	P	A	D	L	A	G	S	2
367	P	A	D	L	A	G	S	G	Y	2
373	S	G	Y	C	G	A	L	W	K	2
376	C	G	A	L	W	K	A	I	E	2
390	L	G	G	K	Q	K	D	K	E	2
395	K	D	K	E	R	K	A	E	N	2
16	I	V	V	E	S	I	R	D	H	1
17	V	V	E	S	I	R	D	H	S	1
19	E	S	I	R	D	H	S	G	Q	1
22	R	D	H	S	G	Q	K	M	K	1
24	H	S	G	Q	K	M	K	Q	D	1
25	S	G	Q	K	M	K	Q	D	K	1
44	T	G	I	I	T	Q	G	A	K	1
55	G	H	V	Q	F	V	G	S	Y	1
56	H	V	Q	F	V	G	S	Y	K	1
61	G	S	Y	K	L	A	Y	S	N	1
63	Y	K	L	A	Y	S	N	D	G	1
71	G	E	H	W	T	V	Y	Q	D	1
72	E	H	W	T	V	Y	Q	D	E	1
77	Y	Q	D	E	K	Q	R	K	D	1
84	K	D	K	V	L	L	G	R	K	1
92	K	A	V	V	V	S	C	E	G	1
98	C	E	G	I	N	I	S	G	S	1
101	I	N	I	S	G	S	F	C	R	1
111	K	L	K	Y	L	A	F	L	H	1
117	F	L	H	K	R	M	N	T	N	1
118	L	H	K	R	M	N	T	N	P	1
121	R	M	N	T	N	P	S	R	R	1
137	S	R	I	F	W	R	Q	E	K	1
151	C	C	P	Q	G	H	A	S	E	1
155	G	H	A	S	E	A	Y	K	K	1
164	V	C	L	S	G	A	P	H	E	1
168	G	A	P	H	E	V	G	W	K	1
180	V	T	A	T	L	E	E	K	R	1
183	T	L	E	E	K	R	K	E	K	1
187	K	R	K	E	K	A	E	I	H	1
191	K	A	E	I	H	Y	R	K	N	1
193	E	I	H	Y	R	K	N	K	Q	1
198	K	N	K	Q	L	M	R	L	Q	1
200	K	Q	L	M	R	L	Q	K	Q	1
203	M	R	L	Q	K	Q	A	E	K	1
206	Q	K	Q	A	E	K	N	M	K	1
208	Q	A	E	K	N	M	K	K	K	1
210	E	K	N	M	K	K	K	I	D	1
212	N	M	K	K	K	I	D	K	Y	1
214	K	K	K	I	D	K	Y	T	E	1
218	D	K	Y	T	E	S	P	G	G	1
219	K	Y	T	E	S	P	G	G	G	1
245	T	R	A	T	R	I	G	H	P	1
255	G	R	T	P	R	A	G	S	S	1
292	T	R	P	S	S	C	P	T	S	1
302	S	T	Y	D	S	L	S	P	Y	1
317	P	N	P	R	H	S	P	S	G	1
334	R	H	C	Q	G	Q	K	H	N	1
339	Q	K	H	N	V	L	A	R	G	1
340	K	H	N	V	L	A	R	G	K	1
341	H	N	V	L	A	R	G	K	P	1
347	G	K	P	Q	R	K	P	K	S	1
350	Q	R	K	P	K	S	E	N	N	1
355	S	E	N	N	S	W	Y	V	E	1
379	L	W	K	A	I	E	S	L	E	1
381	K	A	I	E	S	L	E	E	G	1
392	G	K	Q	K	D	K	E	R	K	1

TABLE XXIX
151P3D4 v.1
HLA Peptide
Scoring Results B*08 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
76	K	I	R	I	K	W	T	K	L	30	Portion
164	F	P	R	L	G	R	Y	N	L	24	of SEQ
243	K	D	K	S	R	Y	D	V	F	24	ID NO:
134	Y	G	R	Y	K	C	E	V	I	23	3; each
232	V	P	G	V	R	N	Y	G	F	23	start
329	E	A	A	V	R	F	V	G	F	22	position
74	I	H	K	I	R	I	K	W	T	21	is
81	W	T	K	L	T	S	D	Y	L	21	specified,
336	G	F	P	D	K	K	H	K	L	21	the length
51	S	H	R	G	G	N	V	T	L	20	of
241	W	D	K	D	K	S	R	Y	D	20	peptide is
320	R	P	R	R	R	C	S	P	T	20	9 amino
339	D	K	K	H	K	L	Y	G	V	20	acids, the
88	Y	L	K	E	V	D	V	F	V	19	end
219	I	T	K	P	R	E	P	C	G	19	position
123	S	L	V	I	T	D	L	T	L	18	for each
256	N	F	N	G	R	F	Y	Y	L	18	peptide is
337	F	P	D	K	K	H	K	L	Y	18	the start
113	F	L	K	G	G	S	D	S	D	17	position
217	Y	P	I	T	K	P	R	E	P	17	plus eight
284	A	Q	I	A	K	V	G	Q	I	17
326	S	P	T	E	A	A	V	R	F	17
58	T	L	P	C	K	F	Y	R	D	16
121	D	A	S	L	V	I	T	D	L	16
286	I	A	K	V	G	Q	I	F	A	16
293	F	A	A	W	K	I	L	G	Y	16
301	Y	D	R	C	D	A	G	W	L	16
46	Q	A	K	V	F	S	H	R	G	15
146	E	D	D	T	V	V	V	A	L	15
291	Q	I	F	A	A	W	K	I	L	15
318	I	S	R	P	R	R	R	C	S	15
24	L	D	H	D	R	A	I	H	I	14
33	Q	A	E	N	G	P	H	L	L	14
78	R	I	K	W	T	K	L	T	S	14
86	S	D	Y	L	K	E	V	D	V	14
153	A	L	D	L	Q	G	V	V	F	14
221	K	P	R	E	P	C	G	G	Q	14
245	K	S	R	Y	D	V	F	C	F	14
316	Y	P	I	S	R	P	R	R	R	14
4	L	L	L	L	V	L	I	S	I	13
32	I	Q	A	E	N	G	P	H	L	13
72	S	G	I	H	K	I	R	I	K	13
137	Y	K	C	E	V	I	E	G	L	13
166	R	L	G	R	Y	N	L	N	F	13
66	D	P	T	A	F	G	S	G	I	12
106	G	G	Y	Q	G	R	V	F	L	12
136	R	Y	K	C	E	V	I	E	G	12
239	G	F	W	D	K	D	K	S	R	12
267	P	T	K	L	T	Y	D	E	A	12
341	K	H	K	L	Y	G	V	Y	C	12
1	M	K	S	L	L	L	L	V	L	11
10	I	S	I	C	W	A	D	H	L	11
16	D	H	L	S	D	N	Y	T	L	11
44	A	E	Q	A	K	V	F	S	H	11
79	I	K	W	T	K	L	T	S	D	11
99	G	Y	H	K	K	T	Y	G	G	11
101	H	K	K	T	Y	G	G	Y	Q	11
111	R	V	F	L	K	G	G	S	D	11
116	G	G	S	D	S	D	A	S	L	11
132	E	D	Y	G	R	Y	K	C	E	11
148	D	T	V	V	V	A	L	D	L	11
159	V	V	F	P	Y	F	P	R	L	11
174	F	H	E	A	Q	Q	A	C	L	11
265	I	H	P	T	K	L	T	Y	D	11
3	S	L	L	L	L	V	L	I	S	10
37	G	P	H	L	L	V	E	A	E	10
42	V	E	A	E	Q	A	K	V	F	10
60	P	C	K	F	Y	R	D	P	T	10
98	M	G	Y	H	K	K	T	Y	G	10
100	Y	H	K	K	T	Y	G	G	Y	10
107	G	Y	Q	G	R	V	F	L	K	10
186	A	V	I	A	S	F	D	Q	L	10
194	L	Y	D	A	W	R	G	G	L	10
202	L	D	W	C	N	A	G	W	L	10
262	Y	Y	L	I	H	P	T	K	L	10
272	Y	D	E	A	V	Q	A	C	L	10
285	Q	I	A	K	V	G	Q	I	F	10
295	A	W	K	I	L	G	Y	D	R	10
313	S	V	R	Y	P	I	S	R	P	10
319	S	R	P	R	R	R	C	S	P	10
338	P	D	K	K	H	K	L	Y	G	10
40	L	L	V	E	A	E	Q	A	K	9
49	V	F	S	H	R	G	G	N	V	9
61	C	K	F	Y	R	D	P	T	A	9
299	L	G	Y	D	R	C	D	A	G	9
311	D	G	S	V	R	Y	P	I	S	9
342	H	K	L	Y	G	V	Y	C	F	9
2	K	S	L	L	L	L	V	L	I	8
5	L	L	L	V	L	I	S	I	C	8
8	V	L	I	S	I	C	W	A	D	8
39	H	L	L	V	E	A	E	Q	A	8
109	Q	G	R	V	F	L	K	G	G	8
118	S	D	S	D	A	S	L	V	I	8
144	G	L	E	D	D	T	V	V	V	8
162	P	Y	F	P	R	L	G	R	Y	8
165	P	R	L	G	R	Y	N	L	N	8
195	Y	D	A	W	R	G	G	L	D	8
201	G	L	D	W	C	N	A	G	W	8
211	S	D	G	S	V	Q	Y	P	I	8
224	E	P	C	G	G	Q	N	T	V	8
253	F	T	S	N	F	N	G	R	F	8
298	I	L	G	Y	D	R	C	D	A	8
6	L	L	V	L	I	S	I	C	W	7
17	H	L	S	D	N	Y	T	L	D	7
22	Y	T	L	D	H	D	R	A	I	7
26	H	D	R	A	I	H	I	Q	A	7
43	E	A	E	Q	A	K	V	F	S	7
55	G	N	V	T	L	P	C	K	F	7
62	K	F	Y	R	D	P	T	A	F	7
63	F	Y	R	D	P	T	A	F	G	7
69	A	F	G	S	G	I	H	K	I	7
71	G	S	G	I	H	K	I	R	I	7
87	D	Y	L	K	E	V	D	V	F	7
105	Y	G	G	Y	Q	G	R	V	F	7
128	D	L	T	L	E	D	Y	G	R	7
155	D	L	Q	G	V	V	F	P	Y	7
156	L	Q	G	V	V	F	P	Y	F	7
161	F	P	Y	F	P	R	L	G	R	7
167	L	G	R	Y	N	L	N	F	H	7
181	C	L	D	Q	D	A	V	I	A	7
183	D	Q	D	A	V	I	A	S	F	7
209	W	L	S	D	G	S	V	Q	Y	7
234	G	V	R	N	Y	G	F	W	D	7
257	F	N	G	R	F	Y	Y	L	I	7
263	Y	L	I	H	P	T	K	L	T	7
266	H	P	T	K	L	T	Y	D	E	7
269	K	L	T	Y	D	E	A	V	Q	7
290	G	Q	I	F	A	A	W	K	I	7
308	W	L	A	D	G	S	V	R	Y	7
322	R	R	R	C	S	P	T	E	A	7
11	S	I	C	W	A	D	H	L	S	6
23	T	L	D	H	D	R	A	I	H	6
31	H	I	Q	A	E	N	G	P	H	6
59	L	P	C	K	F	Y	R	D	P	6
83	K	L	T	S	D	Y	L	K	E	6
125	V	I	T	D	L	T	L	E	D	6
130	T	L	E	D	Y	G	R	Y	K	6
171	N	L	N	F	H	E	A	Q	Q	6
176	E	A	Q	Q	A	C	L	D	Q	6
179	Q	A	C	L	D	Q	D	A	V	6
180	A	C	L	D	Q	D	A	V	I	6
193	Q	L	Y	D	A	W	R	G	G	6
197	A	W	R	G	G	L	D	W	C	6
249	D	V	F	C	F	T	S	N	F	6
258	N	G	R	F	Y	Y	L	I	H	6
274	E	A	V	Q	A	C	L	N	D	6
277	Q	A	C	L	N	D	G	A	Q	6
278	A	C	L	N	D	G	A	Q	I	6
279	C	L	N	D	G	A	Q	I	A	6
283	G	A	Q	I	A	K	V	G	Q	6
310	A	D	G	S	V	R	Y	P	I	6
321	P	R	R	R	C	S	P	T	E	6
331	A	V	R	F	V	G	F	P	D	6
343	K	L	Y	G	V	Y	C	F	R	6
28	R	A	I	H	I	Q	A	E	N	5
73	G	I	H	K	I	R	I	K	W	5
141	V	I	E	G	L	E	D	D	T	5
152	V	A	L	D	L	Q	G	V	V	5
187	V	I	A	S	F	D	Q	L	Y	5
188	I	A	S	F	D	Q	L	Y	D	5
309	L	A	D	G	S	V	R	Y	P	5
330	A	A	V	R	F	V	G	F	P	5
9	L	I	S	I	C	W	A	D	H	4
14	W	A	D	H	L	S	D	N	Y	4
29	A	I	H	I	Q	A	E	N	G	4
68	T	A	F	G	S	G	I	H	K	4
91	E	V	D	V	F	V	S	M	G	4
97	S	M	G	Y	H	K	K	T	Y	4
140	E	V	I	E	G	L	E	D	D	4
143	E	G	L	E	D	D	T	V	V	4
185	D	A	V	I	A	S	F	D	Q	4
196	D	A	W	R	G	G	L	D	W	4
206	N	A	G	W	L	S	D	G	S	4
214	S	V	Q	Y	P	I	T	K	P	4
218	P	I	T	K	P	R	E	P	C	4
264	L	I	H	P	T	K	L	T	Y	4
271	T	Y	D	E	A	V	Q	A	C	4
294	A	A	W	K	I	L	G	Y	D	4
297	K	I	L	G	Y	D	R	C	D	4
305	D	A	G	W	L	A	D	G	S	4
317	P	I	S	R	P	R	R	R	C	4
19	S	D	N	Y	T	L	D	H	D	3
120	S	D	A	S	L	V	I	T	D	3
173	N	F	H	E	A	Q	Q	A	C	3
190	S	F	D	Q	L	Y	D	A	W	3
27	D	R	A	I	H	I	Q	A	E	2
35	E	N	G	P	H	L	L	V	E	2
36	N	G	P	H	L	L	V	E	A	2
38	P	H	L	L	V	E	A	E	Q	2
45	E	Q	A	K	V	F	S	H	R	2
52	H	R	G	G	N	V	T	L	P	2
54	G	G	N	V	T	L	P	C	K	2
56	N	V	T	L	P	C	K	F	Y	2
70	F	G	S	G	I	H	K	I	R	2
77	I	R	I	K	W	T	K	L	T	2
84	L	T	S	D	Y	L	K	E	V	2
89	L	K	E	V	D	V	F	V	S	2
96	V	S	M	G	Y	H	K	K	T	2
126	I	T	D	L	T	L	E	D	Y	2
129	L	T	L	E	D	Y	G	R	Y	2
135	G	R	Y	K	C	E	V	I	E	2
142	I	E	G	L	E	D	D	T	V	2
145	L	E	D	D	T	V	V	V	A	2
147	D	D	T	V	V	V	A	L	D	2
151	V	V	A	L	D	L	Q	G	V	2
154	L	D	L	Q	G	V	V	F	P	2
160	V	F	P	Y	F	P	R	L	G	2
168	G	R	Y	N	L	N	F	H	E	2
169	R	Y	N	L	N	F	H	E	A	2
182	L	D	Q	D	A	V	I	A	S	2
191	F	D	Q	L	Y	D	A	W	R	2
200	G	G	L	D	W	C	N	A	G	2
215	V	Q	Y	P	I	T	K	P	R	2
227	G	G	Q	N	T	V	P	G	V	2
229	Q	N	T	V	P	G	V	R	N	2
235	V	R	N	Y	G	F	W	D	K	2
246	S	R	Y	D	V	F	C	F	T	2
251	F	C	F	T	S	N	F	N	G	2
255	S	N	F	N	G	R	F	Y	Y	2
259	G	R	F	Y	Y	L	I	H	P	2
260	R	F	Y	Y	L	I	H	P	T	2
261	F	Y	Y	L	I	H	P	T	K	2
276	V	Q	A	C	L	N	D	G	A	2
287	A	K	V	G	Q	I	F	A	A	2
332	V	R	F	V	G	F	P	D	K	2
334	F	V	G	F	P	D	K	K	H	2
335	V	G	F	P	D	K	K	H	K	2
345	Y	G	V	Y	C	F	R	A	Y	2
7	L	V	L	I	S	I	C	W	A	1
12	I	C	W	A	D	H	L	S	D	1
15	A	D	H	L	S	D	N	Y	T	1
21	N	Y	T	L	D	H	D	R	A	1
25	D	H	D	R	A	I	H	I	Q	1
30	I	H	I	Q	A	E	N	G	P	1
50	F	S	H	R	G	G	N	V	T	1
57	V	T	L	P	C	K	F	Y	R	1
75	H	K	I	R	I	K	W	T	K	1
85	T	S	D	Y	L	K	E	V	D	1
90	K	E	V	D	V	F	V	S	M	1
92	V	D	V	F	V	S	M	G	Y	1
93	D	V	F	V	S	M	G	Y	H	1
94	V	F	V	S	M	G	Y	H	K	1
95	F	V	S	M	G	Y	H	K	K	1
102	K	K	T	Y	G	G	Y	Q	G	1
110	G	R	V	F	L	K	G	G	S	1
112	V	F	L	K	G	G	S	D	S	1
115	K	G	G	S	D	S	D	A	S	1
117	G	S	D	S	D	A	S	L	V	1
119	D	S	D	A	S	L	V	I	T	1
122	A	S	L	V	I	T	D	L	T	1
131	L	E	D	Y	G	R	Y	K	C	1
133	D	Y	G	R	Y	K	C	E	V	1
138	K	C	E	V	I	E	G	L	E	1
139	C	E	V	I	E	G	L	E	D	1
149	T	V	V	V	A	L	D	L	Q	1
150	V	V	V	A	L	D	L	Q	G	1
157	Q	G	V	V	F	P	Y	F	P	1
158	G	V	V	F	P	Y	F	P	R	1
170	Y	N	L	N	F	H	E	A	Q	1
175	H	E	A	Q	Q	A	C	L	D	1
184	Q	D	A	V	I	A	S	F	D	1
192	D	Q	L	Y	D	A	W	R	G	1
199	R	G	G	L	D	W	C	N	A	1
207	A	G	W	L	S	D	G	S	V	1
208	G	W	L	S	D	G	S	V	Q	1
210	L	S	D	G	S	V	Q	Y	P	1
212	D	G	S	V	Q	Y	P	I	T	1
213	G	S	V	Q	Y	P	I	T	K	1
225	P	C	G	G	Q	N	T	V	P	1
226	C	G	G	Q	N	T	V	P	G	1
228	G	Q	N	T	V	P	G	V	R	1
230	N	T	V	P	G	V	R	N	Y	1	Portion
237	N	Y	G	F	W	D	K	D	K	1	of SEQ
240	F	W	D	K	D	K	S	R	Y	1	ID NO:
244	D	K	S	R	Y	D	V	F	C	1	3; each
247	R	Y	D	V	F	C	F	T	S	1	start
250	V	F	C	F	T	S	N	F	N	1	position
268	T	K	L	T	Y	D	E	A	V	1	is
270	L	T	Y	D	E	A	V	Q	A	1	specified,
273	D	E	A	V	Q	A	C	L	N	1	the length
280	L	N	D	G	A	Q	I	A	K	1	of
281	N	D	G	A	Q	I	A	K	V	1	peptide is
282	D	G	A	Q	I	A	K	V	G	1	9 amino
288	K	V	G	Q	I	F	A	A	W	1	acids, the
289	V	G	Q	I	F	A	A	W	K	1	end
292	I	F	A	A	W	K	I	L	G	1	position
296	W	K	I	L	G	Y	D	R	C	1	for each
300	G	Y	D	R	C	D	A	G	W	1	peptide is
303	R	C	D	A	G	W	L	A	D	1	the start
306	A	G	W	L	A	D	G	S	V	1	position
307	G	W	L	A	D	G	S	V	R	1	plus eight
312	G	S	V	R	Y	P	I	S	R	1
314	V	R	Y	P	I	S	R	P	R	1
323	R	R	C	S	P	T	E	A	A	1
324	R	C	S	P	T	E	A	A	V	1
327	P	T	E	A	A	V	R	F	V	1
344	L	Y	G	V	Y	C	F	R	A	1
346	G	V	Y	C	F	R	A	Y	N	1
151P3D4 v.2
HLA Peptide
Scoring Results B*08 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
107	F	C	R	N	K	L	K	Y	L	28	Portion of
109	R	N	K	L	K	Y	L	A	F	28	SEQ ID
158	S	E	A	Y	K	K	V	C	L	24	NO: 5;
185	E	E	K	R	K	E	K	A	E	24	each start
80	E	K	Q	R	K	D	K	V	L	23	position
194	I	H	Y	R	K	N	K	Q	L	23	is
391	G	G	K	Q	K	D	K	E	R	23	specified,
3	E	H	T	T	K	T	F	P	L	22	the length
187	K	R	K	E	K	A	E	I	H	22	of peptide
26	G	Q	K	M	K	Q	D	K	K	21	is 9
29	M	K	Q	D	K	K	V	D	L	21	amino
30	K	Q	D	K	K	V	D	L	L	21	acids, the
82	Q	R	K	D	K	V	L	L	G	21	end
212	N	M	K	K	K	I	D	K	Y	21	position
262	S	S	A	H	R	P	P	A	L	21	for each
395	K	D	K	E	R	K	A	E	N	21	peptide is
125	N	P	S	R	R	P	Y	H	F	20	the start
183	T	L	E	E	K	R	K	E	K	20	position
196	Y	R	K	N	K	Q	L	M	R	20	plus eight
228	S	P	R	G	L	G	F	I	F	20
336	C	Q	G	Q	K	H	N	V	L	20
344	L	A	R	G	K	P	Q	R	K	20
350	Q	R	K	P	K	S	E	N	N	20
393	K	Q	K	D	K	E	R	K	A	20
362	V	E	N	G	R	P	A	D	L	19
79	D	E	K	Q	R	K	D	K	V	18
242	L	A	A	T	R	A	T	R	I	18
308	S	P	Y	G	P	R	N	P	L	18
389	G	L	G	G	K	Q	K	D	K	18
38	L	V	P	T	K	V	T	G	I	17
81	K	Q	R	K	D	K	V	L	L	17
88	L	L	G	R	K	A	V	V	V	17
111	K	L	K	Y	L	A	F	L	H	17
159	E	A	Y	K	K	V	C	L	S	17
209	A	E	K	N	M	K	K	K	I	17
328	G	L	K	K	P	A	R	H	C	17
348	K	P	Q	R	K	P	K	S	E	17
352	K	P	K	S	E	N	N	S	W	17
378	A	L	W	K	A	I	E	S	L	17
234	F	I	F	K	T	I	A	P	L	16
377	G	A	L	W	K	A	I	E	S	16
8	T	F	P	L	R	A	L	H	I	15
50	G	A	K	D	F	G	H	V	Q	15
87	V	L	L	G	R	K	A	V	V	15
117	F	L	H	K	R	M	N	T	N	15
186	E	K	R	K	E	K	A	E	I	15
193	E	I	H	Y	R	K	N	K	Q	15
226	G	G	S	P	R	G	L	G	F	15
252	H	P	G	G	R	T	P	R	A	15
284	W	L	P	L	R	T	P	W	T	15
231	G	L	G	F	I	F	K	T	I	14
269	A	L	S	A	R	A	P	V	P	14
271	S	A	R	A	P	V	P	A	A	14
277	P	A	A	S	P	A	A	W	L	14
289	T	P	W	T	R	P	S	S	C	14
316	L	P	N	P	R	H	S	P	S	14
382	A	I	E	S	L	E	E	G	L	14
400	K	A	E	N	G	P	H	L	L	14
1	M	L	E	H	T	T	K	T	F	13
13	A	L	H	I	V	V	E	S	I	13
39	V	P	T	K	V	T	G	I	I	13
62	S	Y	K	L	A	Y	S	N	D	13
90	G	R	K	A	V	V	V	S	C	13
172	E	V	G	W	K	Y	Q	A	V	13
174	G	W	K	Y	Q	A	V	T	A	13
207	K	Q	A	E	K	N	M	K	K	13
210	E	K	N	M	K	K	K	I	D	13
257	T	P	R	A	G	S	S	A	H	13
311	G	P	R	N	P	L	P	N	P	13
326	G	G	G	L	K	K	P	A	R	13
338	G	Q	K	H	N	V	L	A	R	13
398	E	R	K	A	E	N	G	P	H	13
10	P	L	R	A	L	H	I	V	V	12
20	S	I	R	D	H	S	G	Q	K	12
24	H	S	G	Q	K	M	K	Q	D	12
46	I	I	T	Q	G	A	K	D	F	12
57	V	Q	F	V	G	S	Y	K	L	12
60	V	G	S	Y	K	L	A	Y	S	12
77	Y	Q	D	E	K	Q	R	K	D	12
104	S	G	S	F	C	R	N	K	L	12
138	R	I	F	W	R	Q	E	K	A	12
141	W	R	Q	E	K	A	D	G	G	12
217	I	D	K	Y	T	E	S	P	G	12
233	G	F	I	F	K	T	I	A	P	12
286	P	L	R	T	P	W	T	R	P	12
318	N	P	R	H	S	P	S	G	G	12
399	R	K	A	E	N	G	P	H	L	12
6	T	K	T	F	P	L	R	A	L	11
28	K	M	K	Q	D	K	K	V	D	11
32	D	K	K	V	D	L	L	V	P	11
40	P	T	K	V	T	G	I	I	T	11
84	K	D	K	V	L	L	G	R	K	11
105	G	S	F	C	R	N	K	L	K	11
118	L	H	K	R	M	N	T	N	P	11
161	Y	K	K	V	C	L	S	G	A	11
189	K	E	K	A	E	I	H	Y	R	11
203	M	R	L	Q	K	Q	A	E	K	11
205	L	Q	K	Q	A	E	K	N	M	11
213	M	K	K	K	I	D	K	Y	T	11
215	K	K	I	D	K	Y	T	E	S	11
235	I	F	K	T	I	A	P	L	A	11
321	H	S	P	S	G	G	G	G	L	11
327	G	G	L	K	K	P	A	R	H	11
346	R	G	K	P	Q	R	K	P	K	11
371	A	G	S	G	Y	C	G	A	L	11
5	T	T	K	T	F	P	L	R	A	10
31	Q	D	K	K	V	D	L	L	V	10
48	T	Q	G	A	K	D	F	G	H	10
110	N	K	L	K	Y	L	A	F	L	10
116	A	F	L	H	K	R	M	N	T	10
143	Q	E	K	A	D	G	G	S	C	10
160	A	Y	K	K	V	C	L	S	G	10
176	K	Y	Q	A	V	T	A	T	L	10
197	R	K	N	K	Q	L	M	R	L	10
198	K	N	K	Q	L	M	R	L	Q	10
211	K	N	M	K	K	K	I	D	K	10
214	K	K	K	I	D	K	Y	T	E	10
224	P	G	G	G	S	P	R	G	L	10
279	A	S	P	A	A	W	L	P	L	10
299	T	S	S	S	T	Y	D	S	L	10
329	L	K	K	P	A	R	H	C	Q	10
332	P	A	R	H	C	Q	G	Q	K	10
379	L	W	K	A	I	E	S	L	E	10
385	S	L	E	E	G	L	G	G	K	10
396	D	K	E	R	K	A	E	N	G	10
18	V	E	S	I	R	D	H	S	G	9
134	Q	V	P	S	R	I	F	W	R	9
245	T	R	A	T	R	I	G	H	P	9
255	G	R	T	P	R	A	G	S	S	9
309	P	Y	G	P	R	N	P	L	P	9
342	N	V	L	A	R	G	K	P	Q	9
347	G	K	P	Q	R	K	P	K	S	9
36	D	L	L	V	P	T	K	V	T	8
64	K	L	A	Y	S	N	D	G	E	8
89	L	G	R	K	A	V	V	V	S	8
99	E	G	I	N	I	S	G	S	F	8
124	T	N	P	S	R	R	P	Y	H	8
127	S	R	R	P	Y	H	F	Q	V	8
132	H	F	Q	V	P	S	R	I	F	8
156	H	A	S	E	A	Y	K	K	V	8
169	A	P	H	E	V	G	W	K	Y	8
184	L	E	E	K	R	K	E	K	A	8
200	K	Q	L	M	R	L	Q	K	Q	8
202	L	M	R	L	Q	K	Q	A	E	8
223	S	P	G	G	G	S	P	R	G	8
267	P	P	A	L	S	A	R	A	P	8
276	V	P	A	A	S	P	A	A	W	8
280	S	P	A	A	W	L	P	L	R	8
306	S	L	S	P	Y	G	P	R	N	8
322	S	P	S	G	G	G	G	L	K	8
330	K	K	P	A	R	H	C	Q	G	8
375	Y	C	G	A	L	W	K	A	I	8
9	F	P	L	R	A	L	H	I	V	7
12	R	A	L	H	I	V	V	E	S	7
37	L	L	V	P	T	K	V	T	G	7
51	A	K	D	F	G	H	V	Q	F	7
93	A	V	V	V	S	C	E	G	I	7
95	V	V	S	C	E	G	I	N	I	7
114	Y	L	A	F	L	H	K	R	M	7
119	H	K	R	M	N	T	N	P	S	7
129	R	P	Y	H	F	Q	V	P	S	7
135	V	P	S	R	I	F	W	R	Q	7
140	F	W	R	Q	E	K	A	D	G	7
152	C	P	Q	G	H	A	S	E	A	7
165	C	L	S	G	A	P	H	E	V	7
195	H	Y	R	K	N	K	Q	L	M	7
201	Q	L	M	R	L	Q	K	Q	A	7
227	G	S	P	R	G	L	G	F	I	7
240	A	P	L	A	A	T	R	A	T	7
254	G	G	R	T	P	R	A	G	S	7
343	V	L	A	R	G	K	P	Q	R	7
349	P	Q	R	K	P	K	S	E	N	7
364	N	G	R	P	A	D	L	A	G	7
381	K	A	I	E	S	L	E	E	G	7
15	H	I	V	V	E	S	I	R	D	6
92	K	A	V	V	V	S	C	E	G	6
126	P	S	R	R	P	Y	H	F	Q	6
131	Y	H	F	Q	V	P	S	R	I	6
136	P	S	R	I	F	W	R	Q	E	6
168	G	A	P	H	E	V	G	W	K	6
181	T	A	T	L	E	E	K	R	K	6
204	R	L	Q	K	Q	A	E	K	N	6
239	I	A	P	L	A	A	T	R	A	6
241	P	L	A	A	T	R	A	T	R	6
244	A	T	R	A	T	R	I	G	H	6
247	A	T	R	I	G	H	P	G	G	6
263	S	A	H	R	P	P	A	L	S	6
264	A	H	R	P	P	A	L	S	A	6
266	R	P	P	A	L	S	A	R	A	6
274	A	P	V	P	A	A	S	P	A	6
285	L	P	L	R	T	P	W	T	R	6
291	W	T	R	P	S	S	C	P	T	6
293	R	P	S	S	C	P	T	S	S	6
297	C	P	T	S	S	S	T	Y	D	6
314	N	P	L	P	N	P	R	H	S	6
315	P	L	P	N	P	R	H	S	P	6
331	K	P	A	R	H	C	Q	G	Q	6
366	R	P	A	D	L	A	G	S	G	6
369	D	L	A	G	S	G	Y	C	G	6
397	K	E	R	K	A	E	N	G	P	6
45	G	I	I	T	Q	G	A	K	D	5
65	L	A	Y	S	N	D	G	E	H	5
100	G	I	N	I	S	G	S	F	C	5
115	L	A	F	L	H	K	R	M	N	5
178	Q	A	V	T	A	T	L	E	E	5
208	Q	A	E	K	N	M	K	K	K	5
273	R	A	P	V	P	A	A	S	P	5
282	A	A	W	L	P	L	R	T	P	5
367	P	A	D	L	A	G	S	G	Y	5
16	I	V	V	E	S	I	R	D	H	4
96	V	S	C	E	G	I	N	I	S	4
102	N	I	S	G	S	F	C	R	N	4
145	K	A	D	G	G	S	C	C	P	4
190	E	K	A	E	I	H	Y	R	K	4
191	K	A	E	I	H	Y	R	K	N	4
216	K	I	D	K	Y	T	E	S	P	4
238	T	I	A	P	L	A	A	T	R	4
243	A	A	T	R	A	T	R	I	G	4
246	R	A	T	R	I	G	H	P	G	4
249	R	I	G	H	P	G	G	R	T	4
259	R	A	G	S	S	A	H	R	P	4
268	P	A	L	S	A	R	A	P	V	4
278	A	A	S	P	A	A	W	L	P	4
281	P	A	A	W	L	P	L	R	T	4
356	E	N	N	S	W	Y	V	E	N	4
359	S	W	Y	V	E	N	G	R	P	4
370	L	A	G	S	G	Y	C	G	A	4
384	E	S	L	E	E	G	L	G	G	4
387	E	E	G	L	G	G	K	Q	K	4
11	L	R	A	L	H	I	V	V	E	3
54	F	G	H	V	Q	F	V	G	S	3
73	H	W	T	V	Y	Q	D	E	K	3
86	K	V	L	L	G	R	K	A	V	3
97	S	C	E	G	I	N	I	S	G	3
137	S	R	I	F	W	R	Q	E	K	3
139	I	F	W	R	Q	E	K	A	D	3
150	S	C	C	P	Q	G	H	A	S	3
167	S	G	A	P	H	E	V	G	W	3
301	S	S	T	Y	D	S	L	S	P	3
324	S	G	G	G	G	L	K	K	P	3
353	P	K	S	E	N	N	S	W	Y	3
19	E	S	I	R	D	H	S	G	Q	2
25	S	G	Q	K	M	K	Q	D	K	2
34	K	V	D	L	L	V	P	T	K	2
35	V	D	L	L	V	P	T	K	V	2
55	G	H	V	Q	F	V	G	S	Y	2
59	F	V	G	S	Y	K	L	A	Y	2
68	S	N	D	G	E	H	W	T	V	2
69	N	D	G	E	H	W	T	V	Y	2
71	G	E	H	W	T	V	Y	Q	D	2
72	E	H	W	T	V	Y	Q	D	E	2
91	R	K	A	V	V	V	S	C	E	2
106	S	F	C	R	N	K	L	K	Y	2
144	E	K	A	D	G	G	S	C	C	2
170	P	H	E	V	G	W	K	Y	Q	2
175	W	K	Y	Q	A	V	T	A	T	2
182	A	T	L	E	E	K	R	K	E	2
219	K	Y	T	E	S	P	G	G	G	2
222	E	S	P	G	G	G	S	P	R	2
236	F	K	T	I	A	P	L	A	A	2
265	H	R	P	P	A	L	S	A	R	2
295	S	S	C	P	T	S	S	S	T	2
296	S	C	P	T	S	S	S	T	Y	2
300	S	S	S	T	Y	D	S	L	S	2
302	S	T	Y	D	S	L	S	P	Y	2
313	R	N	P	L	P	N	P	R	H	2
325	G	G	G	G	L	K	K	P	A	2
337	Q	G	Q	K	H	N	V	L	A	2
341	H	N	V	L	A	R	G	K	P	2
355	S	E	N	N	S	W	Y	V	E	2
360	W	Y	V	E	N	G	R	P	A	2
363	E	N	G	R	P	A	D	L	A	2
372	G	S	G	Y	C	G	A	L	W	2
373	S	G	Y	C	G	A	L	W	K	2
383	I	E	S	L	E	E	G	L	G	2
388	E	G	L	G	G	K	Q	K	D	2
394	Q	K	D	K	E	R	K	A	E	2
4	H	T	T	K	T	F	P	L	R	1
14	L	H	I	V	V	E	S	I	R	1
17	V	V	E	S	I	R	D	H	S	1
21	I	R	D	H	S	G	Q	K	M	1
22	R	D	H	S	G	Q	K	M	K	1
27	Q	K	M	K	Q	D	K	K	V	1
33	K	K	V	D	L	L	V	P	T	1
41	T	K	V	T	G	I	I	T	Q	1
42	K	V	T	G	I	I	T	Q	G	1
43	V	T	G	I	I	T	Q	G	A	1
44	T	G	I	I	T	Q	G	A	K	1
47	I	T	Q	G	A	K	D	F	G	1
52	K	D	F	G	H	V	Q	F	V	1
56	H	V	Q	F	V	G	S	Y	K	1
58	Q	F	V	G	S	Y	K	L	A	1
61	G	S	Y	K	L	A	Y	S	N	1
70	D	G	E	H	W	T	V	Y	Q	1
74	W	T	V	Y	Q	D	E	K	Q	1
75	T	V	Y	Q	D	E	K	Q	R	1
76	V	Y	Q	D	E	K	Q	R	K	1
78	Q	D	E	K	Q	R	K	D	K	1
85	D	K	V	L	L	G	R	K	A	1
94	V	V	V	S	C	E	G	I	N	1
98	C	E	G	I	N	I	S	G	S	1
101	I	N	I	S	G	S	F	C	R	1
103	I	S	G	S	F	C	R	N	K	1
112	L	K	Y	L	A	F	L	H	K	1
120	K	R	M	N	T	N	P	S	R	1
128	R	R	P	Y	H	F	Q	V	P	1
130	P	Y	H	F	Q	V	P	S	R	1
133	F	Q	V	P	S	R	I	F	W	1
148	G	G	S	C	C	P	Q	G	H	1
149	G	S	C	C	P	Q	G	H	A	1
153	P	Q	G	H	A	S	E	A	Y	1
155	G	H	A	S	E	A	Y	K	K	1
157	A	S	E	A	Y	K	K	V	C	1
162	K	K	V	C	L	S	G	A	P	1
163	K	V	C	L	S	G	A	P	H	1
164	V	C	L	S	G	A	P	H	E	1
171	H	E	V	G	W	K	Y	Q	A	1
173	V	G	W	K	Y	Q	A	V	T	1
177	Y	Q	A	V	T	A	T	L	E	1
179	A	V	T	A	T	L	E	E	K	1
180	V	T	A	T	L	E	E	K	R	1
192	A	E	I	H	Y	R	K	N	K	1
199	N	K	Q	L	M	R	L	Q	K	1
225	G	G	G	S	P	R	G	L	G	1
229	P	R	G	L	G	F	I	F	K	1
230	R	G	L	G	F	I	F	K	T	1
237	K	T	I	A	P	L	A	A	T	1
250	I	G	H	P	G	G	R	T	P	1
251	G	H	P	G	G	R	T	P	R	1
253	P	G	G	R	T	P	R	A	G	1
261	G	S	S	A	H	R	P	P	A	1
270	L	S	A	R	A	P	V	P	A	1
272	A	R	A	P	V	P	A	A	S	1
275	P	V	P	A	A	S	P	A	A	1
304	Y	D	S	L	S	P	Y	G	P	1
307	L	S	P	Y	G	P	R	N	P	1
334	R	H	C	Q	G	Q	K	H	N	1
335	H	C	Q	G	Q	K	H	N	V	1
340	K	H	N	V	L	A	R	G	K	1
357	N	N	S	W	Y	V	E	N	G	1
358	N	S	W	Y	V	E	N	G	R	1
361	Y	V	E	N	G	R	P	A	D	1
365	G	R	P	A	D	L	A	G	S	1
374	G	Y	C	G	A	L	W	K	A	1
376	C	G	A	L	W	K	A	I	E	1
380	W	K	A	I	E	S	L	E	E	1
392	G	K	Q	K	D	K	E	R	K	1

TABLE XXX
151P3D4 v.1: HLA Peptide
Scoring Results B*1510 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
51	S	H	R	G	G	N	V	T	L	25	Portion
16	D	H	L	S	D	N	Y	T	L	21	of SEQ
174	F	H	E	A	Q	Q	A	C	L	21	ID NO:
32	I	Q	A	E	N	G	P	H	L	16	3; each
106	G	G	Y	Q	G	R	V	F	L	16	start
146	E	D	D	T	V	V	V	A	L	15	position
159	V	V	F	P	Y	F	P	R	L	15	is
1	M	K	S	L	L	L	L	V	L	13	specified,
30	I	H	I	Q	A	E	N	G	P	13	the length
33	Q	A	E	N	G	P	H	L	L	13	of
74	I	H	K	I	R	I	K	W	T	13	peptide is
116	G	G	S	D	S	D	A	S	L	13	9 amino
137	Y	K	C	E	V	I	E	G	L	13	acids, the
336	G	F	P	D	K	K	H	K	L	13	end
10	I	S	I	C	W	A	D	H	L	12	position
100	Y	H	K	K	T	Y	G	G	Y	12	for each
121	D	A	S	L	V	I	T	D	L	12	peptide is
164	F	P	R	L	G	R	Y	N	L	12	the start
262	Y	Y	L	I	H	P	T	K	L	12	position
265	I	H	P	T	K	L	T	Y	D	12	plus eight
272	Y	D	E	A	V	Q	A	C	L	12
341	K	H	K	L	Y	G	V	Y	C	12
25	D	H	D	R	A	I	H	I	Q	11
38	P	H	L	L	V	E	A	E	Q	11
105	Y	G	G	Y	Q	G	R	V	F	11
123	S	L	V	I	T	D	L	T	L	11
148	D	T	V	V	V	A	L	D	L	11
194	L	Y	D	A	W	R	G	G	L	11
202	L	D	W	C	N	A	G	W	L	11
256	N	F	N	G	R	F	Y	Y	L	11
301	Y	D	R	C	D	A	G	W	L	11
326	S	P	T	E	A	A	V	R	F	11
329	E	A	A	V	R	F	V	G	F	11
42	V	E	A	E	Q	A	K	V	F	10
76	K	I	R	I	K	W	T	K	L	10
81	W	T	K	L	T	S	D	Y	L	10
87	D	Y	L	K	E	V	D	V	F	10
153	A	L	D	L	Q	G	V	V	F	10
186	A	V	I	A	S	F	D	Q	L	10
291	Q	I	F	A	A	W	K	I	L	10
90	K	E	V	D	V	F	V	S	M	9
253	F	T	S	N	F	N	G	R	F	9
55	G	N	V	T	L	P	C	K	F	8
62	K	F	Y	R	D	P	T	A	F	8
156	L	Q	G	V	V	F	P	Y	F	8
243	K	D	K	S	R	Y	D	V	F	8
285	Q	I	A	K	V	G	Q	I	F	8
342	H	K	L	Y	G	V	Y	C	F	8
144	G	L	E	D	D	T	V	V	V	7
183	D	Q	D	A	V	I	A	S	F	7
232	V	P	G	V	R	N	Y	G	F	7
245	K	S	R	Y	D	V	F	C	F	7
308	W	L	A	D	G	S	V	R	Y	7
317	P	I	S	R	P	R	R	R	C	7
318	I	S	R	P	R	R	R	C	S	7
43	E	A	E	Q	A	K	V	F	S	6
145	L	E	D	D	T	V	V	V	A	6
166	R	L	G	R	Y	N	L	N	F	6
229	Q	N	T	V	P	G	V	R	N	6
230	N	T	V	P	G	V	R	N	Y	6
249	D	V	F	C	F	T	S	N	F	6
316	Y	P	I	S	R	P	R	R	R	6
22	Y	T	L	D	H	D	R	A	I	5
35	E	N	G	P	H	L	L	V	E	5
89	L	K	E	V	D	V	F	V	S	5
130	T	L	E	D	Y	G	R	Y	K	5
154	L	D	L	Q	G	V	V	F	P	5
209	W	L	S	D	G	S	V	Q	Y	5
217	Y	P	I	T	K	P	R	E	P	5
219	I	T	K	P	R	E	P	C	G	5
328	T	E	A	A	V	R	F	V	G	5
71	G	S	G	I	H	K	I	R	I	4
85	T	S	D	Y	L	K	E	V	D	4
88	Y	L	K	E	V	D	V	F	V	4
104	T	Y	G	G	Y	Q	G	R	V	4
118	S	D	S	D	A	S	L	V	I	4
135	G	R	Y	K	C	E	V	I	E	4
143	E	G	L	E	D	D	T	V	V	4
162	P	Y	F	P	R	L	G	R	Y	4
213	G	S	V	Q	Y	P	I	T	K	4
216	Q	Y	P	I	T	K	P	R	E	4
224	E	P	C	G	G	Q	N	T	V	4
226	C	G	G	Q	N	T	V	P	G	4
228	G	Q	N	T	V	P	G	V	R	4
240	F	W	D	K	D	K	S	R	Y	4
254	T	S	N	F	N	G	R	F	Y	4
264	L	I	H	P	T	K	L	T	Y	4
271	T	Y	D	E	A	V	Q	A	C	4
282	D	G	A	Q	I	A	K	V	G	4
283	G	A	Q	I	A	K	V	G	Q	4
286	I	A	K	V	G	Q	I	F	A	4
292	I	F	A	A	W	K	I	L	G	4
309	L	A	D	G	S	V	R	Y	P	4
313	S	V	R	Y	P	I	S	R	P	4
314	V	R	Y	P	I	S	R	P	R	4
315	R	Y	P	I	S	R	P	R	R	4
324	R	C	S	P	T	E	A	A	V	4
327	P	T	E	A	A	V	R	F	V	4
345	Y	G	V	Y	C	F	R	A	Y	4
17	H	L	S	D	N	Y	T	L	D	3
27	D	R	A	I	H	I	Q	A	E	3
36	N	G	P	H	L	L	V	E	A	3
37	G	P	H	L	L	V	E	A	E	3
45	E	Q	A	K	V	F	S	H	R	3
46	Q	A	K	V	F	S	H	R	G	3
50	F	S	H	R	G	G	N	V	T	3
52	H	R	G	G	N	V	T	L	P	3
54	G	G	N	V	T	L	P	C	K	3
57	V	T	L	P	C	K	F	Y	R	3
58	T	L	P	C	K	F	Y	R	D	3
59	L	P	C	K	F	Y	R	D	P	3
64	Y	R	D	P	T	A	F	G	S	3
72	S	G	I	H	K	I	R	I	K	3
73	G	I	H	K	I	R	I	K	W	3
77	I	R	I	K	W	T	K	L	T	3
84	L	T	S	D	Y	L	K	E	V	3
91	E	V	D	V	F	V	S	M	G	3
107	G	Y	Q	G	R	V	F	L	K	3
120	S	D	A	S	L	V	I	T	D	3
129	L	T	L	E	D	Y	G	R	Y	3
134	Y	G	R	Y	K	C	E	V	I	3
140	E	V	I	E	G	L	E	D	D	3
142	I	E	G	L	E	D	D	T	V	3
152	V	A	L	D	L	Q	G	V	V	3
160	V	F	P	Y	F	P	R	L	G	3
163	Y	F	P	R	L	G	R	Y	N	3
180	A	C	L	D	Q	D	A	V	I	3
181	C	L	D	Q	D	A	V	I	A	3
182	L	D	Q	D	A	V	I	A	S	3
188	I	A	S	F	D	Q	L	Y	D	3
193	Q	L	Y	D	A	W	R	G	G	3
200	G	G	L	D	W	C	N	A	G	3
208	G	W	L	S	D	G	S	V	Q	3
212	D	G	S	V	Q	Y	P	I	T	3
218	P	I	T	K	P	R	E	P	C	3
222	P	R	E	P	C	G	G	Q	N	3
225	P	C	G	G	Q	N	T	V	P	3
227	G	G	Q	N	T	V	P	G	V	3
231	T	V	P	G	V	R	N	Y	G	3
241	W	D	K	D	K	S	R	Y	D	3
244	D	K	S	R	Y	D	V	F	C	3
270	L	T	Y	D	E	A	V	Q	A	3
287	A	K	V	G	Q	I	F	A	A	3
296	W	K	I	L	G	Y	D	R	C	3
297	K	I	L	G	Y	D	R	C	D	3
298	I	L	G	Y	D	R	C	D	A	3
307	G	W	L	A	D	G	S	V	R	3
311	D	G	S	V	R	Y	P	I	S	3
332	V	R	F	V	G	F	P	D	K	3
335	V	G	F	P	D	K	K	H	K	3
340	K	K	H	K	L	Y	G	V	Y	3
344	L	Y	G	V	Y	C	F	R	A	3
2	K	S	L	L	L	L	V	L	I	2
5	L	L	L	V	L	I	S	I	C	2
12	I	C	W	A	D	H	L	S	D	2
13	C	W	A	D	H	L	S	D	N	2
21	N	Y	T	L	D	H	D	R	A	2
23	T	L	D	H	D	R	A	I	H	2
34	A	E	N	G	P	H	L	L	V	2
40	L	L	V	E	A	E	Q	A	K	2
47	A	K	V	F	S	H	R	G	G	2
61	C	K	F	Y	R	D	P	T	A	2
63	F	Y	R	D	P	T	A	F	G	2
67	P	T	A	F	G	S	G	I	H	2
68	T	A	F	G	S	G	I	H	K	2
69	A	F	G	S	G	I	H	K	I	2
70	F	G	S	G	I	H	K	I	R	2
75	H	K	I	R	I	K	W	T	K	2
78	R	I	K	W	T	K	L	T	S	2
79	I	K	W	T	K	L	T	S	D	2
86	S	D	Y	L	K	E	V	D	V	2
93	D	V	F	V	S	M	G	Y	H	2
95	F	V	S	M	G	Y	H	K	K	2
97	S	M	G	Y	H	K	K	T	Y	2
99	G	Y	H	K	K	T	Y	G	G	2
103	K	T	Y	G	G	Y	Q	G	R	2
110	G	R	V	F	L	K	G	G	S	2
112	V	F	L	K	G	G	S	D	S	2
113	F	L	K	G	G	S	D	S	D	2
119	D	S	D	A	S	L	V	I	T	2
125	V	I	T	D	L	T	L	E	D	2
126	I	T	D	L	T	L	E	D	Y	2
131	L	E	D	Y	G	R	Y	K	C	2
132	E	D	Y	G	R	Y	K	C	E	2
133	D	Y	G	R	Y	K	C	E	V	2
136	R	Y	K	C	E	V	I	E	G	2
138	K	C	E	V	I	E	G	L	E	2
141	V	I	E	G	L	E	D	D	T	2
147	D	D	T	V	V	V	A	L	D	2
149	T	V	V	V	A	L	D	L	Q	2
155	D	L	Q	G	V	V	F	P	Y	2
157	Q	G	V	V	F	P	Y	F	P	2
158	G	V	V	F	P	Y	F	P	R	2
161	F	P	Y	F	P	R	L	G	R	2
169	R	Y	N	L	N	F	H	E	A	2
170	Y	N	L	N	F	H	E	A	Q	2
173	N	F	H	E	A	Q	Q	A	C	2
175	H	E	A	Q	Q	A	C	L	D	2
176	E	A	Q	Q	A	C	L	D	Q	2
184	Q	D	A	V	I	A	S	F	D	2
190	S	F	D	Q	L	Y	D	A	W	2
192	D	Q	L	Y	D	A	W	R	G	2
195	Y	D	A	W	R	G	G	L	D	2
197	A	W	R	G	G	L	D	W	C	2
205	C	N	A	G	W	L	S	D	G	2
210	L	S	D	G	S	V	Q	Y	P	2
214	S	V	Q	Y	P	I	T	K	P	2
215	V	Q	Y	P	I	T	K	P	R	2
220	T	K	P	R	E	P	C	G	G	2
221	K	P	R	E	P	C	G	G	Q	2
238	Y	G	F	W	D	K	D	K	S	2
239	G	F	W	D	K	D	K	S	R	2
242	D	K	D	K	S	R	Y	D	V	2
247	R	Y	D	V	F	C	F	T	S	2
255	S	N	F	N	G	R	F	Y	Y	2
261	F	Y	Y	L	I	H	P	T	K	2
263	Y	L	I	H	P	T	K	L	T	2
268	T	K	L	T	Y	D	E	A	V	2
269	K	L	T	Y	D	E	A	V	Q	2
273	D	E	A	V	Q	A	C	L	N	2
274	E	A	V	Q	A	C	L	N	D	2
277	Q	A	C	L	N	D	G	A	Q	2
279	C	L	N	D	G	A	Q	I	A	2
280	L	N	D	G	A	Q	I	A	K	2
288	K	V	G	Q	I	F	A	A	W	2
293	F	A	A	W	K	I	L	G	Y	2
299	L	G	Y	D	R	C	D	A	G	2
303	R	C	D	A	G	W	L	A	D	2
304	C	D	A	G	W	L	A	D	G	2
312	G	S	V	R	Y	P	I	S	R	2
321	P	R	R	R	C	S	P	T	E	2
322	R	R	R	C	S	P	T	E	A	2
323	R	R	C	S	P	T	E	A	A	2
325	C	S	P	T	E	A	A	V	R	2
333	R	F	V	G	F	P	D	K	K	2
338	P	D	K	K	H	K	L	Y	G	2
346	G	V	Y	C	F	R	A	Y	N	2
3	S	L	L	L	L	V	L	I	S	1
7	L	V	L	I	S	I	C	W	A	1
8	V	L	I	S	I	C	W	A	D	1
9	L	I	S	I	C	W	A	D	H	1
24	L	D	H	D	R	A	I	H	I	1
28	R	A	I	H	I	Q	A	E	N	1
39	H	L	L	V	E	A	E	Q	A	1
41	L	V	E	A	E	Q	A	K	V	1
44	A	E	Q	A	K	V	F	S	H	1
48	K	V	F	S	H	R	G	G	N	1
49	V	F	S	H	R	G	G	N	V	1
56	N	V	T	L	P	C	K	F	Y	1
60	P	C	K	F	Y	R	D	P	T	1
80	K	W	T	K	L	T	S	D	Y	1
82	T	K	L	T	S	D	Y	L	K	1
96	V	S	M	G	Y	H	K	K	T	1
98	M	G	Y	H	K	K	T	Y	G	1
102	K	K	T	Y	G	G	Y	Q	G	1
108	Y	Q	G	R	V	F	L	K	G	1
109	Q	G	R	V	F	L	K	G	G	1
114	L	K	G	G	S	D	S	D	A	1
115	K	G	G	S	D	S	D	A	S	1
117	G	S	D	S	D	A	S	L	V	1
122	A	S	L	V	I	T	D	L	T	1
127	T	D	L	T	L	E	D	Y	G	1
139	C	E	V	I	E	G	L	E	D	1
151	V	V	A	L	D	L	Q	G	V	1
165	P	R	L	G	R	Y	N	L	N	1
167	L	G	R	Y	N	L	N	F	H	1
168	G	R	Y	N	L	N	F	H	E	1
178	Q	Q	A	C	L	D	Q	D	A	1
179	Q	A	C	L	D	Q	D	A	V	1
187	V	I	A	S	F	D	Q	L	Y	1
189	A	S	F	D	Q	L	Y	D	A	1
196	D	A	W	R	G	G	L	D	W	1
198	W	R	G	G	L	D	W	C	N	1
201	G	L	D	W	C	N	A	G	W	1
204	W	C	N	A	G	W	L	S	D	1
223	R	E	P	C	G	G	Q	N	T	1
233	P	G	V	R	N	Y	G	F	W	1
234	G	V	R	N	Y	G	F	W	D	1
235	V	R	N	Y	G	F	W	D	K	1
236	R	N	Y	G	F	W	D	K	D	1
246	S	R	Y	D	V	F	C	F	T	1
248	Y	D	V	F	C	F	T	S	N	1
252	C	F	T	S	N	F	N	G	R	1
259	G	R	F	Y	Y	L	I	H	P	1
260	R	F	Y	Y	L	I	H	P	T	1
266	H	P	T	K	L	T	Y	D	E	1
267	P	T	K	L	T	Y	D	E	A	1
276	V	Q	A	C	L	N	D	G	A	1
281	N	D	G	A	Q	I	A	K	V	1
284	A	Q	I	A	K	V	G	Q	I	1
290	G	Q	I	F	A	A	W	K	I	1
294	A	A	W	K	I	L	G	Y	D	1
300	G	Y	D	R	C	D	A	G	W	1
302	D	R	C	D	A	G	W	L	A	1
310	A	D	G	S	V	R	Y	P	I	1
319	S	R	P	R	R	R	C	S	P	1
330	A	A	V	R	F	V	G	F	P	1
334	F	V	G	F	P	D	K	K	H	1
337	F	P	D	K	K	H	K	L	Y	1
343	K	L	Y	G	V	Y	C	F	R	1
151P3D4 v.2: HLA Peptide
Scoring Results B*1510 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
194	I	H	Y	R	K	N	K	Q	L	22	Portion of
3	E	H	T	T	K	T	F	P	L	21	SEQ ID
6	T	K	T	F	P	L	R	A	L	15	NO: 5;
131	Y	H	F	Q	V	P	S	R	I	15	each start
29	M	K	Q	D	K	K	V	D	L	14	position
81	K	Q	R	K	D	K	V	L	L	14	is
158	S	E	A	Y	K	K	V	C	L	14	specified,
224	P	G	G	G	S	P	R	G	L	14	the length
251	G	H	P	G	G	R	T	P	R	14	of peptide
262	S	S	A	H	R	P	P	A	L	14	is 9
399	R	K	A	E	N	G	P	H	L	14	amino
23	D	H	S	G	Q	K	M	K	Q	13	acids, the
55	G	H	V	Q	F	V	G	S	Y	13	end
80	E	K	Q	R	K	D	K	V	L	13	position
170	P	H	E	V	G	W	K	Y	Q	13	for each
197	R	K	N	K	Q	L	M	R	L	13	peptide is
264	A	H	R	P	P	A	L	S	A	13	the start
308	S	P	Y	G	P	R	N	P	L	13	position
320	R	H	S	P	S	G	G	G	G	13	plus eight
336	C	Q	G	Q	K	H	N	V	L	13
340	K	H	N	V	L	A	R	G	K	13
371	A	G	S	G	Y	C	G	A	L	13
400	K	A	E	N	G	P	H	L	L	13
30	K	Q	D	K	K	V	D	L	L	12
57	V	Q	F	V	G	S	Y	K	L	12
104	S	G	S	F	C	R	N	K	L	12
155	G	H	A	S	E	A	Y	K	K	12
234	F	I	F	K	T	I	A	P	L	12
277	P	A	A	S	P	A	A	W	L	12
299	T	S	S	S	T	Y	D	S	L	12
334	R	H	C	Q	G	Q	K	H	N	12
362	V	E	N	G	R	P	A	D	L	12
378	A	L	W	K	A	I	E	S	L	12
14	L	H	I	V	V	E	S	I	R	11
72	E	H	W	T	V	Y	Q	D	E	11
110	N	K	L	K	Y	L	A	F	L	11
176	K	Y	Q	A	V	T	A	T	L	11
321	H	S	P	S	G	G	G	G	L	11
382	A	I	E	S	L	E	E	G	L	11
46	I	I	T	Q	G	A	K	D	F	10
107	F	C	R	N	K	L	K	Y	L	10
114	Y	L	A	F	L	H	K	R	M	10
118	L	H	K	R	M	N	T	N	P	10
132	H	F	Q	V	P	S	R	I	F	10
226	G	G	S	P	R	G	L	G	F	10
279	A	S	P	A	A	W	L	P	L	10
51	A	K	D	F	G	H	V	Q	F	9
195	H	Y	R	K	N	K	Q	L	M	9
1	M	L	E	H	T	T	K	T	F	8
21	I	R	D	H	S	G	Q	K	M	8
125	N	P	S	R	R	P	Y	H	F	8
250	I	G	H	P	G	G	R	T	P	8
99	E	G	I	N	I	S	G	S	F	7
109	R	N	K	L	K	Y	L	A	F	7
205	L	Q	K	Q	A	E	K	N	M	7
228	S	P	R	G	L	G	F	I	F	7
11	L	R	A	L	H	I	V	V	E	6
16	I	V	V	E	S	I	R	D	H	6
37	L	L	V	P	T	K	V	T	G	6
89	L	G	R	K	A	V	V	V	S	6
306	S	L	S	P	Y	G	P	R	N	6
314	N	P	L	P	N	P	R	H	S	6
361	Y	V	E	N	G	R	P	A	D	6
122	M	N	T	N	P	S	R	R	P	5
123	N	T	N	P	S	R	R	P	Y	5
167	S	G	A	P	H	E	V	G	W	5
183	T	L	E	E	K	R	K	E	K	5
190	E	K	A	E	I	H	Y	R	K	5
221	T	E	S	P	G	G	G	S	P	5
223	S	P	G	G	G	S	P	R	G	5
238	T	I	A	P	L	A	A	T	R	5
272	A	R	A	P	V	P	A	A	S	5
327	G	G	L	K	K	P	A	R	H	5
328	G	L	K	K	P	A	R	H	C	5
392	G	K	Q	K	D	K	E	R	K	5
5	T	T	K	T	F	P	L	R	A	4
12	R	A	L	H	I	V	V	E	S	4
28	K	M	K	Q	D	K	K	V	D	4
36	D	L	L	V	P	T	K	V	T	4
41	T	K	V	T	G	I	I	T	Q	4
47	I	T	Q	G	A	K	D	F	G	4
50	G	A	K	D	F	G	H	V	Q	4
76	V	Y	Q	D	E	K	Q	R	K	4
77	Y	Q	D	E	K	Q	R	K	D	4
87	V	L	L	G	R	K	A	V	V	4
88	L	L	G	R	K	A	V	V	V	4
90	G	R	K	A	V	V	V	S	C	4
102	N	I	S	G	S	F	C	R	N	4
103	I	S	G	S	F	C	R	N	K	4
121	R	M	N	T	N	P	S	R	R	4
144	E	K	A	D	G	G	S	C	C	4
157	A	S	E	A	Y	K	K	V	C	4
165	C	L	S	G	A	P	H	E	V	4
174	G	W	K	Y	Q	A	V	T	A	4
182	A	T	L	E	E	K	R	K	E	4
186	E	K	R	K	E	K	A	E	I	4
198	K	N	K	Q	L	M	R	L	Q	4
208	Q	A	E	K	N	M	K	K	K	4
239	I	A	P	L	A	A	T	R	A	4
252	H	P	G	G	R	T	P	R	A	4
253	P	G	G	R	T	P	R	A	G	4
261	G	S	S	A	H	R	P	P	A	4
267	P	P	A	L	S	A	R	A	P	4
269	A	L	S	A	R	A	P	V	P	4
270	L	S	A	R	A	P	V	P	A	4
271	S	A	R	A	P	V	P	A	A	4
281	P	A	A	W	L	P	L	R	T	4
282	A	A	W	L	P	L	R	T	P	4
287	L	R	T	P	W	T	R	P	S	4
307	L	S	P	Y	G	P	R	N	P	4
313	R	N	P	L	P	N	P	R	H	4
326	G	G	G	L	K	K	P	A	R	4
338	G	Q	K	H	N	V	L	A	R	4
343	V	L	A	R	G	K	P	Q	R	4
344	L	A	R	G	K	P	Q	R	K	4
345	A	R	G	K	P	Q	R	K	P	4
347	G	K	P	Q	R	K	P	K	S	4
349	P	Q	R	K	P	K	S	E	N	4
356	E	N	N	S	W	Y	V	E	N	4
360	W	Y	V	E	N	G	R	P	A	4
388	E	G	L	G	G	K	Q	K	D	4
7	K	T	F	P	L	R	A	L	H	3
15	H	I	V	V	E	S	I	R	D	3
32	D	K	K	V	D	L	L	V	P	3
33	K	K	V	D	L	L	V	P	T	3
34	K	V	D	L	L	V	P	T	K	3
54	F	G	H	V	Q	F	V	G	S	3
67	Y	S	N	D	G	E	H	W	T	3
69	N	D	G	E	H	W	T	V	Y	3
70	D	G	E	H	W	T	V	Y	Q	3
78	Q	D	E	K	Q	R	K	D	K	3
84	K	D	K	V	L	L	G	R	K	3
86	K	V	L	L	G	R	K	A	V	3
91	R	K	A	V	V	V	S	C	E	3
96	V	S	C	E	G	I	N	I	S	3
101	I	N	I	S	G	S	F	C	R	3
115	L	A	F	L	H	K	R	M	N	3
117	F	L	H	K	R	M	N	T	N	3
124	T	N	P	S	R	R	P	Y	H	3
133	F	Q	V	P	S	R	I	F	W	3
135	V	P	S	R	I	F	W	R	Q	3
139	I	F	W	R	Q	E	K	A	D	3
148	G	G	S	C	C	P	Q	G	H	3
150	S	C	C	P	Q	G	H	A	S	3
159	E	A	Y	K	K	V	C	L	S	3
166	L	S	G	A	P	H	E	V	G	3
173	V	G	W	K	Y	Q	A	V	T	3
175	W	K	Y	Q	A	V	T	A	T	3
177	Y	Q	A	V	T	A	T	L	E	3
181	T	A	T	L	E	E	K	R	K	3
184	L	E	E	K	R	K	E	K	A	3
191	K	A	E	I	H	Y	R	K	N	3
220	Y	T	E	S	P	G	G	G	S	3
222	E	S	P	G	G	G	S	P	R	3
225	G	G	G	S	P	R	G	L	G	3
235	I	F	K	T	I	A	P	L	A	3
240	A	P	L	A	A	T	R	A	T	3
241	P	L	A	A	T	R	A	T	R	3
242	L	A	A	T	R	A	T	R	I	3
245	T	R	A	T	R	I	G	H	P	3
248	T	R	I	G	H	P	G	G	R	3
249	R	I	G	H	P	G	G	R	T	3
254	G	G	R	T	P	R	A	G	S	3
255	G	R	T	P	R	A	G	S	S	3
257	T	P	R	A	G	S	S	A	H	3
260	A	G	S	S	A	H	R	P	P	3
265	H	R	P	P	A	L	S	A	R	3
276	V	P	A	A	S	P	A	A	W	3
278	A	A	S	P	A	A	W	L	P	3
283	A	W	L	P	L	R	T	P	W	3
286	P	L	R	T	P	W	T	R	P	3
292	T	R	P	S	S	C	P	T	S	3
304	Y	D	S	L	S	P	Y	G	P	3
309	P	Y	G	P	R	N	P	L	P	3
310	Y	G	P	R	N	P	L	P	N	3
311	G	P	R	N	P	L	P	N	P	3
312	P	R	N	P	L	P	N	P	R	3
322	S	P	S	G	G	G	G	L	K	3
325	G	G	G	G	L	K	K	P	A	3
329	L	K	K	P	A	R	H	C	Q	3
337	Q	G	Q	K	H	N	V	L	A	3
346	R	G	K	P	Q	R	K	P	K	3
353	P	K	S	E	N	N	S	W	Y	3
359	S	W	Y	V	E	N	G	R	P	3
364	N	G	R	P	A	D	L	A	G	3
383	I	E	S	L	E	E	G	L	G	3
385	S	L	E	E	G	L	G	G	K	3
391	G	G	K	Q	K	D	K	E	R	3
393	K	Q	K	D	K	E	R	K	A	3
394	Q	K	D	K	E	R	K	A	E	3
395	K	D	K	E	R	K	A	E	N	3
4	H	T	T	K	T	F	P	L	R	2
10	P	L	R	A	L	H	I	V	V	2
17	V	V	E	S	I	R	D	H	S	2
24	H	S	G	Q	K	M	K	Q	D	2
25	S	G	Q	K	M	K	Q	D	K	2
42	K	V	T	G	I	I	T	Q	G	2
44	T	G	I	I	T	Q	G	A	K	2
49	Q	G	A	K	D	F	G	H	V	2
52	K	D	F	G	H	V	Q	F	V	2
53	D	F	G	H	V	Q	F	V	G	2
59	F	V	G	S	Y	K	L	A	Y	2
61	G	S	Y	K	L	A	Y	S	N	2
65	L	A	Y	S	N	D	G	E	H	2
68	S	N	D	G	E	H	W	T	V	2
71	G	E	H	W	T	V	Y	Q	D	2
73	H	W	T	V	Y	Q	D	E	K	2
75	T	V	Y	Q	D	E	K	Q	R	2
79	D	E	K	Q	R	K	D	K	V	2
82	Q	R	K	D	K	V	L	L	G	2
85	D	K	V	L	L	G	R	K	A	2
92	K	A	V	V	V	S	C	E	G	2
97	S	C	E	G	I	N	I	S	G	2
98	C	E	G	I	N	I	S	G	S	2
106	S	F	C	R	N	K	L	K	Y	2
108	C	R	N	K	L	K	Y	L	A	2
127	S	R	R	P	Y	H	F	Q	V	2
128	R	R	P	Y	H	F	Q	V	P	2
129	R	P	Y	H	F	Q	V	P	S	2
130	P	Y	H	F	Q	V	P	S	R	2
136	P	S	R	I	F	W	R	Q	E	2
137	S	R	I	F	W	R	Q	E	K	2
140	F	W	R	Q	E	K	A	D	G	2
142	R	Q	E	K	A	D	G	G	S	2
145	K	A	D	G	G	S	C	C	P	2
149	G	S	C	C	P	Q	G	H	A	2
151	C	C	P	Q	G	H	A	S	E	2
152	C	P	Q	G	H	A	S	E	A	2
156	H	A	S	E	A	Y	K	K	V	2
161	Y	K	K	V	C	L	S	G	A	2
164	V	C	L	S	G	A	P	H	E	2
168	G	A	P	H	E	V	G	W	K	2
171	H	E	V	G	W	K	Y	Q	A	2
172	E	V	G	W	K	Y	Q	A	V	2
185	E	E	K	R	K	E	K	A	E	2
188	R	K	E	K	A	E	I	H	Y	2
193	E	I	H	Y	R	K	N	K	Q	2
202	L	M	R	L	Q	K	Q	A	E	2
203	M	R	L	Q	K	Q	A	E	K	2
207	K	Q	A	E	K	N	M	K	K	2
210	E	K	N	M	K	K	K	I	D	2
211	K	N	M	K	K	K	I	D	K	2
212	N	M	K	K	K	I	D	K	Y	2
214	K	K	K	I	D	K	Y	T	E	2
215	K	K	I	D	K	Y	T	E	S	2
217	I	D	K	Y	T	E	S	P	G	2
219	K	Y	T	E	S	P	G	G	G	2
227	G	S	P	R	G	L	G	F	I	2
230	R	G	L	G	F	I	F	K	T	2
231	G	L	G	F	I	F	K	T	I	2
233	G	F	I	F	K	T	I	A	P	2
236	F	K	T	I	A	P	L	A	A	2
237	K	T	I	A	P	L	A	A	T	2
243	A	A	T	R	A	T	R	I	G	2
247	A	T	R	I	G	H	P	G	G	2
258	P	R	A	G	S	S	A	H	R	2
259	R	A	G	S	S	A	H	R	P	2
263	S	A	H	R	P	P	A	L	S	2
266	R	P	P	A	L	S	A	R	A	2
273	R	A	P	V	P	A	A	S	P	2
274	A	P	V	P	A	A	S	P	A	2
275	P	V	P	A	A	S	P	A	A	2
280	S	P	A	A	W	L	P	L	R	2
285	L	P	L	R	T	P	W	T	R	2
288	R	T	P	W	T	R	P	S	S	2
289	T	P	W	T	R	P	S	S	C	2
291	W	T	R	P	S	S	C	P	T	2
293	R	P	S	S	C	P	T	S	S	2
294	P	S	S	C	P	T	S	S	S	2
295	S	S	C	P	T	S	S	S	T	2
303	T	Y	D	S	L	S	P	Y	G	2
315	P	L	P	N	P	R	H	S	P	2
316	L	P	N	P	R	H	S	P	S	2
323	P	S	G	G	G	G	L	K	K	2
324	S	G	G	G	G	L	K	K	P	2
335	H	C	Q	G	Q	K	H	N	V	2
339	Q	K	H	N	V	L	A	R	G	2
350	Q	R	K	P	K	S	E	N	N	2
354	K	S	E	N	N	S	W	Y	V	2
355	S	E	N	N	S	W	Y	V	E	2
357	N	N	S	W	Y	V	E	N	G	2
363	E	N	G	R	P	A	D	L	A	2
366	R	P	A	D	L	A	G	S	G	2
369	D	L	A	G	S	G	Y	C	G	2
374	G	Y	C	G	A	L	W	K	A	2
375	Y	C	G	A	L	W	K	A	I	2
376	C	G	A	L	W	K	A	I	E	2
377	G	A	L	W	K	A	I	E	S	2
380	W	K	A	I	E	S	L	E	E	2
381	K	A	I	E	S	L	E	E	G	2
384	E	S	L	E	E	G	L	G	G	2
386	L	E	E	G	L	G	G	K	Q	2
387	E	E	G	L	G	G	K	Q	K	2
389	G	L	G	G	K	Q	K	D	K	2
390	L	G	G	K	Q	K	D	K	E	2
2	L	E	H	T	T	K	T	F	P	1
8	T	F	P	L	R	A	L	H	I	1
13	A	L	H	I	V	V	E	S	I	1
18	V	E	S	I	R	D	H	S	G	1
19	E	S	I	R	D	H	S	G	Q	1
20	S	I	R	D	H	S	G	Q	K	1
22	R	D	H	S	G	Q	K	M	K	1
26	G	Q	K	M	K	Q	D	K	K	1
27	Q	K	M	K	Q	D	K	K	V	1
31	Q	D	K	K	V	D	L	L	V	1
35	V	D	L	L	V	P	T	K	V	1
38	L	V	P	T	K	V	T	G	I	1
39	V	P	T	K	V	T	G	I	I	1
40	P	T	K	V	T	G	I	I	T	1
45	G	I	I	T	Q	G	A	K	D	1
48	T	Q	G	A	K	D	F	G	H	1
58	Q	F	V	G	S	Y	K	L	A	1
60	V	G	S	Y	K	L	A	Y	S	1
63	Y	K	L	A	Y	S	N	D	G	1
64	K	L	A	Y	S	N	D	G	E	1
66	A	Y	S	N	D	G	E	H	W	1
83	R	K	D	K	V	L	L	G	R	1
93	A	V	V	V	S	C	E	G	I	1
95	V	V	S	C	E	G	I	N	I	1
100	G	I	N	I	S	G	S	F	C	1
105	G	S	F	C	R	N	K	L	K	1
116	A	F	L	H	K	R	M	N	T	1
119	H	K	R	M	N	T	N	P	S	1
120	K	R	M	N	T	N	P	S	R	1
126	P	S	R	R	P	Y	H	F	Q	1
134	Q	V	P	S	R	I	F	W	R	1
141	W	R	Q	E	K	A	D	G	G	1
146	A	D	G	G	S	C	C	P	Q	1
147	D	G	G	S	C	C	P	Q	G	1
153	P	Q	G	H	A	S	E	A	Y	1
160	A	Y	K	K	V	C	L	S	G	1
162	K	K	V	C	L	S	G	A	P	1
169	A	P	H	E	V	G	W	K	Y	1
178	Q	A	V	T	A	T	L	E	E	1
179	A	V	T	A	T	L	E	E	K	1
180	V	T	A	T	L	E	E	K	R	1
187	K	R	K	E	K	A	E	I	H	1
189	K	E	K	A	E	I	H	Y	R	1
192	A	E	I	H	Y	R	K	N	K	1
196	Y	R	K	N	K	Q	L	M	R	1
199	N	K	Q	L	M	R	L	Q	K	1
204	R	L	Q	K	Q	A	E	K	N	1
206	Q	K	Q	A	E	K	N	M	K	1
209	A	E	K	N	M	K	K	K	I	1
213	M	K	K	K	I	D	K	Y	T	1
216	K	I	D	K	Y	T	E	S	P	1
218	D	K	Y	T	E	S	P	G	G	1
229	P	R	G	L	G	F	I	F	K	1
232	L	G	F	I	F	K	T	I	A	1
244	A	T	R	A	T	R	I	G	H	1
268	P	A	L	S	A	R	A	P	V	1
284	W	L	P	L	R	T	P	W	T	1
290	P	W	T	R	P	S	S	C	P	1
296	S	C	P	T	S	S	S	T	Y	1
298	P	T	S	S	S	T	Y	D	S	1
300	S	S	S	T	Y	D	S	L	S	1
302	S	T	Y	D	S	L	S	P	Y	1
305	D	S	L	S	P	Y	G	P	R	1
317	P	N	P	R	H	S	P	S	G	1
318	N	P	R	H	S	P	S	G	G	1
319	P	R	H	S	P	S	G	G	G	1
331	K	P	A	R	H	C	Q	G	Q	1
341	H	N	V	L	A	R	G	K	P	1
348	K	P	Q	R	K	P	K	S	E	1
351	R	K	P	K	S	E	N	N	S	1
365	G	R	P	A	D	L	A	G	S	1
368	A	D	L	A	G	S	G	Y	C	1
370	L	A	G	S	G	Y	C	G	A	1
372	G	S	G	Y	C	G	A	L	W	1
373	S	G	Y	C	G	A	L	W	K	1
396	D	K	E	R	K	A	E	N	G	1
397	K	E	R	K	A	E	N	G	P	1
398	E	R	K	A	E	N	G	P	H	1

TABLE XXXI
151P3D4 v.1: HLA Peptide
Scoring Results B*2705 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
332	V	R	F	V	G	F	P	D	K	26	Portion
314	V	R	Y	P	I	S	R	P	R	25	of SEQ
235	V	R	N	Y	G	F	W	D	K	23	ID NO:
106	G	G	Y	Q	G	R	V	F	L	20	3; each
333	R	F	V	G	F	P	D	K	K	19	start
103	K	T	Y	G	G	Y	Q	G	R	18	position
135	G	R	Y	K	C	E	V	I	E	18	is
166	R	L	G	R	Y	N	L	N	F	18	specified,
213	G	S	V	Q	Y	P	I	T	K	18	the length
259	G	R	F	Y	Y	L	I	H	P	18	of
315	R	Y	P	I	S	R	P	R	R	18	peptide is
322	R	R	R	C	S	P	T	E	A	18	9 amino
51	S	H	R	G	G	N	V	T	L	17	acids, the
55	G	N	V	T	L	P	C	K	F	17	end
68	T	A	F	G	S	G	I	H	K	17	position
76	K	I	R	I	K	W	T	K	L	17	for each
87	D	Y	L	K	E	V	D	V	F	17	peptide is
116	G	G	S	D	S	D	A	S	L	17	the start
121	D	A	S	L	V	I	T	D	L	17	position
159	V	V	F	P	Y	F	P	R	L	17	plus eight
168	G	R	Y	N	L	N	F	H	E	17
307	G	W	L	A	D	G	S	V	R	17
336	G	F	P	D	K	K	H	K	L	17
343	K	L	Y	G	V	Y	C	F	R	17
62	K	F	Y	R	D	P	T	A	F	16
72	S	G	I	H	K	I	R	I	K	16
75	H	K	I	R	I	K	W	T	K	16
107	G	Y	Q	G	R	V	F	L	K	16
110	G	R	V	F	L	K	G	G	S	16
164	F	P	R	L	G	R	Y	N	L	16
183	D	Q	D	A	V	I	A	S	F	16
239	G	F	W	D	K	D	K	S	R	16
249	D	V	F	C	F	T	S	N	F	16
261	F	Y	Y	L	I	H	P	T	K	16
262	Y	Y	L	I	H	P	T	K	L	16
312	G	S	V	R	Y	P	I	S	R	16
342	H	K	L	Y	G	V	Y	C	F	16
1	M	K	S	L	L	L	L	V	L	15
16	D	H	L	S	D	N	Y	T	L	15
52	H	R	G	G	N	V	T	L	P	15
54	G	G	N	V	T	L	P	C	K	15
77	I	R	I	K	W	T	K	L	T	15
82	T	K	L	T	S	D	Y	L	K	15
137	Y	K	C	E	V	I	E	G	L	15
158	G	V	V	F	P	Y	F	P	R	15
162	P	Y	F	P	R	L	G	R	Y	15
165	P	R	L	G	R	Y	N	L	N	15
186	A	V	I	A	S	F	D	Q	L	15
198	W	R	G	G	L	D	W	C	N	15
228	G	Q	N	T	V	P	G	V	R	15
230	N	T	V	P	G	V	R	N	Y	15
280	L	N	D	G	A	Q	I	A	K	15
290	G	Q	I	F	A	A	W	K	I	15
323	R	R	C	S	P	T	E	A	A	15
326	S	P	T	E	A	A	V	R	F	15
335	V	G	F	P	D	K	K	H	K	15
2	K	S	L	L	L	L	V	L	I	14
10	I	S	I	C	W	A	D	H	L	14
20	D	N	Y	T	L	D	H	D	R	14
45	E	Q	A	K	V	F	S	H	R	14
57	V	T	L	P	C	K	F	Y	R	14
69	A	F	G	S	G	I	H	K	I	14
80	K	W	T	K	L	T	S	D	Y	14
90	K	E	V	D	V	F	V	S	M	14
95	F	V	S	M	G	Y	H	K	K	14
123	S	L	V	I	T	D	L	T	L	14
128	D	L	T	L	E	D	Y	G	R	14
148	D	T	V	V	V	A	L	D	L	14
153	A	L	D	L	Q	G	V	V	F	14
161	F	P	Y	F	P	R	L	G	R	14
215	V	Q	Y	P	I	T	K	P	R	14
240	F	W	D	K	D	K	S	R	Y	14
272	Y	D	E	A	V	Q	A	C	L	14
308	W	L	A	D	G	S	V	R	Y	14
316	Y	P	I	S	R	P	R	R	R	14
325	C	S	P	T	E	A	A	V	R	14
340	K	K	H	K	L	Y	G	V	Y	14
4	L	L	L	L	V	L	I	S	I	13
27	D	R	A	I	H	I	Q	A	E	13
32	I	Q	A	E	N	G	P	H	L	13
42	V	E	A	E	Q	A	K	V	F	13
70	F	G	S	G	I	H	K	I	R	13
71	G	S	G	I	H	K	I	R	I	13
129	L	T	L	E	D	Y	G	R	Y	13
146	E	D	D	T	V	V	V	A	L	13
174	F	H	E	A	Q	Q	A	C	L	13
191	F	D	Q	L	Y	D	A	W	R	13
209	W	L	S	D	G	S	V	Q	Y	13
243	K	D	K	S	R	Y	D	V	F	13
245	K	S	R	Y	D	V	F	C	F	13
246	S	R	Y	D	V	F	C	F	T	13
253	F	T	S	N	F	N	G	R	F	13
255	S	N	F	N	G	R	F	Y	Y	13
256	N	F	N	G	R	F	Y	Y	L	13
285	Q	I	A	K	V	G	Q	I	F	13
291	Q	I	F	A	A	W	K	I	L	13
293	F	A	A	W	K	I	L	G	Y	13
295	A	W	K	I	L	G	Y	D	R	13
321	P	R	R	R	C	S	P	T	E	13
14	W	A	D	H	L	S	D	N	Y	12
33	Q	A	E	N	G	P	H	L	L	12
40	L	L	V	E	A	E	Q	A	K	12
44	A	E	Q	A	K	V	F	S	H	12
64	Y	R	D	P	T	A	F	G	S	12
81	W	T	K	L	T	S	D	Y	L	12
92	V	D	V	F	V	S	M	G	Y	12
93	D	V	F	V	S	M	G	Y	H	12
94	V	F	V	S	M	G	Y	H	K	12
155	D	L	Q	G	V	V	F	P	Y	12
156	L	Q	G	V	V	F	P	Y	F	12
180	A	C	L	D	Q	D	A	V	I	12
222	P	R	E	P	C	G	G	Q	N	12
232	V	P	G	V	R	N	Y	G	F	12
264	L	I	H	P	T	K	L	T	Y	12
284	A	Q	I	A	K	V	G	Q	I	12
289	V	G	Q	I	F	A	A	W	K	12
334	F	V	G	F	P	D	K	K	H	12
28	R	A	I	H	I	Q	A	E	N	11
67	P	T	A	F	G	S	G	I	H	11
105	Y	G	G	Y	Q	G	R	V	F	11
126	I	T	D	L	T	L	E	D	Y	11
202	L	D	W	C	N	A	G	W	L	11
237	N	Y	G	F	W	D	K	D	K	11
252	C	F	T	S	N	F	N	G	R	11
278	A	C	L	N	D	G	A	Q	I	11
301	Y	D	R	C	D	A	G	W	L	11
302	D	R	C	D	A	G	W	L	A	11
319	S	R	P	R	R	R	C	S	P	11
329	E	A	A	V	R	F	V	G	F	11
337	F	P	D	K	K	H	K	L	Y	11
31	H	I	Q	A	E	N	G	P	H	10
56	N	V	T	L	P	C	K	F	Y	10
97	S	M	G	Y	H	K	K	T	Y	10
100	Y	H	K	K	T	Y	G	G	Y	10
111	R	V	F	L	K	G	G	S	D	10
130	T	L	E	D	Y	G	R	Y	K	10
167	L	G	R	Y	N	L	N	F	H	10
194	L	Y	D	A	W	R	G	G	L	10
211	S	D	G	S	V	Q	Y	P	I	10
236	R	N	Y	G	F	W	D	K	D	10
260	R	F	Y	Y	L	I	H	P	T	10
9	L	I	S	I	C	W	A	D	H	9
18	L	S	D	N	Y	T	L	D	H	9
22	Y	T	L	D	H	D	R	A	I	9
23	T	L	D	H	D	R	A	I	H	9
73	G	I	H	K	I	R	I	K	W	9
118	S	D	S	D	A	S	L	V	I	9
187	V	I	A	S	F	D	Q	L	Y	9
258	N	G	R	F	Y	Y	L	I	H	9
310	A	D	G	S	V	R	Y	P	I	9
345	Y	G	V	Y	C	F	R	A	Y	9
24	L	D	H	D	R	A	I	H	I	8
134	Y	G	R	Y	K	C	E	V	I	8
136	R	Y	K	C	E	V	I	E	G	8
154	L	D	L	Q	G	V	V	F	P	8
214	S	V	Q	Y	P	I	T	K	P	8
223	R	E	P	C	G	G	Q	N	T	8
224	E	P	C	G	G	Q	N	T	V	8
254	T	S	N	F	N	G	R	F	Y	8
5	L	L	L	V	L	I	S	I	C	7
66	D	P	T	A	F	G	S	G	I	7
78	R	I	K	W	T	K	L	T	S	7
99	G	Y	H	K	K	T	Y	G	G	7
112	V	F	L	K	G	G	S	D	S	7
143	E	G	L	E	D	D	T	V	V	7
199	R	G	G	L	D	W	C	N	A	7
208	G	W	L	S	D	G	S	V	Q	7
251	F	C	F	T	S	N	F	N	G	7
257	F	N	G	R	F	Y	Y	L	I	7
287	A	K	V	G	Q	I	F	A	A	7
296	W	K	I	L	G	Y	D	R	C	7
297	K	I	L	G	Y	D	R	C	D	7
303	R	C	D	A	G	W	L	A	D	7
313	S	V	R	Y	P	I	S	R	P	7
3	S	L	L	L	L	V	L	I	S	6
7	L	V	L	I	S	I	C	W	A	6
30	I	H	I	Q	A	E	N	G	P	6
37	G	P	H	L	L	V	E	A	E	6
38	P	H	L	L	V	E	A	E	Q	6
41	L	V	E	A	E	Q	A	K	V	6
53	R	G	G	N	V	T	L	P	C	6
61	C	K	F	Y	R	D	P	T	A	6
79	I	K	W	T	K	L	T	S	D	6
98	M	G	Y	H	K	K	T	Y	G	6
102	K	K	T	Y	G	G	Y	Q	G	6
104	T	Y	G	G	Y	Q	G	R	V	6
113	F	L	K	G	G	S	D	S	D	6
140	E	V	I	E	G	L	E	D	D	6
152	V	A	L	D	L	Q	G	V	V	6
169	R	Y	N	L	N	F	H	E	A	6
172	L	N	F	H	E	A	Q	Q	A	6
189	A	S	F	D	Q	L	Y	D	A	6
192	D	Q	L	Y	D	A	W	R	G	6
197	A	W	R	G	G	L	D	W	C	6
200	G	G	L	D	W	C	N	A	G	6
225	P	C	G	G	Q	N	T	V	P	6
238	Y	G	F	W	D	K	D	K	S	6
270	L	T	Y	D	E	A	V	Q	A	6
274	E	A	V	Q	A	C	L	N	D	6
281	N	D	G	A	Q	I	A	K	V	6
286	I	A	K	V	G	Q	I	F	A	6
288	K	V	G	Q	I	F	A	A	W	6
324	R	C	S	P	T	E	A	A	V	6
346	G	V	Y	C	F	R	A	Y	N	6
6	L	L	V	L	I	S	I	C	W	5
15	A	D	H	L	S	D	N	Y	T	5
34	A	E	N	G	P	H	L	L	V	5
39	H	L	L	V	E	A	E	Q	A	5
48	K	V	F	S	H	R	G	G	N	5
65	R	D	P	T	A	F	G	S	G	5
83	K	L	T	S	D	Y	L	K	E	5
86	S	D	Y	L	K	E	V	D	V	5
114	L	K	G	G	S	D	S	D	A	5
117	G	S	D	S	D	A	S	L	V	5
124	L	V	I	T	D	L	T	L	E	5
131	L	E	D	Y	G	R	Y	K	C	5
142	I	E	G	L	E	D	D	T	V	5
144	G	L	E	D	D	T	V	V	V	5
150	V	V	V	A	L	D	L	Q	G	5
201	G	L	D	W	C	N	A	G	W	5
207	A	G	W	L	S	D	G	S	V	5
227	G	G	Q	N	T	V	P	G	V	5
247	R	Y	D	V	F	C	F	T	S	5
265	I	H	P	T	K	L	T	Y	D	5
282	D	G	A	Q	I	A	K	V	G	5
283	G	A	Q	I	A	K	V	G	Q	5
294	A	A	W	K	I	L	G	Y	D	5
300	G	Y	D	R	C	D	A	G	W	5
320	R	P	R	R	R	C	S	P	T	5
8	V	L	I	S	I	C	W	A	D	4
29	A	I	H	I	Q	A	E	N	G	4
35	E	N	G	P	H	L	L	V	E	4
36	N	G	P	H	L	L	V	E	A	4
43	E	A	E	Q	A	K	V	F	S	4
50	F	S	H	R	G	G	N	V	T	4
58	T	L	P	C	K	F	Y	R	D	4
74	I	H	K	I	R	I	K	W	T	4
88	Y	L	K	E	V	D	V	F	V	4
96	V	S	M	G	Y	H	K	K	T	4
108	Y	Q	G	R	V	F	L	K	G	4
120	S	D	A	S	L	V	I	T	D	4
122	A	S	L	V	I	T	D	L	T	4
132	E	D	Y	G	R	Y	K	C	E	4
139	C	E	V	I	E	G	L	E	D	4
181	C	L	D	Q	D	A	V	I	A	4
188	I	A	S	F	D	Q	L	Y	D	4
204	W	C	N	A	G	W	L	S	D	4
205	C	N	A	G	W	L	S	D	G	4
210	L	S	D	G	S	V	Q	Y	P	4
216	Q	Y	P	I	T	K	P	R	E	4
217	Y	P	I	T	K	P	R	E	P	4
221	K	P	R	E	P	C	G	G	Q	4
229	Q	N	T	V	P	G	V	R	N	4
231	T	V	P	G	V	R	N	Y	G	4
242	D	K	D	K	S	R	Y	D	V	4
248	Y	D	V	F	C	F	T	S	N	4
266	H	P	T	K	L	T	Y	D	E	4
269	K	L	T	Y	D	E	A	V	Q	4
304	C	D	A	G	W	L	A	D	G	4
306	A	G	W	L	A	D	G	S	V	4
309	L	A	D	G	S	V	R	Y	P	4
338	P	D	K	K	H	K	L	Y	G	4
341	K	H	K	L	Y	G	V	Y	C	4
12	I	C	W	A	D	H	L	S	D	3
21	N	Y	T	L	D	H	D	R	A	3
25	D	H	D	R	A	I	H	I	Q	3
26	H	D	R	A	I	H	I	Q	A	3
46	Q	A	K	V	F	S	H	R	G	3
47	A	K	V	F	S	H	R	G	G	3
85	T	S	D	Y	L	K	E	V	D	3
115	K	G	G	S	D	S	D	A	S	3
119	D	S	D	A	S	L	V	I	T	3
125	V	I	T	D	L	T	L	E	D	3
127	T	D	L	T	L	E	D	Y	G	3
138	K	C	E	V	I	E	G	L	E	3
141	V	I	E	G	L	E	D	D	T	3
145	L	E	D	D	T	V	V	V	A	3
147	D	D	T	V	V	V	A	L	D	3
173	N	F	H	E	A	Q	Q	A	C	3
175	H	E	A	Q	Q	A	C	L	D	3
176	E	A	Q	Q	A	C	L	D	Q	3
177	A	Q	Q	A	C	L	D	Q	D	3
179	Q	A	C	L	D	Q	D	A	V	3
184	Q	D	A	V	I	A	S	F	D	3
190	S	F	D	Q	L	Y	D	A	W	3
196	D	A	W	R	G	G	L	D	W	3
218	P	I	T	K	P	R	E	P	C	3
219	I	T	K	P	R	E	P	C	G	3
226	C	G	G	Q	N	T	V	P	G	3
234	G	V	R	N	Y	G	F	W	D	3
263	Y	L	I	H	P	T	K	L	T	3
268	T	K	L	T	Y	D	E	A	V	3
275	A	V	Q	A	C	L	N	D	G	3
279	C	L	N	D	G	A	Q	I	A	3
292	I	F	A	A	W	K	I	L	G	3
317	P	I	S	R	P	R	R	R	C	3
330	A	A	V	R	F	V	G	F	P	3
339	D	K	K	H	K	L	Y	G	V	3
13	C	W	A	D	H	L	S	D	N	2
17	H	L	S	D	N	Y	T	L	D	2
49	V	F	S	H	R	G	G	N	V	2
59	L	P	C	K	F	Y	R	D	P	2
63	F	Y	R	D	P	T	A	F	G	2
84	L	T	S	D	Y	L	K	E	V	2
89	L	K	E	V	D	V	F	V	S	2
91	E	V	D	V	F	V	S	M	G	2
133	D	Y	G	R	Y	K	C	E	V	2
149	T	V	V	V	A	L	D	L	Q	2
151	V	V	A	L	D	L	Q	G	V	2
157	Q	G	V	V	F	P	Y	F	P	2
170	Y	N	L	N	F	H	E	A	Q	2
171	N	L	N	F	H	E	A	Q	Q	2
178	Q	Q	A	C	L	D	Q	D	A	2
182	L	D	Q	D	A	V	I	A	S	2
185	D	A	V	I	A	S	F	D	Q	2
193	Q	L	Y	D	A	W	R	G	G	2
206	N	A	G	W	L	S	D	G	S	2
241	W	D	K	D	K	S	R	Y	D	2
244	D	K	S	R	Y	D	V	F	C	2
250	V	F	C	F	T	S	N	F	N	2
267	P	T	K	L	T	Y	D	E	A	2
271	T	Y	D	E	A	V	Q	A	C	2
276	V	Q	A	C	L	N	D	G	A	2
277	Q	A	C	L	N	D	G	A	Q	2
299	L	G	Y	D	R	C	D	A	G	2
305	D	A	G	W	L	A	D	G	S	2
318	I	S	R	P	R	R	R	C	S	2
328	T	E	A	A	V	R	F	V	G	2
331	A	V	R	F	V	G	F	P	D	2
344	L	Y	G	V	Y	C	F	R	A	2
11	S	I	C	W	A	D	H	L	S	1
19	S	D	N	Y	T	L	D	H	D	1
109	Q	G	R	V	F	L	K	G	G	1
163	Y	F	P	R	L	G	R	Y	N	1
203	D	W	C	N	A	G	W	L	S	1
212	D	G	S	V	Q	Y	P	I	T	1
220	T	K	P	R	E	P	C	G	G	1
233	P	G	V	R	N	Y	G	F	W	1
273	D	E	A	V	Q	A	C	L	N	1
298	I	L	G	Y	D	R	C	D	A	1
311	D	G	S	V	R	Y	P	I	S	1
327	P	T	E	A	A	V	R	F	V	1
151P3D4 v.2: HLA Peptide
Scoring Results B*2705 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
203	M	R	L	Q	K	Q	A	E	K	29	Portion of
120	K	R	M	N	T	N	P	S	R	25	SEQ ID
258	P	R	A	G	S	S	A	H	R	25	NO: 5;
196	Y	R	K	N	K	Q	L	M	R	24	each start
229	P	R	G	L	G	F	I	F	K	24	position
248	T	R	I	G	H	P	G	G	R	24	is
137	S	R	I	F	W	R	Q	E	K	23	specified,
187	K	R	K	E	K	A	E	I	H	23	the length
265	H	R	P	P	A	L	S	A	R	23	of peptide
312	P	R	N	P	L	P	N	P	R	23	is 9
21	I	R	D	H	S	G	Q	K	M	22	amino
333	A	R	H	C	Q	G	Q	K	H	21	acids, the
197	R	K	N	K	Q	L	M	R	L	20	end
398	E	R	K	A	E	N	G	P	H	20	position
57	V	Q	F	V	G	S	Y	K	L	19	for each
83	R	K	D	K	V	L	L	G	R	19	peptide is
234	F	I	F	K	T	I	A	P	L	19	the start
251	G	H	P	G	G	R	T	P	R	19	position
327	G	G	L	K	K	P	A	R	H	19	plus eight
22	R	D	H	S	G	Q	K	M	K	18
26	G	Q	K	M	K	Q	D	K	K	18
155	G	H	A	S	E	A	Y	K	K	18
207	K	Q	A	E	K	N	M	K	K	18
313	R	N	P	L	P	N	P	R	H	18
345	A	R	G	K	P	Q	R	K	P	18
389	G	L	G	G	K	Q	K	D	K	18
391	G	G	K	Q	K	D	K	E	R	18
392	G	K	Q	K	D	K	E	R	K	18
34	K	V	D	L	L	V	P	T	K	17
90	G	R	K	A	V	V	V	S	C	17
105	G	S	F	C	R	N	K	L	K	17
109	R	N	K	L	K	Y	L	A	F	17
113	K	Y	L	A	F	L	H	K	R	17
121	R	M	N	T	N	P	S	R	R	17
211	K	N	M	K	K	K	I	D	K	17
323	P	S	G	G	G	G	L	K	K	17
326	G	G	G	L	K	K	P	A	R	17
378	A	L	W	K	A	I	E	S	L	17
7	K	T	F	P	L	R	A	L	H	16
11	L	R	A	L	H	I	V	V	E	16
30	K	Q	D	K	K	V	D	L	L	16
46	I	I	T	Q	G	A	K	D	F	16
55	G	H	V	Q	F	V	G	S	Y	16
81	K	Q	R	K	D	K	V	L	L	16
84	K	D	K	V	L	L	G	R	K	16
101	I	N	I	S	G	S	F	C	R	16
110	N	K	L	K	Y	L	A	F	L	16
189	K	E	K	A	E	I	H	Y	R	16
194	I	H	Y	R	K	N	K	Q	L	16
212	N	M	K	K	K	I	D	K	Y	16
255	G	R	T	P	R	A	G	S	S	16
308	S	P	Y	G	P	R	N	P	L	16
373	S	G	Y	C	G	A	L	W	K	16
399	R	K	A	E	N	G	P	H	L	16
16	I	V	V	E	S	I	R	D	H	15
51	A	K	D	F	G	H	V	Q	F	15
75	T	V	Y	Q	D	E	K	Q	R	15
99	E	G	I	N	I	S	G	S	F	15
108	C	R	N	K	L	K	Y	L	A	15
128	R	R	P	Y	H	F	Q	V	P	15
131	Y	H	F	Q	V	P	S	R	I	15
168	G	A	P	H	E	V	G	W	K	15
176	K	Y	Q	A	V	T	A	T	L	15
188	R	K	E	K	A	E	I	H	Y	15
190	E	K	A	E	I	H	Y	R	K	15
192	A	E	I	H	Y	R	K	N	K	15
222	E	S	P	G	G	G	S	P	R	15
226	G	G	S	P	R	G	L	G	F	15
238	T	I	A	P	L	A	A	T	R	15
336	C	Q	G	Q	K	H	N	V	L	15
338	G	Q	K	H	N	V	L	A	R	15
343	V	L	A	R	G	K	P	Q	R	15
344	L	A	R	G	K	P	Q	R	K	15
346	R	G	K	P	Q	R	K	P	K	15
350	Q	R	K	P	K	S	E	N	N	15
365	G	R	P	A	D	L	A	G	S	15
14	L	H	I	V	V	E	S	I	R	14
44	T	G	I	I	T	Q	G	A	K	14
76	V	Y	Q	D	E	K	Q	R	K	14
112	L	K	Y	L	A	F	L	H	K	14
169	A	P	H	E	V	G	W	K	Y	14
181	T	A	T	L	E	E	K	R	K	14
208	Q	A	E	K	N	M	K	K	K	14
272	A	R	A	P	V	P	A	A	S	14
285	L	P	L	R	T	P	W	T	R	14
322	S	P	S	G	G	G	G	L	K	14
340	K	H	N	V	L	A	R	G	K	14
385	S	L	E	E	G	L	G	G	K	14
387	E	E	G	L	G	G	K	Q	K	14
400	K	A	E	N	G	P	H	L	L	14
4	H	T	T	K	T	F	P	L	R	13
25	S	G	Q	K	M	K	Q	D	K	13
29	M	K	Q	D	K	K	V	D	L	13
73	H	W	T	V	Y	Q	D	E	K	13
80	E	K	Q	R	K	D	K	V	L	13
82	Q	R	K	D	K	V	L	L	G	13
103	I	S	G	S	F	C	R	N	K	13
104	S	G	S	F	C	R	N	K	L	13
130	P	Y	H	F	Q	V	P	S	R	13
134	Q	V	P	S	R	I	F	W	R	13
141	W	R	Q	E	K	A	D	G	G	13
158	S	E	A	Y	K	K	V	C	L	13
163	K	V	C	L	S	G	A	P	H	13
179	A	V	T	A	T	L	E	E	K	13
180	V	T	A	T	L	E	E	K	R	13
183	T	L	E	E	K	R	K	E	K	13
199	N	K	Q	L	M	R	L	Q	K	13
206	Q	K	Q	A	E	K	N	M	K	13
224	P	G	G	G	S	P	R	G	L	13
228	S	P	R	G	L	G	F	I	F	13
230	R	G	L	G	F	I	F	K	T	13
245	T	R	A	T	R	I	G	H	P	13
277	P	A	A	S	P	A	A	W	L	13
292	T	R	P	S	S	C	P	T	S	13
302	S	T	Y	D	S	L	S	P	Y	13
305	D	S	L	S	P	Y	G	P	R	13
332	P	A	R	H	C	Q	G	Q	K	13
362	V	E	N	G	R	P	A	D	L	13
371	A	G	S	G	Y	C	G	A	L	13
6	T	K	T	F	P	L	R	A	L	12
20	S	I	R	D	H	S	G	Q	K	12
56	H	V	Q	F	V	G	S	Y	K	12
65	L	A	Y	S	N	D	G	E	H	12
69	N	D	G	E	H	W	T	V	Y	12
78	Q	D	E	K	Q	R	K	D	K	12
106	S	F	C	R	N	K	L	K	Y	12
107	F	C	R	N	K	L	K	Y	L	12
111	K	L	K	Y	L	A	F	L	H	12
127	S	R	R	P	Y	H	F	Q	V	12
132	H	F	Q	V	P	S	R	I	F	12
154	Q	G	H	A	S	E	A	Y	K	12
186	E	K	R	K	E	K	A	E	I	12
205	L	Q	K	Q	A	E	K	N	M	12
227	G	S	P	R	G	L	G	F	I	12
241	P	L	A	A	T	R	A	T	R	12
257	T	P	R	A	G	S	S	A	H	12
279	A	S	P	A	A	W	L	P	L	12
280	S	P	A	A	W	L	P	L	R	12
296	S	C	P	T	S	S	S	T	Y	12
319	P	R	H	S	P	S	G	G	G	12
321	H	S	P	S	G	G	G	G	L	12
358	N	S	W	Y	V	E	N	G	R	12
382	A	I	E	S	L	E	E	G	L	12
1	M	L	E	H	T	T	K	T	F	11
3	E	H	T	T	K	T	F	P	L	11
42	K	V	T	G	I	I	T	Q	G	11
61	G	S	Y	K	L	A	Y	S	N	11
114	Y	L	A	F	L	H	K	R	M	11
125	N	P	S	R	R	P	Y	H	F	11
138	R	I	F	W	R	Q	E	K	A	11
148	G	G	S	C	C	P	Q	G	H	11
195	H	Y	R	K	N	K	Q	L	M	11
231	G	L	G	F	I	F	K	T	I	11
242	L	A	A	T	R	A	T	R	I	11
262	S	S	A	H	R	P	P	A	L	11
287	L	R	T	P	W	T	R	P	S	11
299	T	S	S	S	T	Y	D	S	L	11
353	P	K	S	E	N	N	S	W	Y	11
12	R	A	L	H	I	V	V	E	S	10
13	A	L	H	I	V	V	E	S	I	10
38	L	V	P	T	K	V	T	G	I	10
48	T	Q	G	A	K	D	F	G	H	10
59	F	V	G	S	Y	K	L	A	Y	10
95	V	V	S	C	E	G	I	N	I	10
123	N	T	N	P	S	R	R	P	Y	10
209	A	E	K	N	M	K	K	K	I	10
244	A	T	R	A	T	R	I	G	H	10
334	R	H	C	Q	G	Q	K	H	N	10
351	R	K	P	K	S	E	N	N	S	10
367	P	A	D	L	A	G	S	G	Y	10
8	T	F	P	L	R	A	L	H	I	9
39	V	P	T	K	V	T	G	I	I	9
93	A	V	V	V	S	C	E	G	I	9
124	T	N	P	S	R	R	P	Y	H	9
129	R	P	Y	H	F	Q	V	P	S	9
153	P	Q	G	H	A	S	E	A	Y	9
204	R	L	Q	K	Q	A	E	K	N	9
266	R	P	P	A	L	S	A	R	A	9
347	G	K	P	Q	R	K	P	K	S	9
374	G	Y	C	G	A	L	W	K	A	9
377	G	A	L	W	K	A	I	E	S	9
388	E	G	L	G	G	K	Q	K	D	9
35	V	D	L	L	V	P	T	K	V	8
41	T	K	V	T	G	I	I	T	Q	8
45	G	I	I	T	Q	G	A	K	D	8
52	K	D	F	G	H	V	Q	F	V	8
182	A	T	L	E	E	K	R	K	E	8
215	K	K	I	D	K	Y	T	E	S	8
223	S	P	G	G	G	S	P	R	G	8
259	R	A	G	S	S	A	H	R	P	8
273	R	A	P	V	P	A	A	S	P	8
311	G	P	R	N	P	L	P	N	P	8
381	K	A	I	E	S	L	E	E	G	8
86	K	V	L	L	G	R	K	A	V	7
87	V	L	L	G	R	K	A	V	V	7
91	R	K	A	V	V	V	S	C	E	7
96	V	S	C	E	G	I	N	I	S	7
116	A	F	L	H	K	R	M	N	T	7
142	R	Q	E	K	A	D	G	G	S	7
145	K	A	D	G	G	S	C	C	P	7
175	W	K	Y	Q	A	V	T	A	T	7
200	K	Q	L	M	R	L	Q	K	Q	7
233	G	F	I	F	K	T	I	A	P	7
237	K	T	I	A	P	L	A	A	T	7
239	I	A	P	L	A	A	T	R	A	7
249	R	I	G	H	P	G	G	R	T	7
283	A	W	L	P	L	R	T	P	W	7
293	R	P	S	S	C	P	T	S	S	7
324	S	G	G	G	G	L	K	K	P	7
325	G	G	G	G	L	K	K	P	A	7
328	G	L	K	K	P	A	R	H	C	7
366	R	P	A	D	L	A	G	S	G	7
375	Y	C	G	A	L	W	K	A	I	7
15	H	I	V	V	E	S	I	R	D	6
23	D	H	S	G	Q	K	M	K	Q	6
28	K	M	K	Q	D	K	K	V	D	6
33	K	K	V	D	L	L	V	P	T	6
71	G	E	H	W	T	V	Y	Q	D	6
77	Y	Q	D	E	K	Q	R	K	D	6
92	K	A	V	V	V	S	C	E	G	6
97	S	C	E	G	I	N	I	S	G	6
149	G	S	C	C	P	Q	G	H	A	6
151	C	C	P	Q	G	H	A	S	E	6
159	E	A	Y	K	K	V	C	L	S	6
160	A	Y	K	K	V	C	L	S	G	6
164	V	C	L	S	G	A	P	H	E	6
171	H	E	V	G	W	K	Y	Q	A	6
173	V	G	W	K	Y	Q	A	V	T	6
174	G	W	K	Y	Q	A	V	T	A	6
232	L	G	F	I	F	K	T	I	A	6
256	R	T	P	R	A	G	S	S	A	6
264	A	H	R	P	P	A	L	S	A	6
288	R	T	P	W	T	R	P	S	S	6
320	R	H	S	P	S	G	G	G	G	6
349	P	Q	R	K	P	K	S	E	N	6
352	K	P	K	S	E	N	N	S	W	6
359	S	W	Y	V	E	N	G	R	P	6
368	A	D	L	A	G	S	G	Y	C	6
395	K	D	K	E	R	K	A	E	N	6
27	Q	K	M	K	Q	D	K	K	V	5
31	Q	D	K	K	V	D	L	L	V	5
37	L	L	V	P	T	K	V	T	G	5
68	S	N	D	G	E	H	W	T	V	5
79	D	E	K	Q	R	K	D	K	V	5
85	D	K	V	L	L	G	R	K	A	5
89	L	G	R	K	A	V	V	V	S	5
100	G	I	N	I	S	G	S	F	C	5
102	N	I	S	G	S	F	C	R	N	5
115	L	A	F	L	H	K	R	M	N	5
118	L	H	K	R	M	N	T	N	P	5
140	F	W	R	Q	E	K	A	D	G	5
152	C	P	Q	G	H	A	S	E	A	5
162	K	K	V	C	L	S	G	A	P	5
184	L	E	E	K	R	K	E	K	A	5
198	K	N	K	Q	L	M	R	L	Q	5
214	K	K	K	I	D	K	Y	T	E	5
216	K	I	D	K	Y	T	E	S	P	5
218	D	K	Y	T	E	S	P	G	G	5
246	R	A	T	R	I	G	H	P	G	5
250	I	G	H	P	G	G	R	T	P	5
252	H	P	G	G	R	T	P	R	A	5
254	G	G	R	T	P	R	A	G	S	5
274	A	P	V	P	A	A	S	P	A	5
282	A	A	W	L	P	L	R	T	P	5
286	P	L	R	T	P	W	T	R	P	5
335	H	C	Q	G	Q	K	H	N	V	5
339	Q	K	H	N	V	L	A	R	G	5
384	E	S	L	E	E	G	L	G	G	5
386	L	E	E	G	L	G	G	K	Q	5
390	L	G	G	K	Q	K	D	K	E	5
393	K	Q	K	D	K	E	R	K	A	5
397	K	E	R	K	A	E	N	G	P	5
24	H	S	G	Q	K	M	K	Q	D	4
36	D	L	L	V	P	T	K	V	T	4
47	I	T	Q	G	A	K	D	F	G	4
50	G	A	K	D	F	G	H	V	Q	4
53	D	F	G	H	V	Q	F	V	G	4
58	Q	F	V	G	S	Y	K	L	A	4
62	S	Y	K	L	A	Y	S	N	D	4
63	Y	K	L	A	Y	S	N	D	G	4
64	K	L	A	Y	S	N	D	G	E	4
74	W	T	V	Y	Q	D	E	K	Q	4
88	L	L	G	R	K	A	V	V	V	4
98	C	E	G	I	N	I	S	G	S	4
117	F	L	H	K	R	M	N	T	N	4
122	M	N	T	N	P	S	R	R	P	4
133	F	Q	V	P	S	R	I	F	W	4
135	V	P	S	R	I	F	W	R	Q	4
146	A	D	G	G	S	C	C	P	Q	4
191	K	A	E	I	H	Y	R	K	N	4
193	E	I	H	Y	R	K	N	K	Q	4
201	Q	L	M	R	L	Q	K	Q	A	4
213	M	K	K	K	I	D	K	Y	T	4
219	K	Y	T	E	S	P	G	G	G	4
221	T	E	S	P	G	G	G	S	P	4
225	G	G	G	S	P	R	G	L	G	4
235	I	F	K	T	I	A	P	L	A	4
247	A	T	R	I	G	H	P	G	G	4
261	G	S	S	A	H	R	P	P	A	4
269	A	L	S	A	R	A	P	V	P	4
278	A	A	S	P	A	A	W	L	P	4
281	P	A	A	W	L	P	L	R	T	4
295	S	S	C	P	T	S	S	S	T	4
297	C	P	T	S	S	S	T	Y	D	4
306	S	L	S	P	Y	G	P	R	N	4
307	L	S	P	Y	G	P	R	N	P	4
337	Q	G	Q	K	H	N	V	L	A	4
341	H	N	V	L	A	R	G	K	P	4
348	K	P	Q	R	K	P	K	S	E	4
354	K	S	E	N	N	S	W	Y	V	4
369	D	L	A	G	S	G	Y	C	G	4
372	G	S	G	Y	C	G	A	L	W	4
380	W	K	A	I	E	S	L	E	E	4
396	D	K	E	R	K	A	E	N	G	4
2	L	E	H	T	T	K	T	F	P	3
5	T	T	K	T	F	P	L	R	A	3
9	F	P	L	R	A	L	H	I	V	3
10	P	L	R	A	L	H	I	V	V	3
19	E	S	I	R	D	H	S	G	Q	3
32	D	K	K	V	D	L	L	V	P	3
60	V	G	S	Y	K	L	A	Y	S	3
144	E	K	A	D	G	G	S	C	C	3
156	H	A	S	E	A	Y	K	K	V	3
157	A	S	E	A	Y	K	K	V	C	3
165	C	L	S	G	A	P	H	E	V	3
177	Y	Q	A	V	T	A	T	L	E	3
178	Q	A	V	T	A	T	L	E	E	3
240	A	P	L	A	A	T	R	A	T	3
267	P	P	A	L	S	A	R	A	P	3
268	P	A	L	S	A	R	A	P	V	3
271	S	A	R	A	P	V	P	A	A	3
290	P	W	T	R	P	S	S	C	P	3
291	W	T	R	P	S	S	C	P	T	3
294	P	S	S	C	P	T	S	S	S	3
301	S	S	T	Y	D	S	L	S	P	3
303	T	Y	D	S	L	S	P	Y	G	3
304	Y	D	S	L	S	P	Y	G	P	3
309	P	Y	G	P	R	N	P	L	P	3
314	N	P	L	P	N	P	R	H	S	3
317	P	N	P	R	H	S	P	S	G	3
330	K	K	P	A	R	H	C	Q	G	3
355	S	E	N	N	S	W	Y	V	E	3
357	N	N	S	W	Y	V	E	N	G	3
361	Y	V	E	N	G	R	P	A	D	3
364	N	G	R	P	A	D	L	A	G	3
376	C	G	A	L	W	K	A	I	E	3
383	I	E	S	L	E	E	G	L	G	3
394	Q	K	D	K	E	R	K	A	E	3
18	V	E	S	I	R	D	H	S	G	2
49	Q	G	A	K	D	F	G	H	V	2
67	Y	S	N	D	G	E	H	W	T	2
147	D	G	G	S	C	C	P	Q	G	2
161	Y	K	K	V	C	L	S	G	A	2
166	L	S	G	A	P	H	E	V	G	2
167	S	G	A	P	H	E	V	G	W	2
170	P	H	E	V	G	W	K	Y	Q	2
202	L	M	R	L	Q	K	Q	A	E	2
210	E	K	N	M	K	K	K	I	D	2
217	I	D	K	Y	T	E	S	P	G	2
263	S	A	H	R	P	P	A	L	S	2
275	P	V	P	A	A	S	P	A	A	2
276	V	P	A	A	S	P	A	A	W	2
284	W	L	P	L	R	T	P	W	T	2
289	T	P	W	T	R	P	S	S	C	2
298	P	T	S	S	S	T	Y	D	S	2
300	S	S	S	T	Y	D	S	L	S	2
315	P	L	P	N	P	R	H	S	P	2
316	L	P	N	P	R	H	S	P	S	2
318	N	P	R	H	S	P	S	G	G	2
331	K	P	A	R	H	C	Q	G	Q	2
342	N	V	L	A	R	G	K	P	Q	2
356	E	N	N	S	W	Y	V	E	N	2
360	W	Y	V	E	N	G	R	P	A	2
363	E	N	G	R	P	A	D	L	A	2
370	L	A	G	S	G	Y	C	G	A	2
379	L	W	K	A	I	E	S	L	E	2
17	V	V	E	S	I	R	D	H	S	1
40	P	T	K	V	T	G	I	I	T	1
43	V	T	G	I	I	T	Q	G	A	1
54	F	G	H	V	Q	F	V	G	S	1
66	A	Y	S	N	D	G	E	H	W	1
70	D	G	E	H	W	T	V	Y	Q	1
72	E	H	W	T	V	Y	Q	D	E	1
94	V	V	V	S	C	E	G	I	N	1
119	H	K	R	M	N	T	N	P	S	1
126	P	S	R	R	P	Y	H	F	Q	1
136	P	S	R	I	F	W	R	Q	E	1
139	I	F	W	R	Q	E	K	A	D	1
143	Q	E	K	A	D	G	G	S	C	1
150	S	C	C	P	Q	G	H	A	S	1
172	E	V	G	W	K	Y	Q	A	V	1
185	E	E	K	R	K	E	K	A	E	1
220	Y	T	E	S	P	G	G	G	S	1
236	F	K	T	I	A	P	L	A	A	1
243	A	A	T	R	A	T	R	I	G	1
260	A	G	S	S	A	H	R	P	P	1
270	L	S	A	R	A	P	V	P	A	1
310	Y	G	P	R	N	P	L	P	N	1
329	L	K	K	P	A	R	H	C	Q	1

TABLE XXXII
151P3D4 v.1: HLA Peptide
Scoring Results B*2709 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
106	G	G	Y	Q	G	R	V	F	L	16	Portion
135	G	R	Y	K	C	E	V	I	E	16	of SEQ
16	D	H	L	S	D	N	Y	T	L	15	ID NO:
159	V	V	F	P	Y	F	P	R	L	15	3; each
168	G	R	Y	N	L	N	F	H	E	15	start
259	G	R	F	Y	Y	L	I	H	P	15	position
323	R	R	C	S	P	T	E	A	A	15	is
110	G	R	V	F	L	K	G	G	S	14	specified,
117	G	S	D	S	D	A	S	L	V	14	the length
166	R	L	G	R	Y	N	L	N	F	14	of
314	V	R	Y	P	I	S	R	P	R	14	peptide is
322	R	R	R	C	S	P	T	E	A	14	9 amino
2	K	S	L	L	L	L	V	L	I	13	acids, the
10	I	S	I	C	W	A	D	H	L	13	end
62	K	F	Y	R	D	P	T	A	F	13	position
116	G	G	S	D	S	D	A	S	L	13	for each
144	G	L	E	D	D	T	V	V	V	13	peptide is
148	D	T	V	V	V	A	L	D	L	13	the start
186	A	V	I	A	S	F	D	Q	L	13	position
227	G	G	Q	N	T	V	P	G	V	13	plus eight
278	A	C	L	N	D	G	A	Q	I	13
290	G	Q	I	F	A	A	W	K	I	13
324	R	C	S	P	T	E	A	A	V	13
332	V	R	F	V	G	F	P	D	K	13
336	G	F	P	D	K	K	H	K	L	13
32	I	Q	A	E	N	G	P	H	L	12
55	G	N	V	T	L	P	C	K	F	12
64	Y	R	D	P	T	A	F	G	S	12
71	G	S	G	I	H	K	I	R	I	12
76	K	I	R	I	K	W	T	K	L	12
77	I	R	I	K	W	T	K	L	T	12
90	K	E	V	D	V	F	V	S	M	12
123	S	L	V	I	T	D	L	T	L	12
146	E	D	D	T	V	V	V	A	L	12
164	F	P	R	L	G	R	Y	N	L	12
165	P	R	L	G	R	Y	N	L	N	12
222	P	R	E	P	C	G	G	Q	N	12
245	K	S	R	Y	D	V	F	C	F	12
246	S	R	Y	D	V	F	C	F	T	12
262	Y	Y	L	I	H	P	T	K	L	12
284	A	Q	I	A	K	V	G	Q	I	12
291	Q	I	F	A	A	W	K	I	L	12
301	Y	D	R	C	D	A	G	W	L	12
326	S	P	T	E	A	A	V	R	F	12
342	H	K	L	Y	G	V	Y	C	F	12
1	M	K	S	L	L	L	L	V	L	11
51	S	H	R	G	G	N	V	T	L	11
52	H	R	G	G	N	V	T	L	P	11
86	S	D	Y	L	K	E	V	D	V	11
87	D	Y	L	K	E	V	D	V	F	11
143	E	G	L	E	D	D	T	V	V	11
180	A	C	L	D	Q	D	A	V	I	11
202	L	D	W	C	N	A	G	W	L	11
243	K	D	K	S	R	Y	D	V	F	11
249	D	V	F	C	F	T	S	N	F	11
256	N	F	N	G	R	F	Y	Y	L	11
310	A	D	G	S	V	R	Y	P	I	11
321	P	R	R	R	C	S	P	T	E	11
4	L	L	L	L	V	L	I	S	I	10
22	Y	T	L	D	H	D	R	A	I	10
27	D	R	A	I	H	I	Q	A	E	10
33	Q	A	E	N	G	P	H	L	L	10
34	A	E	N	G	P	H	L	L	V	10
69	A	F	G	S	G	I	H	K	I	10
81	W	T	K	L	T	S	D	Y	L	10
121	D	A	S	L	V	I	T	D	L	10
137	Y	K	C	E	V	I	E	G	L	10
152	V	A	L	D	L	Q	G	V	V	10
153	A	L	D	L	Q	G	V	V	F	10
174	F	H	E	A	Q	Q	A	C	L	10
194	L	Y	D	A	W	R	G	G	L	10
198	W	R	G	G	L	D	W	C	N	10
211	S	D	G	S	V	Q	Y	P	I	10
235	V	R	N	Y	G	F	W	D	K	10
268	T	K	L	T	Y	D	E	A	V	10
272	Y	D	E	A	V	Q	A	C	L	10
302	D	R	C	D	A	G	W	L	A	10
319	S	R	P	R	R	R	C	S	P	10
24	L	D	H	D	R	A	I	H	I	9
42	V	E	A	E	Q	A	K	V	F	9
49	V	F	S	H	R	G	G	N	V	9
66	D	P	T	A	F	G	S	G	I	9
88	Y	L	K	E	V	D	V	F	V	9
104	T	Y	G	G	Y	Q	G	R	V	9
118	S	D	S	D	A	S	L	V	I	9
142	I	E	G	L	E	D	D	T	V	9
151	V	V	A	L	D	L	Q	G	V	9
156	L	Q	G	V	V	F	P	Y	F	9
179	Q	A	C	L	D	Q	D	A	V	9
207	A	G	W	L	S	D	G	S	V	9
232	V	P	G	V	R	N	Y	G	F	9
242	D	K	D	K	S	R	Y	D	V	9
253	F	T	S	N	F	N	G	R	F	9
257	F	N	G	R	F	Y	Y	L	I	9
306	A	G	W	L	A	D	G	S	V	9
327	P	T	E	A	A	V	R	F	V	9
329	E	A	A	V	R	F	V	G	F	9
339	D	K	K	H	K	L	Y	G	V	9
41	L	V	E	A	E	Q	A	K	V	8
84	L	T	S	D	Y	L	K	E	V	8
105	Y	G	G	Y	Q	G	R	V	F	8
133	D	Y	G	R	Y	K	C	E	V	8
134	Y	G	R	Y	K	C	E	V	I	8
183	D	Q	D	A	V	I	A	S	F	8
224	E	P	C	G	G	Q	N	T	V	8
281	N	D	G	A	Q	I	A	K	V	8
285	Q	I	A	K	V	G	Q	I	F	8
208	G	W	L	S	D	G	S	V	Q	7
28	R	A	I	H	I	Q	A	E	N	6
83	K	L	T	S	D	Y	L	K	E	6
111	R	V	F	L	K	G	G	S	D	6
199	R	G	G	L	D	W	C	N	A	6
236	R	N	Y	G	F	W	D	K	D	6
260	R	F	Y	Y	L	I	H	P	T	6
307	G	W	L	A	D	G	S	V	R	6
315	R	Y	P	I	S	R	P	R	R	6
48	K	V	F	S	H	R	G	G	N	5
53	R	G	G	N	V	T	L	P	C	5
78	R	I	K	W	T	K	L	T	S	5
102	K	K	T	Y	G	G	Y	Q	G	5
136	R	Y	K	C	E	V	I	E	G	5
192	D	Q	L	Y	D	A	W	R	G	5
200	G	G	L	D	W	C	N	A	G	5
223	R	E	P	C	G	G	Q	N	T	5
270	L	T	Y	D	E	A	V	Q	A	5
303	R	C	D	A	G	W	L	A	D	5
333	R	F	V	G	F	P	D	K	K	5
346	G	V	Y	C	F	R	A	Y	N	5
3	S	L	L	L	L	V	L	I	S	4
37	G	P	H	L	L	V	E	A	E	4
39	H	L	L	V	E	A	E	Q	A	4
54	G	G	N	V	T	L	P	C	K	4
65	R	D	P	T	A	F	G	S	G	4
73	G	I	H	K	I	R	I	K	W	4
99	G	Y	H	K	K	T	Y	G	G	4
103	K	T	Y	G	G	Y	Q	G	R	4
107	G	Y	Q	G	R	V	F	L	K	4
115	K	G	G	S	D	S	D	A	S	4
122	A	S	L	V	I	T	D	L	T	4
129	L	T	L	E	D	Y	G	R	Y	4
154	L	D	L	Q	G	V	V	F	P	4
158	G	V	V	F	P	Y	F	P	R	4
162	P	Y	F	P	R	L	G	R	Y	4
169	R	Y	N	L	N	F	H	E	A	4
172	L	N	F	H	E	A	Q	Q	A	4
189	A	S	F	D	Q	L	Y	D	A	4
213	G	S	V	Q	Y	P	I	T	K	4
215	V	Q	Y	P	I	T	K	P	R	4
230	N	T	V	P	G	V	R	N	Y	4
247	R	Y	D	V	F	C	F	T	S	4
261	F	Y	Y	L	I	H	P	T	K	4
269	K	L	T	Y	D	E	A	V	Q	4
283	G	A	Q	I	A	K	V	G	Q	4
297	K	I	L	G	Y	D	R	C	D	4
312	G	S	V	R	Y	P	I	S	R	4
320	R	P	R	R	R	C	S	P	T	4
335	V	G	F	P	D	K	K	H	K	4
343	K	L	Y	G	V	Y	C	F	R	4
8	V	L	I	S	I	C	W	A	D	3
12	I	C	W	A	D	H	L	S	D	3
21	N	Y	T	L	D	H	D	R	A	3
29	A	I	H	I	Q	A	E	N	G	3
57	V	T	L	P	C	K	F	Y	R	3
61	C	K	F	Y	R	D	P	T	A	3
80	K	W	T	K	L	T	S	D	Y	3
82	T	K	L	T	S	D	Y	L	K	3
94	V	F	V	S	M	G	Y	H	K	3
138	K	C	E	V	I	E	G	L	E	3
150	V	V	V	A	L	D	L	Q	G	3
161	F	P	Y	F	P	R	L	G	R	3
181	C	L	D	Q	D	A	V	I	A	3
188	I	A	S	F	D	Q	L	Y	D	3
201	G	L	D	W	C	N	A	G	W	3
219	I	T	K	P	R	E	P	C	G	3
228	G	Q	N	T	V	P	G	V	R	3
229	Q	N	T	V	P	G	V	R	N	3
234	G	V	R	N	Y	G	F	W	D	3
238	Y	G	F	W	D	K	D	K	S	3
239	G	F	W	D	K	D	K	S	R	3
251	F	C	F	T	S	N	F	N	G	3
274	E	A	V	Q	A	C	L	N	D	3
288	K	V	G	Q	I	F	A	A	W	3
300	G	Y	D	R	C	D	A	G	W	3
316	Y	P	I	S	R	P	R	R	R	3
330	A	A	V	R	F	V	G	F	P	3
341	K	H	K	L	Y	G	V	Y	C	3
5	L	L	L	V	L	I	S	I	C	2
6	L	L	V	L	I	S	I	C	W	2
7	L	V	L	I	S	I	C	W	A	2
20	D	N	Y	T	L	D	H	D	R	2
26	H	D	R	A	I	H	I	Q	A	2
30	I	H	I	Q	A	E	N	G	P	2
35	E	N	G	P	H	L	L	V	E	2
38	P	H	L	L	V	E	A	E	Q	2
44	A	E	Q	A	K	V	F	S	H	2
47	A	K	V	F	S	H	R	G	G	2
58	T	L	P	C	K	F	Y	R	D	2
68	T	A	F	G	S	G	I	H	K	2
75	H	K	I	R	I	K	W	T	K	2
89	L	K	E	V	D	V	F	V	S	2
93	D	V	F	V	S	M	G	Y	H	2
98	M	G	Y	H	K	K	T	Y	G	2
112	V	F	L	K	G	G	S	D	S	2
120	S	D	A	S	L	V	I	T	D	2
124	L	V	I	T	D	L	T	L	E	2
125	V	I	T	D	L	T	L	E	D	2
127	T	D	L	T	L	E	D	Y	G	2
128	D	L	T	L	E	D	Y	G	R	2
132	E	D	Y	G	R	Y	K	C	E	2
139	C	E	V	I	E	G	L	E	D	2
145	L	E	D	D	T	V	V	V	A	2
147	D	D	T	V	V	V	A	L	D	2
157	Q	G	V	V	F	P	Y	F	P	2
170	Y	N	L	N	F	H	E	A	Q	2
177	A	Q	Q	A	C	L	D	Q	D	2
184	Q	D	A	V	I	A	S	F	D	2
193	Q	L	Y	D	A	W	R	G	G	2
209	W	L	S	D	G	S	V	Q	Y	2
216	Q	Y	P	I	T	K	P	R	E	2
221	K	P	R	E	P	C	G	G	Q	2
240	F	W	D	K	D	K	S	R	Y	2
252	C	F	T	S	N	F	N	G	R	2
255	S	N	F	N	G	R	F	Y	Y	2
264	L	I	H	P	T	K	L	T	Y	2
266	H	P	T	K	L	T	Y	D	E	2
282	D	G	A	Q	I	A	K	V	G	2
287	A	K	V	G	Q	I	F	A	A	2
294	A	A	W	K	I	L	G	Y	D	2
295	A	W	K	I	L	G	Y	D	R	2
296	W	K	I	L	G	Y	D	R	C	2
298	I	L	G	Y	D	R	C	D	A	2
299	L	G	Y	D	R	C	D	A	G	2
308	W	L	A	D	G	S	V	R	Y	2
318	I	S	R	P	R	R	R	C	S	2
340	K	K	H	K	L	Y	G	V	Y	2
14	W	A	D	H	L	S	D	N	Y	1
15	A	D	H	L	S	D	N	Y	T	1
18	L	S	D	N	Y	T	L	D	H	1
23	T	L	D	H	D	R	A	I	H	1
36	N	G	P	H	L	L	V	E	A	1
40	L	L	V	E	A	E	Q	A	K	1
43	E	A	E	Q	A	K	V	F	S	1
46	Q	A	K	V	F	S	H	R	G	1
56	N	V	T	L	P	C	K	F	Y	1
70	F	G	S	G	I	H	K	I	R	1
72	S	G	I	H	K	I	R	I	K	1
74	I	H	K	I	R	I	K	W	T	1
79	I	K	W	T	K	L	T	S	D	1
91	E	V	D	V	F	V	S	M	G	1
92	V	D	V	F	V	S	M	G	Y	1
108	Y	Q	G	R	V	F	L	K	G	1
119	D	S	D	A	S	L	V	I	T	1
126	I	T	D	L	T	L	E	D	Y	1
131	L	E	D	Y	G	R	Y	K	C	1
140	E	V	I	E	G	L	E	D	D	1
149	T	V	V	V	A	L	D	L	Q	1
155	D	L	Q	G	V	V	F	P	Y	1
171	N	L	N	F	H	E	A	Q	Q	1
175	H	E	A	Q	Q	A	C	L	D	1
176	E	A	Q	Q	A	C	L	D	Q	1
182	L	D	Q	D	A	V	I	A	S	1
185	D	A	V	I	A	S	F	D	Q	1
187	V	I	A	S	F	D	Q	L	Y	1
196	D	A	W	R	G	G	L	D	W	1
197	A	W	R	G	G	L	D	W	C	1
204	W	C	N	A	G	W	L	S	D	1
210	L	S	D	G	S	V	Q	Y	P	1
212	D	G	S	V	Q	Y	P	I	T	1
217	Y	P	I	T	K	P	R	E	P	1
218	P	I	T	K	P	R	E	P	C	1
226	C	G	G	Q	N	T	V	P	G	1
233	P	G	V	R	N	Y	G	F	W	1
244	D	K	S	R	Y	D	V	F	C	1
248	Y	D	V	F	C	F	T	S	N	1
258	N	G	R	F	Y	Y	L	I	H	1
263	Y	L	I	H	P	T	K	L	T	1
265	I	H	P	T	K	L	T	Y	D	1
271	T	Y	D	E	A	V	Q	A	C	1
273	D	E	A	V	Q	A	C	L	N	1
275	A	V	Q	A	C	L	N	D	G	1
279	C	L	N	D	G	A	Q	I	A	1
286	I	A	K	V	G	Q	I	F	A	1
289	V	G	Q	I	F	A	A	W	K	1
292	I	F	A	A	W	K	I	L	G	1
293	F	A	A	W	K	I	L	G	Y	1
305	D	A	G	W	L	A	D	G	S	1
309	L	A	D	G	S	V	R	Y	P	1
311	D	G	S	V	R	Y	P	I	S	1
313	S	V	R	Y	P	I	S	R	P	1
317	P	I	S	R	P	R	R	R	C	1
325	C	S	P	T	E	A	A	V	R	1
331	A	V	R	F	V	G	F	P	D	1
338	P	D	K	K	H	K	L	Y	G	1
344	L	Y	G	V	Y	C	F	R	A	1
345	Y	G	V	Y	C	F	R	A	Y	1
151P3D4 v.2: HLA Peptide
Scoring Results B*2709 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
127	S	R	R	P	Y	H	F	Q	V	20	Portion of
21	I	R	D	H	S	G	Q	K	M	19	SEQ ID
255	G	R	T	P	R	A	G	S	S	16	NO: 5;
90	G	R	K	A	V	V	V	S	C	15	each start
197	R	K	N	K	Q	L	M	R	L	15	position
399	R	K	A	E	N	G	P	H	L	15	is
81	K	Q	R	K	D	K	V	L	L	14	specified,
128	R	R	P	Y	H	F	Q	V	P	14	the length
194	I	H	Y	R	K	N	K	Q	L	14	of peptide
365	G	R	P	A	D	L	A	G	S	14	is 9
30	K	Q	D	K	K	V	D	L	L	13	amino
52	K	D	F	G	H	V	Q	F	V	13	acids, the
57	V	Q	F	V	G	S	Y	K	L	13	end
109	R	N	K	L	K	Y	L	A	F	13	position
120	K	R	M	N	T	N	P	S	R	13	for each
187	K	R	K	E	K	A	E	I	H	13	peptide is
226	G	G	S	P	R	G	L	G	F	13	the start
82	Q	R	K	D	K	V	L	L	G	12	position
86	K	V	L	L	G	R	K	A	V	12	plus eight
110	N	K	L	K	Y	L	A	F	L	12
176	K	Y	Q	A	V	T	A	T	L	12
203	M	R	L	Q	K	Q	A	E	K	12
231	G	L	G	F	I	F	K	T	I	12
234	F	I	F	K	T	I	A	P	L	12
272	A	R	A	P	V	P	A	A	S	12
277	P	A	A	S	P	A	A	W	L	12
279	A	S	P	A	A	W	L	P	L	12
287	L	R	T	P	W	T	R	P	S	12
292	T	R	P	S	S	C	P	T	S	12
308	S	P	Y	G	P	R	N	P	L	12
350	Q	R	K	P	K	S	E	N	N	12
382	A	I	E	S	L	E	E	G	L	12
400	K	A	E	N	G	P	H	L	L	12
3	E	H	T	T	K	T	F	P	L	11
6	T	K	T	F	P	L	R	A	L	11
11	L	R	A	L	H	I	V	V	E	11
29	M	K	Q	D	K	K	V	D	L	11
46	I	I	T	Q	G	A	K	D	F	11
51	A	K	D	F	G	H	V	Q	F	11
108	C	R	N	K	L	K	Y	L	A	11
131	Y	H	F	Q	V	P	S	R	I	11
137	S	R	I	F	W	R	Q	E	K	11
141	W	R	Q	E	K	A	D	G	G	11
158	S	E	A	Y	K	K	V	C	L	11
196	Y	R	K	N	K	Q	L	M	R	11
227	G	S	P	R	G	L	G	F	I	11
248	T	R	I	G	H	P	G	G	R	11
262	S	S	A	H	R	P	P	A	L	11
265	H	R	P	P	A	L	S	A	R	11
268	P	A	L	S	A	R	A	P	V	11
299	T	S	S	S	T	Y	D	S	L	11
312	P	R	N	P	L	P	N	P	R	11
319	P	R	H	S	P	S	G	G	G	11
321	H	S	P	S	G	G	G	G	L	11
333	A	R	H	C	Q	G	Q	K	H	11
345	A	R	G	K	P	Q	R	K	P	11
371	A	G	S	G	Y	C	G	A	L	11
378	A	L	W	K	A	I	E	S	L	11
8	T	F	P	L	R	A	L	H	I	10
9	F	P	L	R	A	L	H	I	V	10
13	A	L	H	I	V	V	E	S	I	10
35	V	D	L	L	V	P	T	K	V	10
80	E	K	Q	R	K	D	K	V	L	10
87	V	L	L	G	R	K	A	V	V	10
88	L	L	G	R	K	A	V	V	V	10
93	A	V	V	V	S	C	E	G	I	10
99	E	G	I	N	I	S	G	S	F	10
104	S	G	S	F	C	R	N	K	L	10
107	F	C	R	N	K	L	K	Y	L	10
224	P	G	G	G	S	P	R	G	L	10
229	P	R	G	L	G	F	I	F	K	10
242	L	A	A	T	R	A	T	R	I	10
245	T	R	A	T	R	I	G	H	P	10
258	P	R	A	G	S	S	A	H	R	10
336	C	Q	G	Q	K	H	N	V	L	10
354	K	S	E	N	N	S	W	Y	V	10
362	V	E	N	G	R	P	A	D	L	10
398	E	R	K	A	E	N	G	P	H	10
12	R	A	L	H	I	V	V	E	S	9
31	Q	D	K	K	V	D	L	L	V	9
38	L	V	P	T	K	V	T	G	I	9
39	V	P	T	K	V	T	G	I	I	9
49	Q	G	A	K	D	F	G	H	V	9
95	V	V	S	C	E	G	I	N	I	9
114	Y	L	A	F	L	H	K	R	M	9
125	N	P	S	R	R	P	Y	H	F	9
205	L	Q	K	Q	A	E	K	N	M	9
209	A	E	K	N	M	K	K	K	I	9
335	H	C	Q	G	Q	K	H	N	V	9
1	M	L	E	H	T	T	K	T	F	8
10	P	L	R	A	L	H	I	V	V	8
27	Q	K	M	K	Q	D	K	K	V	8
68	S	N	D	G	E	H	W	T	V	8
79	D	E	K	Q	R	K	D	K	V	8
132	H	F	Q	V	P	S	R	I	F	8
156	H	A	S	E	A	Y	K	K	V	8
165	C	L	S	G	A	P	H	E	V	8
172	E	V	G	W	K	Y	Q	A	V	8
186	E	K	R	K	E	K	A	E	I	8
195	H	Y	R	K	N	K	Q	L	M	8
228	S	P	R	G	L	G	F	I	F	8
375	Y	C	G	A	L	W	K	A	I	8
61	G	S	Y	K	L	A	Y	S	N	7
129	R	P	Y	H	F	Q	V	P	S	7
259	R	A	G	S	S	A	H	R	P	7
71	G	E	H	W	T	V	Y	Q	D	6
138	R	I	F	W	R	Q	E	K	A	6
155	G	H	A	S	E	A	Y	K	K	6
230	R	G	L	G	F	I	F	K	T	6
246	R	A	T	R	I	G	H	P	G	6
313	R	N	P	L	P	N	P	R	H	6
327	G	G	L	K	K	P	A	R	H	6
377	G	A	L	W	K	A	I	E	S	6
7	K	T	F	P	L	R	A	L	H	5
22	R	D	H	S	G	Q	K	M	K	5
42	K	V	T	G	I	I	T	Q	G	5
55	G	H	V	Q	F	V	G	S	Y	5
83	R	K	D	K	V	L	L	G	R	5
91	R	K	A	V	V	V	S	C	E	5
105	G	S	F	C	R	N	K	L	K	5
121	R	M	N	T	N	P	S	R	R	5
164	V	C	L	S	G	A	P	H	E	5
174	G	W	K	Y	Q	A	V	T	A	5
204	R	L	Q	K	Q	A	E	K	N	5
249	R	I	G	H	P	G	G	R	T	5
266	R	P	P	A	L	S	A	R	A	5
273	R	A	P	V	P	A	A	S	P	5
288	R	T	P	W	T	R	P	S	S	5
293	R	P	S	S	C	P	T	S	S	5
311	G	P	R	N	P	L	P	N	P	5
320	R	H	S	P	S	G	G	G	G	5
338	G	Q	K	H	N	V	L	A	R	5
346	R	G	K	P	Q	R	K	P	K	5
351	R	K	P	K	S	E	N	N	S	5
366	R	P	A	D	L	A	G	S	G	5
392	G	K	Q	K	D	K	E	R	K	5
33	K	K	V	D	L	L	V	P	T	4
34	K	V	D	L	L	V	P	T	K	4
45	G	I	I	T	Q	G	A	K	D	4
75	T	V	Y	Q	D	E	K	Q	R	4
113	K	Y	L	A	F	L	H	K	R	4
116	A	F	L	H	K	R	M	N	T	4
142	R	Q	E	K	A	D	G	G	S	4
168	G	A	P	H	E	V	G	W	K	4
188	R	K	E	K	A	E	I	H	Y	4
200	K	Q	L	M	R	L	Q	K	Q	4
214	K	K	K	I	D	K	Y	T	E	4
225	G	G	G	S	P	R	G	L	G	4
233	G	F	I	F	K	T	I	A	P	4
235	I	F	K	T	I	A	P	L	A	4
256	R	T	P	R	A	G	S	S	A	4
261	G	S	S	A	H	R	P	P	A	4
264	A	H	R	P	P	A	L	S	A	4
274	A	P	V	P	A	A	S	P	A	4
283	A	W	L	P	L	R	T	P	W	4
326	G	G	G	L	K	K	P	A	R	4
328	G	L	K	K	P	A	R	H	C	4
334	R	H	C	Q	G	Q	K	H	N	4
347	G	K	P	Q	R	K	P	K	S	4
373	S	G	Y	C	G	A	L	W	K	4
26	G	Q	K	M	K	Q	D	K	K	3
28	K	M	K	Q	D	K	K	V	D	3
37	L	L	V	P	T	K	V	T	G	3
50	G	A	K	D	F	G	H	V	Q	3
65	L	A	Y	S	N	D	G	E	H	3
84	K	D	K	V	L	L	G	R	K	3
92	K	A	V	V	V	S	C	E	G	3
100	G	I	N	I	S	G	S	F	C	3
101	I	N	I	S	G	S	F	C	R	3
103	I	S	G	S	F	C	R	N	K	3
111	K	L	K	Y	L	A	F	L	H	3
112	L	K	Y	L	A	F	L	H	K	3
147	D	G	G	S	C	C	P	Q	G	3
148	G	G	S	C	C	P	Q	G	H	3
149	G	S	C	C	P	Q	G	H	A	3
159	E	A	Y	K	K	V	C	L	S	3
162	K	K	V	C	L	S	G	A	P	3
171	H	E	V	G	W	K	Y	Q	A	3
175	W	K	Y	Q	A	V	T	A	T	3
182	A	T	L	E	E	K	R	K	E	3
190	E	K	A	E	I	H	Y	R	K	3
192	A	E	I	H	Y	R	K	N	K	3
215	K	K	I	D	K	Y	T	E	S	3
218	D	K	Y	T	E	S	P	G	G	3
219	K	Y	T	E	S	P	G	G	G	3
237	K	T	I	A	P	L	A	A	T	3
239	I	A	P	L	A	A	T	R	A	3
240	A	P	L	A	A	T	R	A	T	3
251	G	H	P	G	G	R	T	P	R	3
254	G	G	R	T	P	R	A	G	S	3
269	A	L	S	A	R	A	P	V	P	3
278	A	A	S	P	A	A	W	L	P	3
301	S	S	T	Y	D	S	L	S	P	3
305	D	S	L	S	P	Y	G	P	R	3
306	S	L	S	P	Y	G	P	R	N	3
314	N	P	L	P	N	P	R	H	S	3
325	G	G	G	G	L	K	K	P	A	3
330	K	K	P	A	R	H	C	Q	G	3
340	K	H	N	V	L	A	R	G	K	3
352	K	P	K	S	E	N	N	S	W	3
359	S	W	Y	V	E	N	G	R	P	3
368	A	D	L	A	G	S	G	Y	C	3
372	G	S	G	Y	C	G	A	L	W	3
374	G	Y	C	G	A	L	W	K	A	3
381	K	A	I	E	S	L	E	E	G	3
384	E	S	L	E	E	G	L	G	G	3
389	G	L	G	G	K	Q	K	D	K	3
391	G	G	K	Q	K	D	K	E	R	3
4	H	T	T	K	T	F	P	L	R	2
5	T	T	K	T	F	P	L	R	A	2
15	H	I	V	V	E	S	I	R	D	2
16	I	V	V	E	S	I	R	D	H	2
17	V	V	E	S	I	R	D	H	S	2
19	E	S	I	R	D	H	S	G	Q	2
32	D	K	K	V	D	L	L	V	P	2
36	D	L	L	V	P	T	K	V	T	2
59	F	V	G	S	Y	K	L	A	Y	2
63	Y	K	L	A	Y	S	N	D	G	2
64	K	L	A	Y	S	N	D	G	E	2
66	A	Y	S	N	D	G	E	H	W	2
89	L	G	R	K	A	V	V	V	S	2
94	V	V	V	S	C	E	G	I	N	2
115	L	A	F	L	H	K	R	M	N	2
122	M	N	T	N	P	S	R	R	P	2
124	T	N	P	S	R	R	P	Y	H	2
130	P	Y	H	F	Q	V	P	S	R	2
133	F	Q	V	P	S	R	I	F	W	2
135	V	P	S	R	I	F	W	R	Q	2
145	K	A	D	G	G	S	C	C	P	2
160	A	Y	K	K	V	C	L	S	G	2
163	K	V	C	L	S	G	A	P	H	2
167	S	G	A	P	H	E	V	G	W	2
178	Q	A	V	T	A	T	L	E	E	2
179	A	V	T	A	T	L	E	E	K	2
181	T	A	T	L	E	E	K	R	K	2
189	K	E	K	A	E	I	H	Y	R	2
191	K	A	E	I	H	Y	R	K	N	2
198	K	N	K	Q	L	M	R	L	Q	2
199	N	K	Q	L	M	R	L	Q	K	2
207	K	Q	A	E	K	N	M	K	K	2
211	K	N	M	K	K	K	I	D	K	2
216	K	I	D	K	Y	T	E	S	P	2
223	S	P	G	G	G	S	P	R	G	2
232	L	G	F	I	F	K	T	I	A	2
236	F	K	T	I	A	P	L	A	A	2
238	T	I	A	P	L	A	A	T	R	2
243	A	A	T	R	A	T	R	I	G	2
247	A	T	R	I	G	H	P	G	G	2
250	I	G	H	P	G	G	R	T	P	2
252	H	P	G	G	R	T	P	R	A	2
260	A	G	S	S	A	H	R	P	P	2
271	S	A	R	A	P	V	P	A	A	2
281	P	A	A	W	L	P	L	R	T	2
285	L	P	L	R	T	P	W	T	R	2
297	C	P	T	S	S	S	T	Y	D	2
298	P	T	S	S	S	T	Y	D	S	2
302	S	T	Y	D	S	L	S	P	Y	2
303	T	Y	D	S	L	S	P	Y	G	2
309	P	Y	G	P	R	N	P	L	P	2
331	K	P	A	R	H	C	Q	G	Q	2
342	N	V	L	A	R	G	K	P	Q	2
343	V	L	A	R	G	K	P	Q	R	2
348	K	P	Q	R	K	P	K	S	E	2
356	E	N	N	S	W	Y	V	E	N	2
357	N	N	S	W	Y	V	E	N	G	2
364	N	G	R	P	A	D	L	A	G	2
388	E	G	L	G	G	K	Q	K	D	2
393	K	Q	K	D	K	E	R	K	A	2
395	K	D	K	E	R	K	A	E	N	2
396	D	K	E	R	K	A	E	N	G	2
397	K	E	R	K	A	E	N	G	P	2
14	L	H	I	V	V	E	S	I	R	1
20	S	I	R	D	H	S	G	Q	K	1
24	H	S	G	Q	K	M	K	Q	D	1
41	T	K	V	T	G	I	I	T	Q	1
43	V	T	G	I	I	T	Q	G	A	1
44	T	G	I	I	T	Q	G	A	K	1
47	I	T	Q	G	A	K	D	F	G	1
54	F	G	H	V	Q	F	V	G	S	1
58	Q	F	V	G	S	Y	K	L	A	1
62	S	Y	K	L	A	Y	S	N	D	1
70	D	G	E	H	W	T	V	Y	Q	1
73	H	W	T	V	Y	Q	D	E	K	1
74	W	T	V	Y	Q	D	E	K	Q	1
76	V	Y	Q	D	E	K	Q	R	K	1
85	D	K	V	L	L	G	R	K	A	1
97	S	C	E	G	I	N	I	S	G	1
102	N	I	S	G	S	F	C	R	N	1
106	S	F	C	R	N	K	L	K	Y	1
118	L	H	K	R	M	N	T	N	P	1
123	N	T	N	P	S	R	R	P	Y	1
134	Q	V	P	S	R	I	F	W	R	1
136	P	S	R	I	F	W	R	Q	E	1
139	I	F	W	R	Q	E	K	A	D	1
143	Q	E	K	A	D	G	G	S	C	1
146	A	D	G	G	S	C	C	P	Q	1
150	S	C	C	P	Q	G	H	A	S	1
152	C	P	Q	G	H	A	S	E	A	1
157	A	S	E	A	Y	K	K	V	C	1
169	A	P	H	E	V	G	W	K	Y	1
177	Y	Q	A	V	T	A	T	L	E	1
201	Q	L	M	R	L	Q	K	Q	A	1
213	M	K	K	K	I	D	K	Y	T	1
217	I	D	K	Y	T	E	S	P	G	1
220	Y	T	E	S	P	G	G	G	S	1
221	T	E	S	P	G	G	G	S	P	1
244	A	T	R	A	T	R	I	G	H	1
267	P	P	A	L	S	A	R	A	P	1
270	L	S	A	R	A	P	V	P	A	1
275	P	V	P	A	A	S	P	A	A	1
280	S	P	A	A	W	L	P	L	R	1
282	A	A	W	L	P	L	R	T	P	1
284	W	L	P	L	R	T	P	W	T	1
286	P	L	R	T	P	W	T	R	P	1
290	P	W	T	R	P	S	S	C	P	1
291	W	T	R	P	S	S	C	P	T	1
295	S	S	C	P	T	S	S	S	T	1
304	Y	D	S	L	S	P	Y	G	P	1
307	L	S	P	Y	G	P	R	N	P	1
310	Y	G	P	R	N	P	L	P	N	1
316	L	P	N	P	R	H	S	P	S	1	Portion of
317	P	N	P	R	H	S	P	S	G	1	SEQ ID
323	P	S	G	G	G	G	L	K	K	1	NO: 5;
329	L	K	K	P	A	R	H	C	Q	1	each start
332	P	A	R	H	C	Q	G	Q	K	1	position
337	Q	G	Q	K	H	N	V	L	A	1	is
339	Q	K	H	N	V	L	A	R	G	1	specified,
341	H	N	V	L	A	R	G	K	P	1	the length
344	L	A	R	G	K	P	Q	R	K	1	of peptide
355	S	E	N	N	S	W	Y	V	E	1	is 9
360	W	Y	V	E	N	G	R	P	A	1	amino
361	Y	V	E	N	G	R	P	A	D	1	acids, the
363	E	N	G	R	P	A	D	L	A	1	end
369	D	L	A	G	S	G	Y	C	G	1	position
370	L	A	G	S	G	Y	C	G	A	1	for each
379	L	W	K	A	I	E	S	L	E	1	peptide is
380	W	K	A	I	E	S	L	E	E	1	the start
383	I	E	S	L	E	E	G	L	G	1	position
387	E	E	G	L	G	G	K	Q	K	1	plus eight

TABLE XXXIII
151P3D4 v.1: HLA Peptide
Scoring Results B*4402 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
42	V	E	A	E	Q	A	K	V	F	24	Portion
146	E	D	D	T	V	V	V	A	L	18	of SEQ
186	A	V	I	A	S	F	D	Q	L	18	ID NO:
153	A	L	D	L	Q	G	V	V	F	17	3; each
162	P	Y	F	P	R	L	G	R	Y	17	start
34	A	E	N	G	P	H	L	L	V	16	position
69	A	F	G	S	G	I	H	K	I	16	is
159	V	V	F	P	Y	F	P	R	L	16	specified,
230	N	T	V	P	G	V	R	N	Y	16	the length
284	A	Q	I	A	K	V	G	Q	I	16	of
1	M	K	S	L	L	L	L	V	L	15	peptide is
62	K	F	Y	R	D	P	T	A	F	15	9 amino
121	D	A	S	L	V	I	T	D	L	15	acids, the
145	L	E	D	D	T	V	V	V	A	15	end
255	S	N	F	N	G	R	F	Y	Y	15	position
264	L	I	H	P	T	K	L	T	Y	15	for each
288	K	V	G	Q	I	F	A	A	W	15	peptide is
329	E	A	A	V	R	F	V	G	F	15	the start
2	K	S	L	L	L	L	V	L	I	14	position
10	I	S	I	C	W	A	D	H	L	14	plus eight
33	Q	A	E	N	G	P	H	L	L	14
44	A	E	Q	A	K	V	F	S	H	14
51	S	H	R	G	G	N	V	T	L	14
56	N	V	T	L	P	C	K	F	Y	14
73	G	I	H	K	I	R	I	K	W	14
90	K	E	V	D	V	F	V	S	M	14
97	S	M	G	Y	H	K	K	T	Y	14
180	A	C	L	D	Q	D	A	V	I	14
183	D	Q	D	A	V	I	A	S	F	14
190	S	F	D	Q	L	Y	D	A	W	14
209	W	L	S	D	G	S	V	Q	Y	14
256	N	F	N	G	R	F	Y	Y	L	14
278	A	C	L	N	D	G	A	Q	I	14
291	Q	I	F	A	A	W	K	I	L	14
293	F	A	A	W	K	I	L	G	Y	14
336	G	F	P	D	K	K	H	K	L	14
337	F	P	D	K	K	H	K	L	Y	14
345	Y	G	V	Y	C	F	R	A	Y	14
6	L	L	V	L	I	S	I	C	W	13
22	Y	T	L	D	H	D	R	A	I	13
55	G	N	V	T	L	P	C	K	F	13
87	D	Y	L	K	E	V	D	V	F	13
118	S	D	S	D	A	S	L	V	I	13
123	S	L	V	I	T	D	L	T	L	13
126	I	T	D	L	T	L	E	D	Y	13
131	L	E	D	Y	G	R	Y	K	C	13
137	Y	K	C	E	V	I	E	G	L	13
243	K	D	K	S	R	Y	D	V	F	13
249	D	V	F	C	F	T	S	N	F	13
262	Y	Y	L	I	H	P	T	K	L	13
290	G	Q	I	F	A	A	W	K	I	13
326	S	P	T	E	A	A	V	R	F	13
4	L	L	L	L	V	L	I	S	I	12
16	D	H	L	S	D	N	Y	T	L	12
24	L	D	H	D	R	A	I	H	I	12
76	K	I	R	I	K	W	T	K	L	12
80	K	W	T	K	L	T	S	D	Y	12
105	Y	G	G	Y	Q	G	R	V	F	12
106	G	G	Y	Q	G	R	V	F	L	12
116	G	G	S	D	S	D	A	S	L	12
142	I	E	G	L	E	D	D	T	V	12
148	D	T	V	V	V	A	L	D	L	12
155	D	L	Q	G	V	V	F	P	Y	12
164	F	P	R	L	G	R	Y	N	L	12
166	R	L	G	R	Y	N	L	N	F	12
175	H	E	A	Q	Q	A	C	L	D	12
194	L	Y	D	A	W	R	G	G	L	12
196	D	A	W	R	G	G	L	D	W	12
202	L	D	W	C	N	A	G	W	L	12
233	P	G	V	R	N	Y	G	F	W	12
245	K	S	R	Y	D	V	F	C	F	12
253	F	T	S	N	F	N	G	R	F	12
254	T	S	N	F	N	G	R	F	Y	12
273	D	E	A	V	Q	A	C	L	N	12
300	G	Y	D	R	C	D	A	G	W	12
308	W	L	A	D	G	S	V	R	Y	12
310	A	D	G	S	V	R	Y	P	I	12
328	T	E	A	A	V	R	F	V	G	12
340	K	K	H	K	L	Y	G	V	Y	12
342	H	K	L	Y	G	V	Y	C	F	12
14	W	A	D	H	L	S	D	N	Y	11
32	I	Q	A	E	N	G	P	H	L	11
81	W	T	K	L	T	S	D	Y	L	11
129	L	T	L	E	D	Y	G	R	Y	11
139	C	E	V	I	E	G	L	E	D	11
156	L	Q	G	V	V	F	P	Y	F	11
187	V	I	A	S	F	D	Q	L	Y	11
201	G	L	D	W	C	N	A	G	W	11
223	R	E	P	C	G	G	Q	N	T	11
232	V	P	G	V	R	N	Y	G	F	11
240	F	W	D	K	D	K	S	R	Y	11
301	Y	D	R	C	D	A	G	W	L	11
92	V	D	V	F	V	S	M	G	Y	10
100	Y	H	K	K	T	Y	G	G	Y	10
174	F	H	E	A	Q	Q	A	C	L	10
257	F	N	G	R	F	Y	Y	L	I	10
272	Y	D	E	A	V	Q	A	C	L	10
285	Q	I	A	K	V	G	Q	I	F	10
71	G	S	G	I	H	K	I	R	I	9
134	Y	G	R	Y	K	C	E	V	I	9
211	S	D	G	S	V	Q	Y	P	I	9
287	A	K	V	G	Q	I	F	A	A	9
35	E	N	G	P	H	L	L	V	E	8
66	D	P	T	A	F	G	S	G	I	8
72	S	G	I	H	K	I	R	I	K	8
77	I	R	I	K	W	T	K	L	T	7
122	A	S	L	V	I	T	D	L	T	7
189	A	S	F	D	Q	L	Y	D	A	7
215	V	Q	Y	P	I	T	K	P	R	7
263	Y	L	I	H	P	T	K	L	T	7
335	V	G	F	P	D	K	K	H	K	7
8	V	L	I	S	I	C	W	A	D	6
25	D	H	D	R	A	I	H	I	Q	6
74	I	H	K	I	R	I	K	W	T	6
75	H	K	I	R	I	K	W	T	K	6
124	L	V	I	T	D	L	T	L	E	6
132	E	D	Y	G	R	Y	K	C	E	6
140	E	V	I	E	G	L	E	D	D	6
217	Y	P	I	T	K	P	R	E	P	6
316	Y	P	I	S	R	P	R	R	R	6
318	I	S	R	P	R	R	R	C	S	6
324	R	C	S	P	T	E	A	A	V	6
3	S	L	L	L	L	V	L	I	S	5
15	A	D	H	L	S	D	N	Y	T	5
27	D	R	A	I	H	I	Q	A	E	5
64	Y	R	D	P	T	A	F	G	S	5
70	F	G	S	G	I	H	K	I	R	5
84	L	T	S	D	Y	L	K	E	V	5
96	V	S	M	G	Y	H	K	K	T	5
165	P	R	L	G	R	Y	N	L	N	5
177	A	Q	Q	A	C	L	D	Q	D	5
182	L	D	Q	D	A	V	I	A	S	5
197	A	W	R	G	G	L	D	W	C	5
200	G	G	L	D	W	C	N	A	G	5
214	S	V	Q	Y	P	I	T	K	P	5
224	E	P	C	G	G	Q	N	T	V	5
275	A	V	Q	A	C	L	N	D	G	5
280	L	N	D	G	A	Q	I	A	K	5
281	N	D	G	A	Q	I	A	K	V	5
282	D	G	A	Q	I	A	K	V	G	5
294	A	A	W	K	I	L	G	Y	D	5
314	V	R	Y	P	I	S	R	P	R	5
319	S	R	P	R	R	R	C	S	P	5
330	A	A	V	R	F	V	G	F	P	5
5	L	L	L	V	L	I	S	I	C	4
7	L	V	L	I	S	I	C	W	A	4
17	H	L	S	D	N	Y	T	L	D	4
18	L	S	D	N	Y	T	L	D	H	4
28	R	A	I	H	I	Q	A	E	N	4
29	A	I	H	I	Q	A	E	N	G	4
30	I	H	I	Q	A	E	N	G	P	4
36	N	G	P	H	L	L	V	E	A	4
37	G	P	H	L	L	V	E	A	E	4
47	A	K	V	F	S	H	R	G	G	4
48	K	V	F	S	H	R	G	G	N	4
52	H	R	G	G	N	V	T	L	P	4
57	V	T	L	P	C	K	F	Y	R	4
61	C	K	F	Y	R	D	P	T	A	4
68	T	A	F	G	S	G	I	H	K	4
91	E	V	D	V	F	V	S	M	G	4
107	G	Y	Q	G	R	V	F	L	K	4
108	Y	Q	G	R	V	F	L	K	G	4
120	S	D	A	S	L	V	I	T	D	4
143	E	G	L	E	D	D	T	V	V	4
144	G	L	E	D	D	T	V	V	V	4
160	V	F	P	Y	F	P	R	L	G	4
169	R	Y	N	L	N	F	H	E	A	4
170	Y	N	L	N	F	H	E	A	Q	4
172	L	N	F	H	E	A	Q	Q	A	4
207	A	G	W	L	S	D	G	S	V	4
219	I	T	K	P	R	E	P	C	G	4
222	P	R	E	P	C	G	G	Q	N	4
231	T	V	P	G	V	R	N	Y	G	4
259	G	R	F	Y	Y	L	I	H	P	4
260	R	F	Y	Y	L	I	H	P	T	4
268	T	K	L	T	Y	D	E	A	V	4
270	L	T	Y	D	E	A	V	Q	A	4
271	T	Y	D	E	A	V	Q	A	C	4
277	Q	A	C	L	N	D	G	A	Q	4
296	W	K	I	L	G	Y	D	R	C	4
297	K	I	L	G	Y	D	R	C	D	4
299	L	G	Y	D	R	C	D	A	G	4
303	R	C	D	A	G	W	L	A	D	4
306	A	G	W	L	A	D	G	S	V	4
309	L	A	D	G	S	V	R	Y	P	4
313	S	V	R	Y	P	I	S	R	P	4
317	P	I	S	R	P	R	R	R	C	4
325	C	S	P	T	E	A	A	V	R	4
11	S	I	C	W	A	D	H	L	S	3
26	H	D	R	A	I	H	I	Q	A	3
39	H	L	L	V	E	A	E	Q	A	3
43	E	A	E	Q	A	K	V	F	S	3
45	E	Q	A	K	V	F	S	H	R	3
50	F	S	H	R	G	G	N	V	T	3
53	R	G	G	N	V	T	L	P	C	3
65	R	D	P	T	A	F	G	S	G	3
82	T	K	L	T	S	D	Y	L	K	3
83	K	L	T	S	D	Y	L	K	E	3
86	S	D	Y	L	K	E	V	D	V	3
95	F	V	S	M	G	Y	H	K	K	3
109	Q	G	R	V	F	L	K	G	G	3
111	R	V	F	L	K	G	G	S	D	3
115	K	G	G	S	D	S	D	A	S	3
117	G	S	D	S	D	A	S	L	V	3
119	D	S	D	A	S	L	V	I	T	3
125	V	I	T	D	L	T	L	E	D	3
138	K	C	E	V	I	E	G	L	E	3
152	V	A	L	D	L	Q	G	V	V	3
154	L	D	L	Q	G	V	V	F	P	3
163	Y	F	P	R	L	G	R	Y	N	3
167	L	G	R	Y	N	L	N	F	H	3
173	N	F	H	E	A	Q	Q	A	C	3
176	E	A	Q	Q	A	C	L	D	Q	3
179	Q	A	C	L	D	Q	D	A	V	3
181	C	L	D	Q	D	A	V	I	A	3
210	L	S	D	G	S	V	Q	Y	P	3
213	G	S	V	Q	Y	P	I	T	K	3
220	T	K	P	R	E	P	C	G	G	3
226	C	G	G	Q	N	T	V	P	G	3
228	G	Q	N	T	V	P	G	V	R	3
237	N	Y	G	F	W	D	K	D	K	3
238	Y	G	F	W	D	K	D	K	S	3
239	G	F	W	D	K	D	K	S	R	3
244	D	K	S	R	Y	D	V	F	C	3
246	S	R	Y	D	V	F	C	F	T	3
251	F	C	F	T	S	N	F	N	G	3
252	C	F	T	S	N	F	N	G	R	3
261	F	Y	Y	L	I	H	P	T	K	3
265	I	H	P	T	K	L	T	Y	D	3
274	E	A	V	Q	A	C	L	N	D	3
295	A	W	K	I	L	G	Y	D	R	3
312	G	S	V	R	Y	P	I	S	R	3
323	R	R	C	S	P	T	E	A	A	3
331	A	V	R	F	V	G	F	P	D	3
332	V	R	F	V	G	F	P	D	K	3
333	R	F	V	G	F	P	D	K	K	3
334	F	V	G	F	P	D	K	K	H	3
341	K	H	K	L	Y	G	V	Y	C	3
13	C	W	A	D	H	L	S	D	N	2
19	S	D	N	Y	T	L	D	H	D	2
20	D	N	Y	T	L	D	H	D	R	2
21	N	Y	T	L	D	H	D	R	A	2
23	T	L	D	H	D	R	A	I	H	2
38	P	H	L	L	V	E	A	E	Q	2
40	L	L	V	E	A	E	Q	A	K	2
49	V	F	S	H	R	G	G	N	V	2
58	T	L	P	C	K	F	Y	R	D	2
63	F	Y	R	D	P	T	A	F	G	2
78	R	I	K	W	T	K	L	T	S	2
79	I	K	W	T	K	L	T	S	D	2
85	T	S	D	Y	L	K	E	V	D	2
89	L	K	E	V	D	V	F	V	S	2
93	D	V	F	V	S	M	G	Y	H	2
102	K	K	T	Y	G	G	Y	Q	G	2
103	K	T	Y	G	G	Y	Q	G	R	2
127	T	D	L	T	L	E	D	Y	G	2
130	T	L	E	D	Y	G	R	Y	K	2
136	R	Y	K	C	E	V	I	E	G	2
147	D	D	T	V	V	V	A	L	D	2
149	T	V	V	V	A	L	D	L	Q	2
150	V	V	V	A	L	D	L	Q	G	2
151	V	V	A	L	D	L	Q	G	V	2
161	F	P	Y	F	P	R	L	G	R	2
171	N	L	N	F	H	E	A	Q	Q	2
184	Q	D	A	V	I	A	S	F	D	2
188	I	A	S	F	D	Q	L	Y	D	2
192	D	Q	L	Y	D	A	W	R	G	2
193	Q	L	Y	D	A	W	R	G	G	2
195	Y	D	A	W	R	G	G	L	D	2
203	D	W	C	N	A	G	W	L	S	2
205	C	N	A	G	W	L	S	D	G	2
208	G	W	L	S	D	G	S	V	Q	2
225	P	C	G	G	Q	N	T	V	P	2
227	G	G	Q	N	T	V	P	G	V	2
236	R	N	Y	G	F	W	D	K	D	2
241	W	D	K	D	K	S	R	Y	D	2
242	D	K	D	K	S	R	Y	D	V	2
247	R	Y	D	V	F	C	F	T	S	2
258	N	G	R	F	Y	Y	L	I	H	2
269	K	L	T	Y	D	E	A	V	Q	2
279	C	L	N	D	G	A	Q	I	A	2
292	I	F	A	A	W	K	I	L	G	2
302	D	R	C	D	A	G	W	L	A	2
304	C	D	A	G	W	L	A	D	G	2
307	G	W	L	A	D	G	S	V	R	2
311	D	G	S	V	R	Y	P	I	S	2
315	R	Y	P	I	S	R	P	R	R	2
320	R	P	R	R	R	C	S	P	T	2
321	P	R	R	R	C	S	P	T	E	2
327	P	T	E	A	A	V	R	F	V	2
343	K	L	Y	G	V	Y	C	F	R	2
9	L	I	S	I	C	W	A	D	H	1
12	I	C	W	A	D	H	L	S	D	1
41	L	V	E	A	E	Q	A	K	V	1
46	Q	A	K	V	F	S	H	R	G	1
54	G	G	N	V	T	L	P	C	K	1
59	L	P	C	K	F	Y	R	D	P	1
60	P	C	K	F	Y	R	D	P	T	1
88	Y	L	K	E	V	D	V	F	V	1
99	G	Y	H	K	K	T	Y	G	G	1
101	H	K	K	T	Y	G	G	Y	Q	1
104	T	Y	G	G	Y	Q	G	R	V	1
112	V	F	L	K	G	G	S	D	S	1
113	F	L	K	G	G	S	D	S	D	1
114	L	K	G	G	S	D	S	D	A	1
128	D	L	T	L	E	D	Y	G	R	1
133	D	Y	G	R	Y	K	C	E	V	1
135	G	R	Y	K	C	E	V	I	E	1
141	V	I	E	G	L	E	D	D	T	1
157	Q	G	V	V	F	P	Y	F	P	1
168	G	R	Y	N	L	N	F	H	E	1
191	F	D	Q	L	Y	D	A	W	R	1
198	W	R	G	G	L	D	W	C	N	1
199	R	G	G	L	D	W	C	N	A	1
204	W	C	N	A	G	W	L	S	D	1
206	N	A	G	W	L	S	D	G	S	1
212	D	G	S	V	Q	Y	P	I	T	1
216	Q	Y	P	I	T	K	P	R	E	1
218	P	I	T	K	P	R	E	P	C	1
221	K	P	R	E	P	C	G	G	Q	1
229	Q	N	T	V	P	G	V	R	N	1
234	G	V	R	N	Y	G	F	W	D	1
235	V	R	N	Y	G	F	W	D	K	1
248	Y	D	V	F	C	F	T	S	N	1
250	V	F	C	F	T	S	N	F	N	1
266	H	P	T	K	L	T	Y	D	E	1
267	P	T	K	L	T	Y	D	E	A	1
283	G	A	Q	I	A	K	V	G	Q	1
286	I	A	K	V	G	Q	I	F	A	1
289	V	G	Q	I	F	A	A	W	K	1
298	I	L	G	Y	D	R	C	D	A	1
305	D	A	G	W	L	A	D	G	S	1
322	R	R	R	C	S	P	T	E	A	1
338	P	D	K	K	H	K	L	Y	G	1
339	D	K	K	H	K	L	Y	G	V	1
346	G	V	Y	C	F	R	A	Y	N	1
151P3D4 v.2: HLA Peptide
Scoring Results B*4402 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
209	A	E	K	N	M	K	K	K	I	25	Portion of
362	V	E	N	G	R	P	A	D	L	23	SEQ ID
158	S	E	A	Y	K	K	V	C	L	22	NO: 5;
192	A	E	I	H	Y	R	K	N	K	19	each start
283	A	W	L	P	L	R	T	P	W	18	position
99	E	G	I	N	I	S	G	S	F	17	is
185	E	E	K	R	K	E	K	A	E	17	specified,
371	A	G	S	G	Y	C	G	A	L	17	the length
51	A	K	D	F	G	H	V	Q	F	16	of peptide
80	E	K	Q	R	K	D	K	V	L	16	is 9
123	N	T	N	P	S	R	R	P	Y	16	amino
226	G	G	S	P	R	G	L	G	F	16	acids, the
378	A	L	W	K	A	I	E	S	L	16	end
387	E	E	G	L	G	G	K	Q	K	16	position
66	A	Y	S	N	D	G	E	H	W	15	for each
104	S	G	S	F	C	R	N	K	L	15	peptide is
106	S	F	C	R	N	K	L	K	Y	15	the start
125	N	P	S	R	R	P	Y	H	F	15	position
133	F	Q	V	P	S	R	I	F	W	15	plus eight
167	S	G	A	P	H	E	V	G	W	15
189	K	E	K	A	E	I	H	Y	R	15
212	N	M	K	K	K	I	D	K	Y	15
234	F	I	F	K	T	I	A	P	L	15
262	S	S	A	H	R	P	P	A	L	15
279	A	S	P	A	A	W	L	P	L	15
400	K	A	E	N	G	P	H	L	L	15
1	M	L	E	H	T	T	K	T	F	14
3	E	H	T	T	K	T	F	P	L	14
6	T	K	T	F	P	L	R	A	L	14
30	K	Q	D	K	K	V	D	L	L	14
98	C	E	G	I	N	I	S	G	S	14
107	F	C	R	N	K	L	K	Y	L	14
109	R	N	K	L	K	Y	L	A	F	14
169	A	P	H	E	V	G	W	K	Y	14
194	I	H	Y	R	K	N	K	Q	L	14
221	T	E	S	P	G	G	G	S	P	14
296	S	C	P	T	S	S	S	T	Y	14
308	S	P	Y	G	P	R	N	P	L	14
8	T	F	P	L	R	A	L	H	I	13
18	V	E	S	I	R	D	H	S	G	13
46	I	I	T	Q	G	A	K	D	F	13
57	V	Q	F	V	G	S	Y	K	L	13
59	F	V	G	S	Y	K	L	A	Y	13
81	K	Q	R	K	D	K	V	L	L	13
110	N	K	L	K	Y	L	A	F	L	13
176	K	Y	Q	A	V	T	A	T	L	13
224	P	G	G	G	S	P	R	G	L	13
231	G	L	G	F	I	F	K	T	I	13
276	V	P	A	A	S	P	A	A	W	13
302	S	T	Y	D	S	L	S	P	Y	13
355	S	E	N	N	S	W	Y	V	E	13
382	A	I	E	S	L	E	E	G	L	13
383	I	E	S	L	E	E	G	L	G	13
13	A	L	H	I	V	V	E	S	I	12
29	M	K	Q	D	K	K	V	D	L	12
69	N	D	G	E	H	W	T	V	Y	12
71	G	E	H	W	T	V	Y	Q	D	12
79	D	E	K	Q	R	K	D	K	V	12
153	P	Q	G	H	A	S	E	A	Y	12
171	H	E	V	G	W	K	Y	Q	A	12
184	L	E	E	K	R	K	E	K	A	12
228	S	P	R	G	L	G	F	I	F	12
336	C	Q	G	Q	K	H	N	V	L	12
352	K	P	K	S	E	N	N	S	W	12
353	P	K	S	E	N	N	S	W	Y	12
367	P	A	D	L	A	G	S	G	Y	12
375	Y	C	G	A	L	W	K	A	I	12
386	L	E	E	G	L	G	G	K	Q	12
397	K	E	R	K	A	E	N	G	P	12
2	L	E	H	T	T	K	T	F	P	11
38	L	V	P	T	K	V	T	G	I	11
55	G	H	V	Q	F	V	G	S	Y	11
93	A	V	V	V	S	C	E	G	I	11
131	Y	H	F	Q	V	P	S	R	I	11
132	H	F	Q	V	P	S	R	I	F	11
188	R	K	E	K	A	E	I	H	Y	11
197	R	K	N	K	Q	L	M	R	L	11
227	G	S	P	R	G	L	G	F	I	11
242	L	A	A	T	R	A	T	R	I	11
277	P	A	A	S	P	A	A	W	L	11
299	T	S	S	S	T	Y	D	S	L	11
321	H	S	P	S	G	G	G	G	L	11
372	G	S	G	Y	C	G	A	L	W	11
399	R	K	A	E	N	G	P	H	L	11
95	V	V	S	C	E	G	I	N	I	10
143	Q	E	K	A	D	G	G	S	C	10
186	E	K	R	K	E	K	A	E	I	10
39	V	P	T	K	V	T	G	I	I	9
272	A	R	A	P	V	P	A	A	S	9
278	A	A	S	P	A	A	W	L	P	9
7	K	T	F	P	L	R	A	L	H	8
86	K	V	L	L	G	R	K	A	V	8
240	A	P	L	A	A	T	R	A	T	8
264	A	H	R	P	P	A	L	S	A	8
314	N	P	L	P	N	P	R	H	S	8
42	K	V	T	G	I	I	T	Q	G	7
150	S	C	C	P	Q	G	H	A	S	7
233	G	F	I	F	K	T	I	A	P	7
237	K	T	I	A	P	L	A	A	T	7
265	H	R	P	P	A	L	S	A	R	7
269	A	L	S	A	R	A	P	V	P	7
274	A	P	V	P	A	A	S	P	A	7
282	A	A	W	L	P	L	R	T	P	7
364	N	G	R	P	A	D	L	A	G	7
11	L	R	A	L	H	I	V	V	E	6
19	E	S	I	R	D	H	S	G	Q	6
41	T	K	V	T	G	I	I	T	Q	6
105	G	S	F	C	R	N	K	L	K	6
157	A	S	E	A	Y	K	K	V	C	6
182	A	T	L	E	E	K	R	K	E	6
230	R	G	L	G	F	I	F	K	T	6
243	A	A	T	R	A	T	R	I	G	6
324	S	G	G	G	G	L	K	K	P	6
346	R	G	K	P	Q	R	K	P	K	6
394	Q	K	D	K	E	R	K	A	E	6
34	K	V	D	L	L	V	P	T	K	5
36	D	L	L	V	P	T	K	V	T	5
37	L	L	V	P	T	K	V	T	G	5
44	T	G	I	I	T	Q	G	A	K	5
45	G	I	I	T	Q	G	A	K	D	5
52	K	D	F	G	H	V	Q	F	V	5
113	K	Y	L	A	F	L	H	K	R	5
116	A	F	L	H	K	R	M	N	T	5
127	S	R	R	P	Y	H	F	Q	V	5
134	Q	V	P	S	R	I	F	W	R	5
137	S	R	I	F	W	R	Q	E	K	5
139	I	F	W	R	Q	E	K	A	D	5
193	E	I	H	Y	R	K	N	K	Q	5
199	N	K	Q	L	M	R	L	Q	K	5
200	K	Q	L	M	R	L	Q	K	Q	5
201	Q	L	M	R	L	Q	K	Q	A	5
215	K	K	I	D	K	Y	T	E	S	5
238	T	I	A	P	L	A	A	T	R	5
244	A	T	R	A	T	R	I	G	H	5
245	T	R	A	T	R	I	G	H	P	5
248	T	R	I	G	H	P	G	G	R	5
250	I	G	H	P	G	G	R	T	P	5
253	P	G	G	R	T	P	R	A	G	5
255	G	R	T	P	R	A	G	S	S	5
260	A	G	S	S	A	H	R	P	P	5
267	P	P	A	L	S	A	R	A	P	5
287	L	R	T	P	W	T	R	P	S	5
306	S	L	S	P	Y	G	P	R	N	5
309	P	Y	G	P	R	N	P	L	P	5
310	Y	G	P	R	N	P	L	P	N	5
312	P	R	N	P	L	P	N	P	R	5
329	L	K	K	P	A	R	H	C	Q	5
338	G	Q	K	H	N	V	L	A	R	5
342	N	V	L	A	R	G	K	P	Q	5
345	A	R	G	K	P	Q	R	K	P	5
348	K	P	Q	R	K	P	K	S	E	5
363	E	N	G	R	P	A	D	L	A	5
381	K	A	I	E	S	L	E	E	G	5
388	E	G	L	G	G	K	Q	K	D	5
9	F	P	L	R	A	L	H	I	V	4
12	R	A	L	H	I	V	V	E	S	4
16	I	V	V	E	S	I	R	D	H	4
27	Q	K	M	K	Q	D	K	K	V	4
28	K	M	K	Q	D	K	K	V	D	4
33	K	K	V	D	L	L	V	P	T	4
35	V	D	L	L	V	P	T	K	V	4
58	Q	F	V	G	S	Y	K	L	A	4
68	S	N	D	G	E	H	W	T	V	4
82	Q	R	K	D	K	V	L	L	G	4
87	V	L	L	G	R	K	A	V	V	4
88	L	L	G	R	K	A	V	V	V	4
96	V	S	C	E	G	I	N	I	S	4
97	S	C	E	G	I	N	I	S	G	4
102	N	I	S	G	S	F	C	R	N	4
115	L	A	F	L	H	K	R	M	N	4
135	V	P	S	R	I	F	W	R	Q	4
138	R	I	F	W	R	Q	E	K	A	4
146	A	D	G	G	S	C	C	P	Q	4
156	H	A	S	E	A	Y	K	K	V	4
159	E	A	Y	K	K	V	C	L	S	4
160	A	Y	K	K	V	C	L	S	G	4
165	C	L	S	G	A	P	H	E	V	4
172	E	V	G	W	K	Y	Q	A	V	4
179	A	V	T	A	T	L	E	E	K	4
208	Q	A	E	K	N	M	K	K	K	4
210	E	K	N	M	K	K	K	I	D	4
222	E	S	P	G	G	G	S	P	R	4
235	I	F	K	T	I	A	P	L	A	4
236	F	K	T	I	A	P	L	A	A	4
263	S	A	H	R	P	P	A	L	S	4
271	S	A	R	A	P	V	P	A	A	4
284	W	L	P	L	R	T	P	W	T	4
285	L	P	L	R	T	P	W	T	R	4
295	S	S	C	P	T	S	S	S	T	4
300	S	S	S	T	Y	D	S	L	S	4
315	P	L	P	N	P	R	H	S	P	4
316	L	P	N	P	R	H	S	P	S	4
320	R	H	S	P	S	G	G	G	G	4
322	S	P	S	G	G	G	G	L	K	4
330	K	K	P	A	R	H	C	Q	G	4
333	A	R	H	C	Q	G	Q	K	H	4
361	Y	V	E	N	G	R	P	A	D	4
368	A	D	L	A	G	S	G	Y	C	4
384	E	S	L	E	E	G	L	G	G	4
393	K	Q	K	D	K	E	R	K	A	4
5	T	T	K	T	F	P	L	R	A	3
14	L	H	I	V	V	E	S	I	R	3
20	S	I	R	D	H	S	G	Q	K	3
23	D	H	S	G	Q	K	M	K	Q	3
24	H	S	G	Q	K	M	K	Q	D	3
32	D	K	K	V	D	L	L	V	P	3
50	G	A	K	D	F	G	H	V	Q	3
72	E	H	W	T	V	Y	Q	D	E	3
75	T	V	Y	Q	D	E	K	Q	R	3
77	Y	Q	D	E	K	Q	R	K	D	3
78	Q	D	E	K	Q	R	K	D	K	3
83	R	K	D	K	V	L	L	G	R	3
85	D	K	V	L	L	G	R	K	A	3
89	L	G	R	K	A	V	V	V	S	3
101	I	N	I	S	G	S	F	C	R	3
111	K	L	K	Y	L	A	F	L	H	3
112	L	K	Y	L	A	F	L	H	K	3
117	F	L	H	K	R	M	N	T	N	3
119	H	K	R	M	N	T	N	P	S	3
120	K	R	M	N	T	N	P	S	R	3
121	R	M	N	T	N	P	S	R	R	3
124	T	N	P	S	R	R	P	Y	H	3
128	R	R	P	Y	H	F	Q	V	P	3
144	E	K	A	D	G	G	S	C	C	3
145	K	A	D	G	G	S	C	C	P	3
162	K	K	V	C	L	S	G	A	P	3
174	G	W	K	Y	Q	A	V	T	A	3
175	W	K	Y	Q	A	V	T	A	T	3
178	Q	A	V	T	A	T	L	E	E	3
181	T	A	T	L	E	E	K	R	K	3
183	T	L	E	E	K	R	K	E	K	3
190	E	K	A	E	I	H	Y	R	K	3
191	K	A	E	I	H	Y	R	K	N	3
198	K	N	K	Q	L	M	R	L	Q	3
202	L	M	R	L	Q	K	Q	A	E	3
211	K	N	M	K	K	K	I	D	K	3
213	M	K	K	K	I	D	K	Y	T	3
216	K	I	D	K	Y	T	E	S	P	3
229	P	R	G	L	G	F	I	F	K	3
239	I	A	P	L	A	A	T	R	A	3
246	R	A	T	R	I	G	H	P	G	3
247	A	T	R	I	G	H	P	G	G	3
251	G	H	P	G	G	R	T	P	R	3
252	H	P	G	G	R	T	P	R	A	3
270	L	S	A	R	A	P	V	P	A	3
275	P	V	P	A	A	S	P	A	A	3
280	S	P	A	A	W	L	P	L	R	3
289	T	P	W	T	R	P	S	S	C	3
291	W	T	R	P	S	S	C	P	T	3
304	Y	D	S	L	S	P	Y	G	P	3
307	L	S	P	Y	G	P	R	N	P	3
323	P	S	G	G	G	G	L	K	K	3
325	G	G	G	G	L	K	K	P	A	3
326	G	G	G	L	K	K	P	A	R	3
340	K	H	N	V	L	A	R	G	K	3
341	H	N	V	L	A	R	G	K	P	3
347	G	K	P	Q	R	K	P	K	S	3
350	Q	R	K	P	K	S	E	N	N	3
354	K	S	E	N	N	S	W	Y	V	3
356	E	N	N	S	W	Y	V	E	N	3
357	N	N	S	W	Y	V	E	N	G	3
373	S	G	Y	C	G	A	L	W	K	3
374	G	Y	C	G	A	L	W	K	A	3
377	G	A	L	W	K	A	I	E	S	3
389	G	L	G	G	K	Q	K	D	K	3
4	H	T	T	K	T	F	P	L	R	2
10	P	L	R	A	L	H	I	V	V	2
17	V	V	E	S	I	R	D	H	S	2
21	I	R	D	H	S	G	Q	K	M	2
22	R	D	H	S	G	Q	K	M	K	2
31	Q	D	K	K	V	D	L	L	V	2
43	V	T	G	I	I	T	Q	G	A	2
54	F	G	H	V	Q	F	V	G	S	2
60	V	G	S	Y	K	L	A	Y	S	2
62	S	Y	K	L	A	Y	S	N	D	2
63	Y	K	L	A	Y	S	N	D	G	2
67	Y	S	N	D	G	E	H	W	T	2
70	D	G	E	H	W	T	V	Y	Q	2
84	K	D	K	V	L	L	G	R	K	2
90	G	R	K	A	V	V	V	S	C	2
114	Y	L	A	F	L	H	K	R	M	2
122	M	N	T	N	P	S	R	R	P	2
126	P	S	R	R	P	Y	H	F	Q	2
136	P	S	R	I	F	W	R	Q	E	2
148	G	G	S	C	C	P	Q	G	H	2
152	C	P	Q	G	H	A	S	E	A	2
155	G	H	A	S	E	A	Y	K	K	2
163	K	V	C	L	S	G	A	P	H	2
164	V	C	L	S	G	A	P	H	E	2
168	G	A	P	H	E	V	G	W	K	2
170	P	H	E	V	G	W	K	Y	Q	2
177	Y	Q	A	V	T	A	T	L	E	2
180	V	T	A	T	L	E	E	K	R	2
187	K	R	K	E	K	A	E	I	H	2
195	H	Y	R	K	N	K	Q	L	M	2
196	Y	R	K	N	K	Q	L	M	R	2
204	R	L	Q	K	Q	A	E	K	N	2
205	L	Q	K	Q	A	E	K	N	M	2
207	K	Q	A	E	K	N	M	K	K	2
214	K	K	K	I	D	K	Y	T	E	2
219	K	Y	T	E	S	P	G	G	G	2
223	S	P	G	G	G	S	P	R	G	2
225	G	G	G	S	P	R	G	L	G	2
232	L	G	F	I	F	K	T	I	A	2
241	P	L	A	A	T	R	A	T	R	2
254	G	G	R	T	P	R	A	G	S	2
256	R	T	P	R	A	G	S	S	A	2
257	T	P	R	A	G	S	S	A	H	2
259	R	A	G	S	S	A	H	R	P	2
261	G	S	S	A	H	R	P	P	A	2
268	P	A	L	S	A	R	A	P	V	2
273	R	A	P	V	P	A	A	S	P	2
281	P	A	A	W	L	P	L	R	T	2
288	R	T	P	W	T	R	P	S	S	2
292	T	R	P	S	S	C	P	T	S	2
293	R	P	S	S	C	P	T	S	S	2
294	P	S	S	C	P	T	S	S	S	2
298	P	T	S	S	S	T	Y	D	S	2
301	S	S	T	Y	D	S	L	S	P	2
311	G	P	R	N	P	L	P	N	P	2
313	R	N	P	L	P	N	P	R	H	2
317	P	N	P	R	H	S	P	S	G	2
318	N	P	R	H	S	P	S	G	G	2
327	G	G	L	K	K	P	A	R	H	2
328	G	L	K	K	P	A	R	H	C	2
331	K	P	A	R	H	C	Q	G	Q	2
334	R	H	C	Q	G	Q	K	H	N	2
335	H	C	Q	G	Q	K	H	N	V	2
337	Q	G	Q	K	H	N	V	L	A	2
339	Q	K	H	N	V	L	A	R	G	2
343	V	L	A	R	G	K	P	Q	R	2
344	L	A	R	G	K	P	Q	R	K	2
351	R	K	P	K	S	E	N	N	S	2
358	N	S	W	Y	V	E	N	G	R	2
360	W	Y	V	E	N	G	R	P	A	2
365	G	R	P	A	D	L	A	G	S	2
366	R	P	A	D	L	A	G	S	G	2
379	L	W	K	A	I	E	S	L	E	2
385	S	L	E	E	G	L	G	G	K	2
391	G	G	K	Q	K	D	K	E	R	2
395	K	D	K	E	R	K	A	E	N	2
396	D	K	E	R	K	A	E	N	G	2
398	E	R	K	A	E	N	G	P	H	2
15	H	I	V	V	E	S	I	R	D	1
25	S	G	Q	K	M	K	Q	D	K	1
26	G	Q	K	M	K	Q	D	K	K	1
40	P	T	K	V	T	G	I	I	T	1
47	I	T	Q	G	A	K	D	F	G	1
49	Q	G	A	K	D	F	G	H	V	1
53	D	F	G	H	V	Q	F	V	G	1
61	G	S	Y	K	L	A	Y	S	N	1
64	K	L	A	Y	S	N	D	G	E	1
65	L	A	Y	S	N	D	G	E	H	1
74	W	T	V	Y	Q	D	E	K	Q	1
76	V	Y	Q	D	E	K	Q	R	K	1
91	R	K	A	V	V	V	S	C	E	1
92	K	A	V	V	V	S	C	E	G	1
103	I	S	G	S	F	C	R	N	K	1
108	C	R	N	K	L	K	Y	L	A	1
118	L	H	K	R	M	N	T	N	P	1
129	R	P	Y	H	F	Q	V	P	S	1
130	P	Y	H	F	Q	V	P	S	R	1
141	W	R	Q	E	K	A	D	G	G	1
147	D	G	G	S	C	C	P	Q	G	1
151	C	C	P	Q	G	H	A	S	E	1
161	Y	K	K	V	C	L	S	G	A	1
166	L	S	G	A	P	H	E	V	G	1
173	V	G	W	K	Y	Q	A	V	T	1
203	M	R	L	Q	K	Q	A	E	K	1
206	Q	K	Q	A	E	K	N	M	K	1
218	D	K	Y	T	E	S	P	G	G	1
258	P	R	A	G	S	S	A	H	R	1
266	R	P	P	A	L	S	A	R	A	1
286	P	L	R	T	P	W	T	R	P	1
290	P	W	T	R	P	S	S	C	P	1
303	T	Y	D	S	L	S	P	Y	G	1
305	D	S	L	S	P	Y	G	P	R	1
332	P	A	R	H	C	Q	G	Q	K	1
359	S	W	Y	V	E	N	G	R	P	1
369	D	L	A	G	S	G	Y	C	G	1
376	C	G	A	L	W	K	A	I	E	1
380	W	K	A	I	E	S	L	E	E	1
390	L	G	G	K	Q	K	D	K	E	1

TABLE XXXIV
151P3D4 v.1: HLA Peptide
Scoring Results B*5101 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
66	D	P	T	A	F	G	S	G	I	25	Portion
152	V	A	L	D	L	Q	G	V	V	25	of SEQ
121	D	A	S	L	V	I	T	D	L	24	ID NO:
134	Y	G	R	Y	K	C	E	V	I	22	3; each
143	E	G	L	E	D	D	T	V	V	22	start
224	E	P	C	G	G	Q	N	T	V	22	position
4	L	L	L	L	V	L	I	S	I	18	is
179	Q	A	C	L	D	Q	D	A	V	18	specified,
33	Q	A	E	N	G	P	H	L	L	17	the length
106	G	G	Y	Q	G	R	V	F	L	17	of
164	F	P	R	L	G	R	Y	N	L	17	peptide is
227	G	G	Q	N	T	V	P	G	V	17	9 amino
309	L	A	D	G	S	V	R	Y	P	17	acids, the
22	Y	T	L	D	H	D	R	A	I	16	end
24	L	D	H	D	R	A	I	H	I	16	position
68	T	A	F	G	S	G	I	H	K	16	for each
161	F	P	Y	F	P	R	L	G	R	16	peptide is
180	A	C	L	D	Q	D	A	V	I	16	the start
196	D	A	W	R	G	G	L	D	W	16	position
207	A	G	W	L	S	D	G	S	V	16	plus eight
217	Y	P	I	T	K	P	R	E	P	16
16	D	H	L	S	D	N	Y	T	L	15
88	Y	L	K	E	V	D	V	F	V	15
118	S	D	S	D	A	S	L	V	I	15
282	D	G	A	Q	I	A	K	V	G	15
305	D	A	G	W	L	A	D	G	S	15
306	A	G	W	L	A	D	G	S	V	15
316	Y	P	I	S	R	P	R	R	R	15
326	S	P	T	E	A	A	V	R	F	15
2	K	S	L	L	L	L	V	L	I	14
59	L	P	C	K	F	Y	R	D	P	14
84	L	T	S	D	Y	L	K	E	V	14
86	S	D	Y	L	K	E	V	D	V	14
116	G	G	S	D	S	D	A	S	L	14
148	D	T	V	V	V	A	L	D	L	14
185	D	A	V	I	A	S	F	D	Q	14
242	D	K	D	K	S	R	Y	D	V	14
262	Y	Y	L	I	H	P	T	K	L	14
284	A	Q	I	A	K	V	G	Q	I	14
293	F	A	A	W	K	I	L	G	Y	14
337	F	P	D	K	K	H	K	L	Y	14
339	D	K	K	H	K	L	Y	G	V	14
41	L	V	E	A	E	Q	A	K	V	13
69	A	F	G	S	G	I	H	K	I	13
98	M	G	Y	H	K	K	T	Y	G	13
133	D	Y	G	R	Y	K	C	E	V	13
137	Y	K	C	E	V	I	E	G	L	13
144	G	L	E	D	D	T	V	V	V	13
188	I	A	S	F	D	Q	L	Y	D	13
268	T	K	L	T	Y	D	E	A	V	13
281	N	D	G	A	Q	I	A	K	V	13
286	I	A	K	V	G	Q	I	F	A	13
290	G	Q	I	F	A	A	W	K	I	13
294	A	A	W	K	I	L	G	Y	D	13
299	L	G	Y	D	R	C	D	A	G	13
1	M	K	S	L	L	L	L	V	L	12
37	G	P	H	L	L	V	E	A	E	12
71	G	S	G	I	H	K	I	R	I	12
87	D	Y	L	K	E	V	D	V	F	12
104	T	Y	G	G	Y	Q	G	R	V	12
105	Y	G	G	Y	Q	G	R	V	F	12
142	I	E	G	L	E	D	D	T	V	12
146	E	D	D	T	V	V	V	A	L	12
211	S	D	G	S	V	Q	Y	P	I	12
221	K	P	R	E	P	C	G	G	Q	12
232	V	P	G	V	R	N	Y	G	F	12
278	A	C	L	N	D	G	A	Q	I	12
310	A	D	G	S	V	R	Y	P	I	12
327	P	T	E	A	A	V	R	F	V	12
329	E	A	A	V	R	F	V	G	F	12
330	A	A	V	R	F	V	G	F	P	12
32	I	Q	A	E	N	G	P	H	L	11
43	E	A	E	Q	A	K	V	F	S	11
46	Q	A	K	V	F	S	H	R	G	11
51	S	H	R	G	G	N	V	T	L	11
159	V	V	F	P	Y	F	P	R	L	11
176	E	A	Q	Q	A	C	L	D	Q	11
206	N	A	G	W	L	S	D	G	S	11
238	Y	G	F	W	D	K	D	K	S	11
257	F	N	G	R	F	Y	Y	L	I	11
266	H	P	T	K	L	T	Y	D	E	11
272	Y	D	E	A	V	Q	A	C	L	11
274	E	A	V	Q	A	C	L	N	D	11
283	G	A	Q	I	A	K	V	G	Q	11
336	G	F	P	D	K	K	H	K	L	11
10	I	S	I	C	W	A	D	H	L	10
14	W	A	D	H	L	S	D	N	Y	10
28	R	A	I	H	I	Q	A	E	N	10
34	A	E	N	G	P	H	L	L	V	10
36	N	G	P	H	L	L	V	E	A	10
76	K	I	R	I	K	W	T	K	L	10
123	S	L	V	I	T	D	L	T	L	10
145	L	E	D	D	T	V	V	V	A	10
151	V	V	A	L	D	L	Q	G	V	10
167	L	G	R	Y	N	L	N	F	H	10
200	G	G	L	D	W	C	N	A	G	10
202	L	D	W	C	N	A	G	W	L	10
212	D	G	S	V	Q	Y	P	I	T	10
277	Q	A	C	L	N	D	G	A	Q	10
311	D	G	S	V	R	Y	P	I	S	10
320	R	P	R	R	R	C	S	P	T	10
335	V	G	F	P	D	K	K	H	K	10
345	Y	G	V	Y	C	F	R	A	Y	10
20	D	N	Y	T	L	D	H	D	R	9
49	V	F	S	H	R	G	G	N	V	9
53	R	G	G	N	V	T	L	P	C	9
70	F	G	S	G	I	H	K	I	R	9
72	S	G	I	H	K	I	R	I	K	9
117	G	S	D	S	D	A	S	L	V	9
155	D	L	Q	G	V	V	F	P	Y	9
186	A	V	I	A	S	F	D	Q	L	9
194	L	Y	D	A	W	R	G	G	L	9
256	N	F	N	G	R	F	Y	Y	L	9
258	N	G	R	F	Y	Y	L	I	H	9
270	L	T	Y	D	E	A	V	Q	A	9
291	Q	I	F	A	A	W	K	I	L	9
301	Y	D	R	C	D	A	G	W	L	9
324	R	C	S	P	T	E	A	A	V	9
42	V	E	A	E	Q	A	K	V	F	8
54	G	G	N	V	T	L	P	C	K	8
108	Y	Q	G	R	V	F	L	K	G	8
109	Q	G	R	V	F	L	K	G	G	8
119	D	S	D	A	S	L	V	I	T	8
147	D	D	T	V	V	V	A	L	D	8
174	F	H	E	A	Q	Q	A	C	L	8
183	D	Q	D	A	V	I	A	S	F	8
192	D	Q	L	Y	D	A	W	R	G	8
246	S	R	Y	D	V	F	C	F	T	8
289	V	G	Q	I	F	A	A	W	K	8
79	I	K	W	T	K	L	T	S	D	7
81	W	T	K	L	T	S	D	Y	L	7
89	L	K	E	V	D	V	F	V	S	7
129	L	T	L	E	D	Y	G	R	Y	7
154	L	D	L	Q	G	V	V	F	P	7
157	Q	G	V	V	F	P	Y	F	P	7
226	C	G	G	Q	N	T	V	P	G	7
228	G	Q	N	T	V	P	G	V	R	7
236	R	N	Y	G	F	W	D	K	D	7
261	F	Y	Y	L	I	H	P	T	K	7
265	I	H	P	T	K	L	T	Y	D	7
328	T	E	A	A	V	R	F	V	G	7
343	K	L	Y	G	V	Y	C	F	R	7
7	L	V	L	I	S	I	C	W	A	6
62	K	F	Y	R	D	P	T	A	F	6
93	D	V	F	V	S	M	G	Y	H	6
96	V	S	M	G	Y	H	K	K	T	6
115	K	G	G	S	D	S	D	A	S	6
132	E	D	Y	G	R	Y	K	C	E	6
135	G	R	Y	K	C	E	V	I	E	6
168	G	R	Y	N	L	N	F	H	E	6
182	L	D	Q	D	A	V	I	A	S	6
193	Q	L	Y	D	A	W	R	G	G	6
199	R	G	G	L	D	W	C	N	A	6
210	L	S	D	G	S	V	Q	Y	P	6
215	V	Q	Y	P	I	T	K	P	R	6
225	P	C	G	G	Q	N	T	V	P	6
231	T	V	P	G	V	R	N	Y	G	6
233	P	G	V	R	N	Y	G	F	W	6
244	D	K	S	R	Y	D	V	F	C	6
264	L	I	H	P	T	K	L	T	Y	6
307	G	W	L	A	D	G	S	V	R	6
314	V	R	Y	P	I	S	R	P	R	6
325	C	S	P	T	E	A	A	V	R	6
3	S	L	L	L	L	V	L	I	S	5
5	L	L	L	V	L	I	S	I	C	5
12	I	C	W	A	D	H	L	S	D	5
25	D	H	D	R	A	I	H	I	Q	5
27	D	R	A	I	H	I	Q	A	E	5
35	E	N	G	P	H	L	L	V	E	5
45	E	Q	A	K	V	F	S	H	R	5
50	F	S	H	R	G	G	N	V	T	5
58	T	L	P	C	K	F	Y	R	D	5
82	T	K	L	T	S	D	Y	L	K	5
90	K	E	V	D	V	F	V	S	M	5
103	K	T	Y	G	G	Y	Q	G	R	5
120	S	D	A	S	L	V	I	T	D	5
124	L	V	I	T	D	L	T	L	E	5
156	L	Q	G	V	V	F	P	Y	F	5
208	G	W	L	S	D	G	S	V	Q	5
213	G	S	V	Q	Y	P	I	T	K	5
249	D	V	F	C	F	T	S	N	F	5
251	F	C	F	T	S	N	F	N	G	5
259	G	R	F	Y	Y	L	I	H	P	5
260	R	F	Y	Y	L	I	H	P	T	5
271	T	Y	D	E	A	V	Q	A	C	5
273	D	E	A	V	Q	A	C	L	N	5
297	K	I	L	G	Y	D	R	C	D	5
302	D	R	C	D	A	G	W	L	A	5
18	L	S	D	N	Y	T	L	D	H	4
38	P	H	L	L	V	E	A	E	Q	4
40	L	L	V	E	A	E	Q	A	K	4
44	A	E	Q	A	K	V	F	S	H	4
52	H	R	G	G	N	V	T	L	P	4
55	G	N	V	T	L	P	C	K	F	4
64	Y	R	D	P	T	A	F	G	S	4
73	G	I	H	K	I	R	I	K	W	4
74	I	H	K	I	R	I	K	W	T	4
77	I	R	I	K	W	T	K	L	T	4
78	R	I	K	W	T	K	L	T	S	4
85	T	S	D	Y	L	K	E	V	D	4
100	Y	H	K	K	T	Y	G	G	Y	4
112	V	F	L	K	G	G	S	D	S	4
114	L	K	G	G	S	D	S	D	A	4
126	I	T	D	L	T	L	E	D	Y	4
127	T	D	L	T	L	E	D	Y	G	4
128	D	L	T	L	E	D	Y	G	R	4
130	T	L	E	D	Y	G	R	Y	K	4
131	L	E	D	Y	G	R	Y	K	C	4
153	A	L	D	L	Q	G	V	V	F	4
160	V	F	P	Y	F	P	R	L	G	4
163	Y	F	P	R	L	G	R	Y	N	4
165	P	R	L	G	R	Y	N	L	N	4
170	Y	N	L	N	F	H	E	A	Q	4
172	L	N	F	H	E	A	Q	Q	A	4
203	D	W	C	N	A	G	W	L	S	4
214	S	V	Q	Y	P	I	T	K	P	4
230	N	T	V	P	G	V	R	N	Y	4
239	G	F	W	D	K	D	K	S	R	4
248	Y	D	V	F	C	F	T	S	N	4
280	L	N	D	G	A	Q	I	A	K	4
292	I	F	A	A	W	K	I	L	G	4
333	R	F	V	G	F	P	D	K	K	4
334	F	V	G	F	P	D	K	K	H	4
340	K	K	H	K	L	Y	G	V	Y	4
342	H	K	L	Y	G	V	Y	C	F	4
344	L	Y	G	V	Y	C	F	R	A	4
346	G	V	Y	C	F	R	A	Y	N	4
6	L	L	V	L	I	S	I	C	W	3
19	S	D	N	Y	T	L	D	H	D	3
30	I	H	I	Q	A	E	N	G	P	3
39	H	L	L	V	E	A	E	Q	A	3
57	V	T	L	P	C	K	F	Y	R	3
61	C	K	F	Y	R	D	P	T	A	3
65	R	D	P	T	A	F	G	S	G	3
83	K	L	T	S	D	Y	L	K	E	3
92	V	D	V	F	V	S	M	G	Y	3
94	V	F	V	S	M	G	Y	H	K	3
95	F	V	S	M	G	Y	H	K	K	3
97	S	M	G	Y	H	K	K	T	Y	3
107	G	Y	Q	G	R	V	F	L	K	3
125	V	I	T	D	L	T	L	E	D	3
136	R	Y	K	C	E	V	I	E	G	3
140	E	V	I	E	G	L	E	D	D	3
150	V	V	V	A	L	D	L	Q	G	3
162	P	Y	F	P	R	L	G	R	Y	3
166	R	L	G	R	Y	N	L	N	F	3
173	N	F	H	E	A	Q	Q	A	C	3
189	A	S	F	D	Q	L	Y	D	A	3
216	Q	Y	P	I	T	K	P	R	E	3
220	T	K	P	R	E	P	C	G	G	3
240	F	W	D	K	D	K	S	R	Y	3
241	W	D	K	D	K	S	R	Y	D	3
243	K	D	K	S	R	Y	D	V	F	3
250	V	F	C	F	T	S	N	F	N	3
253	F	T	S	N	F	N	G	R	F	3
263	Y	L	I	H	P	T	K	L	T	3
269	K	L	T	Y	D	E	A	V	Q	3
275	A	V	Q	A	C	L	N	D	G	3
285	Q	I	A	K	V	G	Q	I	F	3
308	W	L	A	D	G	S	V	R	Y	3
312	G	S	V	R	Y	P	I	S	R	3
315	R	Y	P	I	S	R	P	R	R	3
318	I	S	R	P	R	R	R	C	S	3
322	R	R	R	C	S	P	T	E	A	3
332	V	R	F	V	G	F	P	D	K	3
9	L	I	S	I	C	W	A	D	H	2
13	C	W	A	D	H	L	S	D	N	2
15	A	D	H	L	S	D	N	Y	T	2
17	H	L	S	D	N	Y	T	L	D	2
21	N	Y	T	L	D	H	D	R	A	2
26	H	D	R	A	I	H	I	Q	A	2
31	H	I	Q	A	E	N	G	P	H	2
47	A	K	V	F	S	H	R	G	G	2
56	N	V	T	L	P	C	K	F	Y	2
63	F	Y	R	D	P	T	A	F	G	2
75	H	K	I	R	I	K	W	T	K	2
91	E	V	D	V	F	V	S	M	G	2
99	G	Y	H	K	K	T	Y	G	G	2
101	H	K	K	T	Y	G	G	Y	Q	2
111	R	V	F	L	K	G	G	S	D	2
113	F	L	K	G	G	S	D	S	D	2
122	A	S	L	V	I	T	D	L	T	2
141	V	I	E	G	L	E	D	D	T	2
149	T	V	V	V	A	L	D	L	Q	2
177	A	Q	Q	A	C	L	D	Q	D	2
181	C	L	D	Q	D	A	V	I	A	2
191	F	D	Q	L	Y	D	A	W	R	2
195	Y	D	A	W	R	G	G	L	D	2
197	A	W	R	G	G	L	D	W	C	2
204	W	C	N	A	G	W	L	S	D	2
205	C	N	A	G	W	L	S	D	G	2
209	W	L	S	D	G	S	V	Q	Y	2
219	I	T	K	P	R	E	P	C	G	2
229	Q	N	T	V	P	G	V	R	N	2
235	V	R	N	Y	G	F	W	D	K	2
237	N	Y	G	F	W	D	K	D	K	2
245	K	S	R	Y	D	V	F	C	F	2
247	R	Y	D	V	F	C	F	T	S	2
252	C	F	T	S	N	F	N	G	R	2
254	T	S	N	F	N	G	R	F	Y	2
276	V	Q	A	C	L	N	D	G	A	2
279	C	L	N	D	G	A	Q	I	A	2
287	A	K	V	G	Q	I	F	A	A	2
298	I	L	G	Y	D	R	C	D	A	2
303	R	C	D	A	G	W	L	A	D	2
304	C	D	A	G	W	L	A	D	G	2
313	S	V	R	Y	P	I	S	R	P	2
317	P	I	S	R	P	R	R	R	C	2	Portion
321	P	R	R	R	C	S	P	T	E	2	of SEQ
331	A	V	R	F	V	G	F	P	D	2	ID NO:
338	P	D	K	K	H	K	L	Y	G	2	3; each
341	K	H	K	L	Y	G	V	Y	C	2	start
8	V	L	I	S	I	C	W	A	D	1	position
23	T	L	D	H	D	R	A	I	H	1	is
29	A	I	H	I	Q	A	E	N	G	1	specified,
48	K	V	F	S	H	R	G	G	N	1	the length
60	P	C	K	F	Y	R	D	P	T	1	of
80	K	W	T	K	L	T	S	D	Y	1	peptide is
139	C	E	V	I	E	G	L	E	D	1	9 amino
169	R	Y	N	L	N	F	H	E	A	1	acids, the
171	N	L	N	F	H	E	A	Q	Q	1	end
175	H	E	A	Q	Q	A	C	L	D	1	position
184	Q	D	A	V	I	A	S	F	D	1	for each
187	V	I	A	S	F	D	Q	L	Y	1	peptide is
198	W	R	G	G	L	D	W	C	N	1	the start
201	G	L	D	W	C	N	A	G	W	1	position
218	P	I	T	K	P	R	E	P	C	1	plus eight
223	R	E	P	C	G	G	Q	N	T	1
234	G	V	R	N	Y	G	F	W	D	1
255	S	N	F	N	G	R	F	Y	Y	1
267	P	T	K	L	T	Y	D	E	A	1
288	K	V	G	Q	I	F	A	A	W	1
296	W	K	I	L	G	Y	D	R	C	1
319	S	R	P	R	R	R	C	S	P	1
151P3D4 v.2: HLA Peptide
Scoring Results B*5101 9-mers SYFPEITHI
											SEQ. ID
Pos	1	2	3	4	5	6	7	8	9	score	NO.
242	L	A	A	T	R	A	T	R	I	26	Portion of
39	V	P	T	K	V	T	G	I	I	24	SEQ ID
156	H	A	S	E	A	Y	K	K	V	23	NO: 5;
9	F	P	L	R	A	L	H	I	V	22	each start
308	S	P	Y	G	P	R	N	P	L	22	position
268	P	A	L	S	A	R	A	P	V	20	is
38	L	V	P	T	K	V	T	G	I	18	specified,
159	E	A	Y	K	K	V	C	L	S	18	the length
285	L	P	L	R	T	P	W	T	R	18	of peptide
35	V	D	L	L	V	P	T	K	V	17	is 9
49	Q	G	A	K	D	F	G	H	V	17	amino
131	Y	H	F	Q	V	P	S	R	I	17	acids, the
277	P	A	A	S	P	A	A	W	L	17	end
400	K	A	E	N	G	P	H	L	L	17	position
65	L	A	Y	S	N	D	G	E	H	16	for each
88	L	L	G	R	K	A	V	V	V	16	peptide is
169	A	P	H	E	V	G	W	K	Y	16	the start
224	P	G	G	G	S	P	R	G	L	16	position
239	I	A	P	L	A	A	T	R	A	16	plus eight
314	N	P	L	P	N	P	R	H	S	16
344	L	A	R	G	K	P	Q	R	K	16
8	T	F	P	L	R	A	L	H	I	15
12	R	A	L	H	I	V	V	E	S	15
87	V	L	L	G	R	K	A	V	V	15
89	L	G	R	K	A	V	V	V	S	15
104	S	G	S	F	C	R	N	K	L	15
129	R	P	Y	H	F	Q	V	P	S	15
194	I	H	Y	R	K	N	K	Q	L	15
282	A	A	W	L	P	L	R	T	P	15
377	G	A	L	W	K	A	I	E	S	15
13	A	L	H	I	V	V	E	S	I	14
50	G	A	K	D	F	G	H	V	Q	14
79	D	E	K	Q	R	K	D	K	V	14
115	L	A	F	L	H	K	R	M	N	14
208	Q	A	E	K	N	M	K	K	K	14
209	A	E	K	N	M	K	K	K	I	14
231	G	L	G	F	I	F	K	T	I	14
240	A	P	L	A	A	T	R	A	T	14
276	V	P	A	A	S	P	A	A	W	14
289	T	P	W	T	R	P	S	S	C	14
371	A	G	S	G	Y	C	G	A	L	14
375	Y	C	G	A	L	W	K	A	I	14
381	K	A	I	E	S	L	E	E	G	14
10	P	L	R	A	L	H	I	V	V	13
125	N	P	S	R	R	P	Y	H	F	13
135	V	P	S	R	I	F	W	R	Q	13
168	G	A	P	H	E	V	G	W	K	13
173	V	G	W	K	Y	Q	A	V	T	13
181	T	A	T	L	E	E	K	R	K	13
191	K	A	E	I	H	Y	R	K	N	13
259	R	A	G	S	S	A	H	R	P	13
266	R	P	P	A	L	S	A	R	A	13
267	P	P	A	L	S	A	R	A	P	13
271	S	A	R	A	P	V	P	A	A	13
281	P	A	A	W	L	P	L	R	T	13
318	N	P	R	H	S	P	S	G	G	13
348	K	P	Q	R	K	P	K	S	E	13
27	Q	K	M	K	Q	D	K	K	V	12
31	Q	D	K	K	V	D	L	L	V	12
52	K	D	F	G	H	V	Q	F	V	12
92	K	A	V	V	V	S	C	E	G	12
95	V	V	S	C	E	G	I	N	I	12
110	N	K	L	K	Y	L	A	F	L	12
152	C	P	Q	G	H	A	S	E	A	12
178	Q	A	V	T	A	T	L	E	E	12
223	S	P	G	G	G	S	P	R	G	12
227	G	S	P	R	G	L	G	F	I	12
230	R	G	L	G	F	I	F	K	T	12
252	H	P	G	G	R	T	P	R	A	12
257	T	P	R	A	G	S	S	A	H	12
273	R	A	P	V	P	A	A	S	P	12
280	S	P	A	A	W	L	P	L	R	12
293	R	P	S	S	C	P	T	S	S	12
297	C	P	T	S	S	S	T	Y	D	12
316	L	P	N	P	R	H	S	P	S	12
327	G	G	L	K	K	P	A	R	H	12
352	K	P	K	S	E	N	N	S	W	12
366	R	P	A	D	L	A	G	S	G	12
370	L	A	G	S	G	Y	C	G	A	12
373	S	G	Y	C	G	A	L	W	K	12
68	S	N	D	G	E	H	W	T	V	11
70	D	G	E	H	W	T	V	Y	Q	11
80	E	K	Q	R	K	D	K	V	L	11
86	K	V	L	L	G	R	K	A	V	11
93	A	V	V	V	S	C	E	G	I	11
145	K	A	D	G	G	S	C	C	P	11
176	K	Y	Q	A	V	T	A	T	L	11
186	E	K	R	K	E	K	A	E	I	11
228	S	P	R	G	L	G	F	I	F	11
234	F	I	F	K	T	I	A	P	L	11
243	A	A	T	R	A	T	R	I	G	11
250	I	G	H	P	G	G	R	T	P	11
263	S	A	H	R	P	P	A	L	S	11
274	A	P	V	P	A	A	S	P	A	11
278	A	A	S	P	A	A	W	L	P	11
310	Y	G	P	R	N	P	L	P	N	11
311	G	P	R	N	P	L	P	N	P	11
322	S	P	S	G	G	G	G	L	K	11
324	S	G	G	G	G	L	K	K	P	11
336	C	Q	G	Q	K	H	N	V	L	11
388	E	G	L	G	G	K	Q	K	D	11
390	L	G	G	K	Q	K	D	K	E	11
29	M	K	Q	D	K	K	V	D	L	10
30	K	Q	D	K	K	V	D	L	L	10
36	D	L	L	V	P	T	K	V	T	10
57	V	Q	F	V	G	S	Y	K	L	10
107	F	C	R	N	K	L	K	Y	L	10
147	D	G	G	S	C	C	P	Q	G	10
165	C	L	S	G	A	P	H	E	V	10
232	L	G	F	I	F	K	T	I	A	10
246	R	A	T	R	I	G	H	P	G	10
331	K	P	A	R	H	C	Q	G	Q	10
332	P	A	R	H	C	Q	G	Q	K	10
367	P	A	D	L	A	G	S	G	Y	10
6	T	K	T	F	P	L	R	A	L	9
32	D	K	K	V	D	L	L	V	P	9
53	D	F	G	H	V	Q	F	V	G	9
54	F	G	H	V	Q	F	V	G	S	9
60	V	G	S	Y	K	L	A	Y	S	9
112	L	K	Y	L	A	F	L	H	K	9
127	S	R	R	P	Y	H	F	Q	V	9
172	E	V	G	W	K	Y	Q	A	V	9
197	R	K	N	K	Q	L	M	R	L	9
218	D	K	Y	T	E	S	P	G	G	9
253	P	G	G	R	T	P	R	A	G	9
279	A	S	P	A	A	W	L	P	L	9
335	H	C	Q	G	Q	K	H	N	V	9
337	Q	G	Q	K	H	N	V	L	A	9
362	V	E	N	G	R	P	A	D	L	9
378	A	L	W	K	A	I	E	S	L	9
399	R	K	A	E	N	G	P	H	L	9
3	E	H	T	T	K	T	F	P	L	8
25	S	G	Q	K	M	K	Q	D	K	8
44	T	G	I	I	T	Q	G	A	K	8
77	Y	Q	D	E	K	Q	R	K	D	8
81	K	Q	R	K	D	K	V	L	L	8
154	Q	G	H	A	S	E	A	Y	K	8
158	S	E	A	Y	K	K	V	C	L	8
299	T	S	S	S	T	Y	D	S	L	8
325	G	G	G	G	L	K	K	P	A	8
354	K	S	E	N	N	S	W	Y	V	8
364	N	G	R	P	A	D	L	A	G	8
391	G	G	K	Q	K	D	K	E	R	8
11	L	R	A	L	H	I	V	V	E	7
16	I	V	V	E	S	I	R	D	H	7
23	D	H	S	G	Q	K	M	K	Q	7
63	Y	K	L	A	Y	S	N	D	G	7
69	N	D	G	E	H	W	T	V	Y	7
85	D	K	V	L	L	G	R	K	A	7
148	G	G	S	C	C	P	Q	G	H	7
167	S	G	A	P	H	E	V	G	W	7
175	W	K	Y	Q	A	V	T	A	T	7
182	A	T	L	E	E	K	R	K	E	7
226	G	G	S	P	R	G	L	G	F	7
254	G	G	R	T	P	R	A	G	S	7
260	A	G	S	S	A	H	R	P	P	7
262	S	S	A	H	R	P	P	A	L	7
302	S	T	Y	D	S	L	S	P	Y	7
321	H	S	P	S	G	G	G	G	L	7
326	G	G	G	L	K	K	P	A	R	7
346	R	G	K	P	Q	R	K	P	K	7
37	L	L	V	P	T	K	V	T	G	6
41	T	K	V	T	G	I	I	T	Q	6
61	G	S	Y	K	L	A	Y	S	N	6
75	T	V	Y	Q	D	E	K	Q	R	6
90	G	R	K	A	V	V	V	S	C	6
99	E	G	I	N	I	S	G	S	F	6
113	K	Y	L	A	F	L	H	K	R	6
157	A	S	E	A	Y	K	K	V	C	6
166	L	S	G	A	P	H	E	V	G	6
207	K	Q	A	E	K	N	M	K	K	6
212	N	M	K	K	K	I	D	K	Y	6
225	G	G	G	S	P	R	G	L	G	6
305	D	S	L	S	P	Y	G	P	R	6
359	S	W	Y	V	E	N	G	R	P	6
369	D	L	A	G	S	G	Y	C	G	6
376	C	G	A	L	W	K	A	I	E	6
382	A	I	E	S	L	E	E	G	L	6
396	D	K	E	R	K	A	E	N	G	6
1	M	L	E	H	T	T	K	T	F	5
2	L	E	H	T	T	K	T	F	P	5
5	T	T	K	T	F	P	L	R	A	5
21	I	R	D	H	S	G	Q	K	M	5
82	Q	R	K	D	K	V	L	L	G	5
83	R	K	D	K	V	L	L	G	R	5
96	V	S	C	E	G	I	N	I	S	5
102	N	I	S	G	S	F	C	R	N	5
117	F	L	H	K	R	M	N	T	N	5
118	L	H	K	R	M	N	T	N	P	5
128	R	R	P	Y	H	F	Q	V	P	5
164	V	C	L	S	G	A	P	H	E	5
177	Y	Q	A	V	T	A	T	L	E	5
183	T	L	E	E	K	R	K	E	K	5
184	L	E	E	K	R	K	E	K	A	5
200	K	Q	L	M	R	L	Q	K	Q	5
269	A	L	S	A	R	A	P	V	P	5
292	T	R	P	S	S	C	P	T	S	5
296	S	C	P	T	S	S	S	T	Y	5
307	L	S	P	Y	G	P	R	N	P	5
342	N	V	L	A	R	G	K	P	Q	5
358	N	S	W	Y	V	E	N	G	R	5
384	E	S	L	E	E	G	L	G	G	5
386	L	E	E	G	L	G	G	K	Q	5
393	K	Q	K	D	K	E	R	K	A	5
14	L	H	I	V	V	E	S	I	R	4
28	K	M	K	Q	D	K	K	V	D	4
34	K	V	D	L	L	V	P	T	K	4
46	I	I	T	Q	G	A	K	D	F	4
72	E	H	W	T	V	Y	Q	D	E	4
91	R	K	A	V	V	V	S	C	E	4
114	Y	L	A	F	L	H	K	R	M	4
139	I	F	W	R	Q	E	K	A	D	4
141	W	R	Q	E	K	A	D	G	G	4
160	A	Y	K	K	V	C	L	S	G	4
174	G	W	K	Y	Q	A	V	T	A	4
180	V	T	A	T	L	E	E	K	R	4
187	K	R	K	E	K	A	E	I	H	4
196	Y	R	K	N	K	Q	L	M	R	4
203	M	R	L	Q	K	Q	A	E	K	4
204	R	L	Q	K	Q	A	E	K	N	4
219	K	Y	T	E	S	P	G	G	G	4
235	I	F	K	T	I	A	P	L	A	4
238	T	I	A	P	L	A	A	T	R	4
241	P	L	A	A	T	R	A	T	R	4
245	T	R	A	T	R	I	G	H	P	4
270	L	S	A	R	A	P	V	P	A	4
304	Y	D	S	L	S	P	Y	G	P	4
323	P	S	G	G	G	G	L	K	K	4
328	G	L	K	K	P	A	R	H	C	4
339	Q	K	H	N	V	L	A	R	G	4
345	A	R	G	K	P	Q	R	K	P	4
351	R	K	P	K	S	E	N	N	S	4
355	S	E	N	N	S	W	Y	V	E	4
357	N	N	S	W	Y	V	E	N	G	4
374	G	Y	C	G	A	L	W	K	A	4
4	H	T	T	K	T	F	P	L	R	3
26	G	Q	K	M	K	Q	D	K	K	3
33	K	K	V	D	L	L	V	P	T	3
42	K	V	T	G	I	I	T	Q	G	3
45	G	I	I	T	Q	G	A	K	D	3
47	I	T	Q	G	A	K	D	F	G	3
48	T	Q	G	A	K	D	F	G	H	3
58	Q	F	V	G	S	Y	K	L	A	3
59	F	V	G	S	Y	K	L	A	Y	3
67	Y	S	N	D	G	E	H	W	T	3
71	G	E	H	W	T	V	Y	Q	D	3
76	V	Y	Q	D	E	K	Q	R	K	3
97	S	C	E	G	I	N	I	S	G	3
103	I	S	G	S	F	C	R	N	K	3
105	G	S	F	C	R	N	K	L	K	3
106	S	F	C	R	N	K	L	K	Y	3
116	A	F	L	H	K	R	M	N	T	3
121	R	M	N	T	N	P	S	R	R	3
122	M	N	T	N	P	S	R	R	P	3
123	N	T	N	P	S	R	R	P	Y	3
133	F	Q	V	P	S	R	I	F	W	3
138	R	I	F	W	R	Q	E	K	A	3
155	G	H	A	S	E	A	Y	K	K	3
161	Y	K	K	V	C	L	S	G	A	3
179	A	V	T	A	T	L	E	E	K	3
188	R	K	E	K	A	E	I	H	Y	3
190	E	K	A	E	I	H	Y	R	K	3
193	E	I	H	Y	R	K	N	K	Q	3
199	N	K	Q	L	M	R	L	Q	K	3
205	L	Q	K	Q	A	E	K	N	M	3
211	K	N	M	K	K	K	I	D	K	3
213	M	K	K	K	I	D	K	Y	T	3
215	K	K	I	D	K	Y	T	E	S	3
217	I	D	K	Y	T	E	S	P	G	3
236	F	K	T	I	A	P	L	A	A	3
244	A	T	R	A	T	R	I	G	H	3
248	T	R	I	G	H	P	G	G	R	3
251	G	H	P	G	G	R	T	P	R	3
258	P	R	A	G	S	S	A	H	R	3
272	A	R	A	P	V	P	A	A	S	3
283	A	W	L	P	L	R	T	P	W	3
286	P	L	R	T	P	W	T	R	P	3
287	L	R	T	P	W	T	R	P	S	3
313	R	N	P	L	P	N	P	R	H	3
338	G	Q	K	H	N	V	L	A	R	3
347	G	K	P	Q	R	K	P	K	S	3
353	P	K	S	E	N	N	S	W	Y	3
360	W	Y	V	E	N	G	R	P	A	3
365	G	R	P	A	D	L	A	G	S	3
368	A	D	L	A	G	S	G	Y	C	3
379	L	W	K	A	I	E	S	L	E	3
385	S	L	E	E	G	L	G	G	K	3
389	G	L	G	G	K	Q	K	D	K	3
15	H	I	V	V	E	S	I	R	D	2
17	V	V	E	S	I	R	D	H	S	2
24	H	S	G	Q	K	M	K	Q	D	2
40	P	T	K	V	T	G	I	I	T	2
55	G	H	V	Q	F	V	G	S	Y	2
56	H	V	Q	F	V	G	S	Y	K	2
64	K	L	A	Y	S	N	D	G	E	2
74	W	T	V	Y	Q	D	E	K	Q	2
78	Q	D	E	K	Q	R	K	D	K	2
84	K	D	K	V	L	L	G	R	K	2
101	I	N	I	S	G	S	F	C	R	2
109	R	N	K	L	K	Y	L	A	F	2
120	K	R	M	N	T	N	P	S	R	2
124	T	N	P	S	R	R	P	Y	H	2
130	P	Y	H	F	Q	V	P	S	R	2
134	Q	V	P	S	R	I	F	W	R	2
146	A	D	G	G	S	C	C	P	Q	2
185	E	E	K	R	K	E	K	A	E	2
189	K	E	K	A	E	I	H	Y	R	2
192	A	E	I	H	Y	R	K	N	K	2
202	L	M	R	L	Q	K	Q	A	E	2
206	Q	K	Q	A	E	K	N	M	K	2
210	E	K	N	M	K	K	K	I	D	2
214	K	K	K	I	D	K	Y	T	E	2
216	K	I	D	K	Y	T	E	S	P	2
220	Y	T	E	S	P	G	G	G	S	2
222	E	S	P	G	G	G	S	P	R	2
229	P	R	G	L	G	F	I	F	K	2
233	G	F	I	F	K	T	I	A	P	2
237	K	T	I	A	P	L	A	A	T	2
264	A	H	R	P	P	A	L	S	A	2
265	H	R	P	P	A	L	S	A	R	2
275	P	V	P	A	A	S	P	A	A	2
288	R	T	P	W	T	R	P	S	S	2
300	S	S	S	T	Y	D	S	L	S	2
306	S	L	S	P	Y	G	P	R	N	2
312	P	R	N	P	L	P	N	P	R	2
329	L	K	K	P	A	R	H	C	Q	2
330	K	K	P	A	R	H	C	Q	G	2
333	A	R	H	C	Q	G	Q	K	H	2
334	R	H	C	Q	G	Q	K	H	N	2
340	K	H	N	V	L	A	R	G	K	2
341	H	N	V	L	A	R	G	K	P	2
361	Y	V	E	N	G	R	P	A	D	2
383	I	E	S	L	E	E	G	L	G	2
392	G	K	Q	K	D	K	E	R	K	2
394	Q	K	D	K	E	R	K	A	E	2
395	K	D	K	E	R	K	A	E	N	2
397	K	E	R	K	A	E	N	G	P	2
398	E	R	K	A	E	N	G	P	H	2
7	K	T	F	P	L	R	A	L	H	1
18	V	E	S	I	R	D	H	S	G	1
20	S	I	R	D	H	S	G	Q	K	1
22	R	D	H	S	G	Q	K	M	K	1
43	V	T	G	I	I	T	Q	G	A	1
51	A	K	D	F	G	H	V	Q	F	1
66	A	Y	S	N	D	G	E	H	W	1
73	H	W	T	V	Y	Q	D	E	K	1
94	V	V	V	S	C	E	G	I	N	1
98	C	E	G	I	N	I	S	G	S	1
100	G	I	N	I	S	G	S	F	C	1
108	C	R	N	K	L	K	Y	L	A	1
111	K	L	K	Y	L	A	F	L	H	1
119	H	K	R	M	N	T	N	P	S	1
132	H	F	Q	V	P	S	R	I	F	1
136	P	S	R	I	F	W	R	Q	E	1
140	F	W	R	Q	E	K	A	D	G	1
142	R	Q	E	K	A	D	G	G	S	1
143	Q	E	K	A	D	G	G	S	C	1
144	E	K	A	D	G	G	S	C	C	1
149	G	S	C	C	P	Q	G	H	A	1
151	C	C	P	Q	G	H	A	S	E	1
163	K	V	C	L	S	G	A	P	H	1
170	P	H	E	V	G	W	K	Y	Q	1
171	H	E	V	G	W	K	Y	Q	A	1
195	H	Y	R	K	N	K	Q	L	M	1
198	K	N	K	Q	L	M	R	L	Q	1
201	Q	L	M	R	L	Q	K	Q	A	1
221	T	E	S	P	G	G	G	S	P	1
249	R	I	G	H	P	G	G	R	T	1
255	G	R	T	P	R	A	G	S	S	1
256	R	T	P	R	A	G	S	S	A	1
261	G	S	S	A	H	R	P	P	A	1
284	W	L	P	L	R	T	P	W	T	1
291	W	T	R	P	S	S	C	P	T	1
295	S	S	C	P	T	S	S	S	T	1
298	P	T	S	S	S	T	Y	D	S	1
301	S	S	T	Y	D	S	L	S	P	1
303	T	Y	D	S	L	S	P	Y	G	1
309	P	Y	G	P	R	N	P	L	P	1
315	P	L	P	N	P	R	H	S	P	1
317	P	N	P	R	H	S	P	S	G	1
320	R	H	S	P	S	G	G	G	G	1
343	V	L	A	R	G	K	P	Q	R	1
349	P	Q	R	K	P	K	S	E	N	1
350	Q	R	K	P	K	S	E	N	N	1
356	E	N	N	S	W	Y	V	E	N	1
363	E	N	G	R	P	A	D	L	A	1
380	W	K	A	I	E	S	L	E	E	1
387	E	E	G	L	G	G	K	Q	K	1

TABLE XXXV

151P3D4 v.1: HLA Peptide

Scoring Results A1 10-mers SYFPEITHI

SEQ. ID

Pos

1

2

3

4

5

6

7

8

9

0

score

NO.

91

E

V

D

V

F

V

S

M

G

Y

25

Portion

263

Y

L

I

H

P

T

K

L

T

Y

24

of SEQ

253

F

T

S

N

F

N

G

R

F

Y

23

ID NO:

96

V

S

M

G

Y

H

K

K

T

Y

21

3; each

117

G

S

D

S

D

A

S

L

V

I

21

start

292

I

F

A

A

W

K

I

L

G

Y

21

position

254

T

S

N

F

N

G

R

F

Y

Y

20

is

64

Y

R

D

P

T

A

F

G

S

G

19

specified,

119

D

S

D

A

S

L

V

I

T

D

19

the length

33

Q

A

E

N

G

P

H

L

L

V

18

of

186

A

V

I

A

S

F

D

Q

L

Y

18

peptide is

327

P

T

E

A

A

V

R

F

V

G

18

10 amino

344

L

Y

G

V

Y

C

F

R

A

Y

18

acids, the

138

K

C

E

V

I

E

G

L

E

D

17

end

336

G

F

P

D

K

K

H

K

L

Y

17

position

337

F

P

D

K

K

H

K

L

Y

G

17

for each

125

V

I

T

D

L

T

L

E

D

Y

16

peptide is

126

I

T

D

L

T

L

E

D

Y

G

16

the start

128

D

L

T

L

E

D

Y

G

R

Y

16

position

154

L

D

L

Q

G

V

V

F

P

Y

16

plus nine

161

F

P

Y

F

P

R

L

G

R

Y

16

181

C

L

D

Q

D

A

V

I

A

S

16

229

Q

N

T

V

P

G

V

R

N

Y

16

339

D

K

K

H

K

L

Y

G

V

Y

16

13

C

W

A

D

H

L

S

D

N

Y

15

23

T

L

D

H

D

R

A

I

H

I

15

55

G

N

V

T

L

P

C

K

F

Y

15

79

I

K

W

T

K

L

T

S

D

Y

15

99

G

Y

H

K

K

T

Y

G

G

Y

15

208

G

W

L

S

D

G

S

V

Q

Y

15

210

L

S

D

G

S

V

Q

Y

P

I

15

222

P

R

E

P

C

G

G

Q

N

T

15

239

G

F

W

D

K

D

K

S

R

Y

15

307

G

W

L

A

D

G

S

V

R

Y

15

18

L

S

D

N

Y

T

L

D

H

D

14

25

D

H

D

R

A

I

H

I

Q

A

14

57

V

T

L

P

C

K

F

Y

R

D

14

85

T

S

D

Y

L

K

E

V

D

V

14

130

T

L

E

D

Y

G

R

Y

K

C

14

272

Y

D

E

A

V

Q

A

C

L

N

14

89

L

K

E

V

D

V

F

V

S

M

13

144

G

L

E

D

D

T

V

V

V

A

13

146

E

D

D

T

V

V

V

A

L

D

13

153

A

L

D

L

Q

G

V

V

F

P

13

174

F

H

E

A

Q

Q

A

C

L

D

13

194

L

Y

D

A

W

R

G

G

L

D

13

247

R

Y

D

V

F

C

F

T

S

N

13

280

L

N

D

G

A

Q

I

A

K

V

13

107

G

Y

Q

G

R

V

F

L

K

G

12

141

V

I

E

G

L

E

D

D

T

V

12

190

S

F

D

Q

L

Y

D

A

W

R

12

309

L

A

D

G

S

V

R

Y

P

I

12

2

K

S

L

L

L

L

V

L

I

S

11

41

L

V

E

A

E

Q

A

K

V

F

11

43

E

A

E

Q

A

K

V

F

S

H

11

67

P

T

A

F

G

S

G

I

H

K

11

122

A

S

L

V

I

T

D

L

T

L

11

145

L

E

D

D

T

V

V

V

A

L

11

201

G

L

D

W

C

N

A

G

W

L

11

230

N

T

V

P

G

V

R

N

Y

G

11

240

F

W

D

K

D

K

S

R

Y

D

11

242

D

K

D

K

S

R

Y

D

V

F

11

14

W

A

D

H

L

S

D

N

Y

T

10

131

L

E

D

Y

G

R

Y

K

C

E

10

183

D

Q

D

A

V

I

A

S

F

D

10

219

I

T

K

P

R

E

P

C

G

G

10

271

T

Y

D

E

A

V

Q

A

C

L

10

300

G

Y

D

R

C

D

A

G

W

L

10

303

R

C

D

A

G

W

L

A

D

G

10

22

Y

T

L

D

H

D

R

A

I

H

9

34

A

E

N

G

P

H

L

L

V

E

9

72

S

G

I

H

K

I

R

I

K

W

9

195

Y

D

A

W

R

G

G

L

D

W

9

318

I

S

R

P

R

R

R

C

S

P

9

11

S

I

C

W

A

D

H

L

S

D

8

81

W

T

K

L

T

S

D

Y

L

K

8

82

T

K

L

T

S

D

Y

L

K

E

8

148

D

T

V

V

V

A

L

D

L

Q

8

160

V

F

P

Y

F

P

R

L

G

R

8

165

P

R

L

G

R

Y

N

L

N

F

8

3

S

L

L

L

L

V

L

I

S

I

7

17

H

L

S

D

N

Y

T

L

D

H

7

52

H

R

G

G

N

V

T

L

P

C

7

84

L

T

S

D

Y

L

K

E

V

D

7

103

K

T

Y

G

G

Y

Q

G

R

V

7

129

L

T

L

E

D

Y

G

R

Y

K

7

159

V

V

F

P

Y

F

P

R

L

G

7

187

V

I

A

S

F

D

Q

L

Y

D

7

245

K

S

R

Y

D

V

F

C

F

T

7

257

F

N

G

R

F

Y

Y

L

I

H

7

270

L

T

Y

D

E

A

V

Q

A

C

7

335

V

G

F

P

D

K

K

H

K

L

7

10

I

S

I

C

W

A

D

H

L

S

6

50

F

S

H

R

G

G

N

V

T

L

6

51

S

H

R

G

G

N

V

T

L

P

6

70

F

G

S

G

I

H

K

I

R

I

6

77

I

R

I

K

W

T

K

L

T

S

6

124

L

V

I

T

D

L

T

L

E

D

6

147

D

D

T

V

V

V

A

L

D

L

6

149

T

V

V

V

A

L

D

L

Q

G

6

175

H

E

A

Q

Q

A

C

L

D

Q

6

203

D

W

C

N

A

G

W

L

S

D

6

213

G

S

V

Q

Y

P

I

T

K

P

6

267

P

T

K

L

T

Y

D

E

A

V

6

273

D

E

A

V

Q

A

C

L

N

D

6

291

Q

I

F

A

A

W

K

I

L

G

6

302

D

R

C

D

A

G

W

L

A

D

6

314

V

R

Y

P

I

S

R

P

R

R

6

5

L

L

L

V

L

I

S

I

C

W

5

88

Y

L

K

E

V

D

V

F

V

S

5

123

S

L

V

I

T

D

L

T

L

E

5

135

G

R

Y

K

C

E

V

I

E

G

5

155

D

L

Q

G

V

V

F

P

Y

F

5

162

P

Y

F

P

R

L

G

R

Y

N

5

189

A

S

F

D

Q

L

Y

D

A

W

5

215

V

Q

Y

P

I

T

K

P

R

E

5

255

S

N

F

N

G

R

F

Y

Y

L

5

279

C

L

N

D

G

A

Q

I

A

K

5

287

A

K

V

G

Q

I

F

A

A

W

5

301

Y

D

R

C

D

A

G

W

L

A

5

324

R

C

S

P

T

E

A

A

V

R

5

35

E

N

G

P

H

L

L

V

E

A

4

44

A

E

Q

A

K

V

F

S

H

R

4

71

G

S

G

I

H

K

I

R

I

K

4

86

S

D

Y

L

K

E

V

D

V

F

4

137

Y

K

C

E

V

I

E

G

L

E

4

212

D

G

S

V

Q

Y

P

I

T

K

4

251

F

C

F

T

S

N

F

N

G

R

4

258

N

G

R

F

Y

Y

L

I

H

P

4

262

Y

Y

L

I

H

P

T

K

L

T

4

264

L

I

H

P

T

K

L

T

Y

D

4

285

Q

I

A

K

V

G

Q

I

F

A

4

311

D

G

S

V

R

Y

P

I

S

R

4

312

G

S

V

R

Y

P

I

S

R

P

4

325

C

S

P

T

E

A

A

V

R

F

4

331

A

V

R

F

V

G

F

P

D

K

4

40

L

L

V

E

A

E

Q

A

K

V

3

49

V

F

S

H

R

G

G

N

V

T

3

68

T

A

F

G

S

G

I

H

K

I

3

94

V

F

V

S

M

G

Y

H

K

K

3

95

F

V

S

M

G

Y

H

K

K

T

3

100

Y

H

K

K

T

Y

G

G

Y

Q

3

104

T

Y

G

G

Y

Q

G

R

V

F

3

105

Y

G

G

Y

Q

G

R

V

F

L

3

106

G

G

Y

Q

G

R

V

F

L

K

3

113

F

L

K

G

G

S

D

S

D

A

3

152

V

A

L

D

L

Q

G

V

V

F

3

158

G

V

V

F

P

Y

F

P

R

L

3

163

Y

F

P

R

L

G

R

Y

N

L

3

164

F

P

R

L

G

R

Y

N

L

N

3

168

G

R

Y

N

L

N

F

H

E

A

3

185

D

A

V

I

A

S

F

D

Q

L

3

202

L

D

W

C

N

A

G

W

L

S

3

207

A

G

W

L

S

D

G

S

V

Q

3

217

Y

P

I

T

K

P

R

E

P

C

3

224

E

P

C

G

G

Q

N

T

V

P

3

234

G

V

R

N

Y

G

F

W

D

K

3

235

V

R

N

Y

G

F

W

D

K

D

3

256

N

F

N

G

R

F

Y

Y

L

I

3

261

F

Y

Y

L

I

H

P

T

K

L

3

289

V

G

Q

I

F

A

A

W

K

I

3

306

A

G

W

L

A

D

G

S

V

R

3

316

Y

P

I

S

R

P

R

R

R

C

3

326

S

P

T

E

A

A

V

R

F

V

3

328

T

E

A

A

V

R

F

V

G

F

3

332

V

R

F

V

G

F

P

D

K

K

3

333

R

F

V

G

F

P

D

K

K

H

3

345

Y

G

V

Y

C

F

R

A

Y

N

3

1

M

K

S

L

L

L

L

V

L

I

2

8

V

L

I

S

I

C

W

A

D

H

2

15

A

D

H

L

S

D

N

Y

T

L

2

16

D

H

L

S

D

N

Y

T

L

D

2

19

S

D

N

Y

T

L

D

H

D

R

2

32

I

Q

A

E

N

G

P

H

L

L

2

47

A

K

V

F

S

H

R

G

G

N

2

54

G

G

N

V

T

L

P

C

K

F

2

75

H

K

I

R

I

K

W

T

K

L

2

76

K

I

R

I

K

W

T

K

L

T

2

90

K

E

V

D

V

F

V

S

M

G

2

97

S

M

G

Y

H

K

K

T

Y

G

2

108

Y

Q

G

R

V

F

L

K

G

G

2

116

G

G

S

D

S

D

A

S

L

V

2

118

S

D

S

D

A

S

L

V

I

T

2

120

S

D

A

S

L

V

I

T

D

L

2

121

D

A

S

L

V

I

T

D

L

T

2

134

Y

G

R

Y

K

C

E

V

I

E

2

151

V

V

A

L

D

L

Q

G

V

V

2

170

Y

N

L

N

F

H

E

A

Q

Q

2

193

Q

L

Y

D

A

W

R

G

G

L

2

197

A

W

R

G

G

L

D

W

C

N

2

209

W

L

S

D

G

S

V

Q

Y

P

2

211

S

D

G

S

V

Q

Y

P

I

T

2

214

S

V

Q

Y

P

I

T

K

P

R

2

231

T

V

P

G

V

R

N

Y

G

F

2

237

N

Y

G

F

W

D

K

D

K

S

2

238

Y

G

F

W

D

K

D

K

S

R

2

246

S

R

Y

D

V

F

C

F

T

S

2

248

Y

D

V

F

C

F

T

S

N

F

2

250

V

F

C

F

T

S

N

F

N

G

2

275

A

V

Q

A

C

L

N

D

G

A

2

284

A

Q

I

A

K

V

G

Q

I

F

2

294

A

A

W

K

I

L

G

Y

D

R

2

297

K

I

L

G

Y

D

R

C

D

A

2

308

W

L

A

D

G

S

V

R

Y

P

2

313

S

V

R

Y

P

I

S

R

P

R

2

319

S

R

P

R

R

R

C

S

P

T

2

330

A

A

V

R

F

V

G

F

P

D

2

343

K

L

Y

G

V

Y

C

F

R

A

2

4

L

L

L

L

V

L

I

S

I

C

1

6

L

L

V

L

I

S

I

C

W

A

1

29

A

I

H

I

Q

A

E

N

G

P

1

30

I

H

I

Q

A

E

N

G

P

H

1

31

H

I

Q

A

E

N

G

P

H

L

1

36

N

G

P

H

L

L

V

E

A

E

1

39

H

L

L

V

E

A

E

Q

A

K

1

42

V

E

A

E

Q

A

K

V

F

S

1

48

K

V

F

S

H

R

G

G

N

V

1

58

T

L

P

C

K

F

Y

R

D

P

1

59

L

P

C

K

F

Y

R

D

P

T

1

63

F

Y

R

D

P

T

A

F

G

S

1

65

R

D

P

T

A

F

G

S

G

I

1

69

A

F

G

S

G

I

H

K

I

R

1

83

K

L

T

S

D

Y

L

K

E

V

1

92

V

D

V

F

V

S

M

G

Y

H

1

93

D

V

F

V

S

M

G

Y

H

K

1

101

H

K

K

T

Y

G

G

Y

Q

G

1

110

G

R

V

F

L

K

G

G

S

D

1

111

R

V

F

L

K

G

G

S

D

S

1

112

V

F

L

K

G

G

S

D

S

D

1

114

L

K

G

G

S

D

S

D

A

S

1

132

E

D

Y

G

R

Y

K

C

E

V

1

133

D

Y

G

R

Y

K

C

E

V

I

1

142

I

E

G

L

E

D

D

T

V

V

1

143

E

G

L

E

D

D

T

V

V

V

1

150

V

V

V

A

L

D

L

Q

G

V

1

166

R

L

G

R

Y

N

L

N

F

H

1

167

L

G

R

Y

N

L

N

F

H

E

1

171

N

L

N

F

H

E

A

Q

Q

A

1

177

A

Q

Q

A

C

L

D

Q

D

A

1

179

Q

A

C

L

D

Q

D

A

V

I

1

180

A

C

L

D

Q

D

A

V

I

A

1

191

F

D

Q

L

Y

D

A

W

R

G

1

198

W

R

G

G

L

D

W

C

N

A

1

200

G

G

L

D

W

C

N

A

G

W

1

205

C

N

A

G

W

L

S

D

G

S

1

221

K

P

R

E

P

C

G

G

Q

N

1

225

P

C

G

G

Q

N

T

V

P

G

1

226

C

G

G

Q

N

T

V

P

G

V

1

227

G

G

Q

N

T

V

P

G

V

R

1

228

G

Q

N

T

V

P

G

V

R

N

1

232

V

P

G

V

R

N

Y

G

F

W

1

233

P

G

V

R

N

Y

G

F

W

D

1

236

R

N

Y

G

F

W

D

K

D

K

1

241

W

D

K

D

K

S

R

Y

D

V

1

244

D

K

S

R

Y

D

V

F

C

F

1

252

C

F

T

S

N

F

N

G

R

F

1

268

T

K

L

T

Y

D

E

A

V

Q

1

269

K

L

T

Y

D

E

A

V

Q

A

1

276

V

Q

A

C

L

N

D

G

A

Q

1

277

Q

A

C

L

N

D

G

A

Q

I

1

278

A

C

L

N

D

G

A

Q

I

A

1

281

N

D

G

A

Q

I

A

K

V

G

1

283

G

A

Q

I

A

K

V

G

Q

I

1

293

F

A

A

W

K

I

L

G

Y

D

1

295

A

W

K

I

L

G

Y

D

R

C

1

298

I

L

G

Y

D

R

C

D

A

G

1

304

C

D

A

G

W

L

A

D

G

S

1

310

A

D

G

S

V

R

Y

P

I

S

1

317

P

I

S

R

P

R

R

R

C

S

1

329

E

A

A

V

R

F

V

G

F

P

1

334

F

V

G

F

P

D

K

K

H

K

1

340

K

K

H

K

L

Y

G

V

Y

C

1

341

K

H

K

L

Y

G

V

Y

C

F

1

151P3D4 v.2: HLA Peptide

Scoring Results A1 10-mers SYFPEITHI

SEQ. ID

Pos

1

2

3

4

5

6

7

8

9

0

score

NO.

68

S

N

D

G

E

H

W

T

V

Y

29

Portion

105

G

S

F

C

R

N

K

L

K

Y

27

of SEQ

295

S

S

C

P

T

S

S

S

T

Y

25

ID NO:

58

Q

F

V

G

S

Y

K

L

A

Y

22

5; each

301

S

S

T

Y

D

S

L

S

P

Y

21

start

187

K

R

K

E

K

A

E

I

H

Y

19

position

220

Y

T

E

S

P

G

G

G

S

P

19

is

30

K

Q

D

K

K

V

D

L

L

V

18

specified,

168

G

A

P

H

E

V

G

W

K

Y

18

the length

54

F

G

H

V

Q

F

V

G

S

Y

17

of

211

K

N

M

K

K

K

I

D

K

Y

17

peptide is

7

K

T

F

P

L

R

A

L

H

I

16

10 amino

122

M

N

T

N

P

S

R

R

P

Y

16

acids, the

152

C

P

Q

G

H

A

S

E

A

Y

16

end

352

K

P

K

S

E

N

N

S

W

Y

16

position

366

R

P

A

D

L

A

G

S

G

Y

16

for each

385

S

L

E

E

G

L

G

G

K

Q

16

peptide is

157

A

S

E

A

Y

K

K

V

C

L

15

the start

354

K

S

E

N

N

S

W

Y

V

E

15

position

77

Y

Q

D

E

K

Q

R

K

D

K

13

plus nine

97

S

C

E

G

I

N

I

S

G

S

13

183

T

L

E

E

K

R

K

E

K

A

13

382

A

I

E

S

L

E

E

G

L

G

13

4

H

T

T

K

T

F

P

L

R

A

12

34

K

V

D

L

L

V

P

T

K

V

12

51

A

K

D

F

G

H

V

Q

F

V

12

78

Q

D

E

K

Q

R

K

D

K

V

12

208

Q

A

E

K

N

M

K

K

K

I

12

300

S

S

S

T

Y

D

S

L

S

P

12

322

S

P

S

G

G

G

G

L

K

K

12

361

Y

V

E

N

G

R

P

A

D

L

12

386

L

E

E

G

L

G

G

K

Q

K

12

1

M

L

E

H

T

T

K

T

F

P

11

17

V

V

E

S

I

R

D

H

S

G

11

21

I

R

D

H

S

G

Q

K

M

K

11

70

D

G

E

H

W

T

V

Y

Q

D

11

123

N

T

N

P

S

R

R

P

Y

H

11

142

R

Q

E

K

A

D

G

G

S

C

11

145

K

A

D

G

G

S

C

C

P

Q

11

191

K

A

E

I

H

Y

R

K

N

K

11

278

A

A

S

P

A

A

W

L

P

L

11

40

P

T

K

V

T

G

I

I

T

Q

10

83

R

K

D

K

V

L

L

G

R

K

10

96

V

S

C

E

G

I

N

I

S

G

10

111

K

L

K

Y

L

A

F

L

H

K

10

127

S

R

R

P

Y

H

F

Q

V

P

10

170

P

H

E

V

G

W

K

Y

Q

A

10

184

L

E

E

K

R

K

E

K

A

E

10

188

R

K

E

K

A

E

I

H

Y

R

10

216

K

I

D

K

Y

T

E

S

P

G

10

228

S

P

R

G

L

G

F

I

F

K

10

291

W

T

R

P

S

S

C

P

T

S

10

303

T

Y

D

S

L

S

P

Y

G

P

10

309

P

Y

G

P

R

N

P

L

P

N

10

367

P

A

D

L

A

G

S

G

Y

C

10

372

G

S

G

Y

C

G

A

L

W

K

10

394

Q

K

D

K

E

R

K

A

E

N

10

396

D

K

E

R

K

A

E

N

G

P

10

81

K

Q

R

K

D

K

V

L

L

G

9

177

Y

Q

A

V

T

A

T

L

E

E

8

182

A

T

L

E

E

K

R

K

E

K

8

262

S

S

A

H

R

P

P

A

L

S

8

263

S

A

H

R

P

P

A

L

S

A

8

280

S

P

A

A

W

L

P

L

R

T

8

302

S

T

Y

D

S

L

S

P

Y

G

8

31

Q

D

K

K

V

D

L

L

V

P

7

43

V

T

G

I

I

T

Q

G

A

K

7

47

I

T

Q

G

A

K

D

F

G

H

7

103

I

S

G

S

F

C

R

N

K

L

7

167

S

G

A

P

H

E

V

G

W

K

7

180

V

T

A

T

L

E

E

K

R

K

7

195

H

Y

R

K

N

K

Q

L

M

R

7

198

K

N

K

Q

L

M

R

L

Q

K

7

225

G

G

G

S

P

R

G

L

G

F

7

244

A

T

R

A

T

R

I

G

H

P

7

247

A

T

R

I

G

H

P

G

G

R

7

279

A

S

P

A

A

W

L

P

L

R

7

306

S

L

S

P

Y

G

P

R

N

P

7

321

H

S

P

S

G

G

G

G

L

K

7

323

P

S

G

G

G

G

L

K

K

P

7

337

Q

G

Q

K

H

N

V

L

A

R

7

383

I

E

S

L

E

E

G

L

G

G

7

5

T

T

K

T

F

P

L

R

A

L

6

9

F

P

L

R

A

L

H

I

V

V

6

37

L

L

V

P

T

K

V

T

G

I

6

39

V

P

T

K

V

T

G

I

I

T

6

67

Y

S

N

D

G

E

H

W

T

V

6

74

W

T

V

Y

Q

D

E

K

Q

R

6

82

Q

R

K

D

K

V

L

L

G

R

6

94

V

V

V

S

C

E

G

I

N

I

6

108

C

R

N

K

L

K

Y

L

A

F

6

150

S

C

C

P

Q

G

H

A

S

E

6

159

E

A

Y

K

K

V

C

L

S

G

6

235

I

F

K

T

I

A

P

L

A

A

6

237

K

T

I

A

P

L

A

A

T

R

6

243

A

A

T

R

A

T

R

I

G

H

6

256

R

T

P

R

A

G

S

S

A

H

6

288

R

T

P

W

T

R

P

S

S

C

6

298

P

T

S

S

S

T

Y

D

S

L

6

299

T

S

S

S

T

Y

D

S

L

S

6

308

S

P

Y

G

P

R

N

P

L

P

6

346

R

G

K

P

Q

R

K

P

K

S

6

363

E

N

G

R

P

A

D

L

A

G

6

379

L

W

K

A

I

E

S

L

E

E

6

3

E

H

T

T

K

T

F

P

L

R

5

20

S

I

R

D

H

S

G

Q

K

M

5

104

S

G

S

F

C

R

N

K

L

K

5

132

H

F

Q

V

P

S

R

I

F

W

5

133

F

Q

V

P

S

R

I

F

W

R

5

136

P

S

R

I

F

W

R

Q

E

K

5

149

G

S

C

C

P

Q

G

H

A

S

5

158

S

E

A

Y

K

K

V

C

L

S

5

221

T

E

S

P

G

G

G

S

P

R

5

222

E

S

P

G

G

G

S

P

R

G

5

227

G

S

P

R

G

L

G

F

I

F

5

250

I

G

H

P

G

G

R

T

P

R

5

255

G

R

T

P

R

A

G

S

S

A

5

264

A

H

R

P

P

A

L

S

A

R

5

270

L

S

A

R

A

P

V

P

A

A

5

272

A

R

A

P

V

P

A

A

S

P

5

274

A

P

V

P

A

A

S

P

A

A

5

283

A

W

L

P

L

R

T

P

W

T

5

287

L

R

T

P

W

T

R

P

S

S

5

305

D

S

L

S

P

Y

G

P

R

N

5

307

L

S

P

Y

G

P

R

N

P

L

5

312

P

R

N

P

L

P

N

P

R

H

5

314

N

P

L

P

N

P

R

H

S

P

5

320

R

H

S

P

S

G

G

G

G

L

5

358

N

S

W

Y

V

E

N

G

R

P

5

371

A

G

S

G

Y

C

G

A

L

W

5

14

L

H

I

V

V

E

S

I

R

D

4

19

E

S

I

R

D

H

S

G

Q

K

4

24

H

S

G

Q

K

M

K

Q

D

K

4

25

S

G

Q

K

M

K

Q

D

K

K

4

61

G

S

Y

K

L

A

Y

S

N

D

4

87

V

L

L

G

R

K

A

V

V

V

4

114

Y

L

A

F

L

H

K

R

M

N

4

126

P

S

R

R

P

Y

H

F

Q

V

4

137

S

R

I

F

W

R

Q

E

K

A

4

166

L

S

G

A

P

H

E

V

G

W

4

210

E

K

N

M

K

K

K

I

D

K

4

224

P

G

G

G

S

P

R

G

L

G

4

226

G

G

S

P

R

G

L

G

F

I

4

230

R

G

L

G

F

I

F

K

T

I

4

232

L

G

F

I

F

K

T

I

A

P

4

238

T

I

A

P

L

A

A

T

R

A

4

261

G

S

S

A

H

R

P

P

A

L

4

265

H

R

P

P

A

L

S

A

R

A

4

294

P

S

S

C

P

T

S

S

S

T

4

316

L

P

N

P

R

H

S

P

S

G

4

329

L

K

K

P

A

R

H

C

Q

G

4

350

Q

R

K

P

K

S

E

N

N

S

4

362

V

E

N

G

R

P

A

D

L

A

4

364

N

G

R

P

A

D

L

A

G

S

4

373

S

G

Y

C

G

A

L

W

K

A

4

376

C

G

A

L

W

K

A

I

E

S

4

378

A

L

W

K

A

I

E

S

L

E

4

384

E

S

L

E

E

G

L

G

G

K

4

389

G

L

G

G

K

Q

K

D

K

E

4

6

T

K

T

F

P

L

R

A

L

H

3

29

M

K

Q

D

K

K

V

D

L

L

3

44

T

G

I

I

T

Q

G

A

K

D

3

48

T

Q

G

A

K

D

F

G

H

V

3

53

D

F

G

H

V

Q

F

V

G

S

3

57

V

Q

F

V

G

S

Y

K

L

A

3

63

Y

K

L

A

Y

S

N

D

G

E

3

76

V

Y

Q

D

E

K

Q

R

K

D

3

84

K

D

K

V

L

L

G

R

K

A

3

88

L

L

G

R

K

A

V

V

V

S

3

101

I

N

I

S

G

S

F

C

R

N

3

107

F

C

R

N

K

L

K

Y

L

A

3

117

F

L

H

K

R

M

N

T

N

P

3

134

Q

V

P

S

R

I

F

W

R

Q

3

165

C

L

S

G

A

P

H

E

V

G

3

179

A

V

T

A

T

L

E

E

K

R

3

192

A

E

I

H

Y

R

K

N

K

Q

3

206

Q

K

Q

A

E

K

N

M

K

K

3

223

S

P

G

G

G

S

P

R

G

L

3

234

F

I

F

K

T

I

A

P

L

A

3

324

S

G

G

G

G

L

K

K

P

A

3

332

P

A

R

H

C

Q

G

Q

K

H

3

336

C

Q

G

Q

K

H

N

V

L

A

3

340

K

H

N

V

L

A

R

G

K

P

3

344

L

A

R

G

K

P

Q

R

K

P

3

359

S

W

Y

V

E

N

G

R

P

A

3

10

P

L

R

A

L

H

I

V

V

E

2

13

A

L

H

I

V

V

E

S

I

R

2

22

R

D

H

S

G

Q

K

M

K

Q

2

26

G

Q

K

M

K

Q

D

K

K

V

2

35

V

D

L

L

V

P

T

K

V

T

2

49

Q

G

A

K

D

F

G

H

V

Q

2

52

K

D

F

G

H

V

Q

F

V

G

2

56

H

V

Q

F

V

G

S

Y

K

L

2

62

S

Y

K

L

A

Y

S

N

D

G

2

73

H

W

T

V

Y

Q

D

E

K

Q

2

80

E

K

Q

R

K

D

K

V

L

L

2

106

S

F

C

R

N

K

L

K

Y

L

2

110

N

K

L

K

Y

L

A

F

L

H

2

112

L

K

Y

L

A

F

L

H

K

R

2

131

Y

H

F

Q

V

P

S

R

I

F

2

146

A

D

G

G

S

C

C

P

Q

G

2

154

Q

G

H

A

S

E

A

Y

K

K

2

155

G

H

A

S

E

A

Y

K

K

V

2

161

Y

K

K

V

C

L

S

G

A

P

2

176

K

Y

Q

A

V

T

A

T

L

E

2

181

T

A

T

L

E

E

K

R

K

E

2

190

E

K

A

E

I

H

Y

R

K

N

2

194

I

H

Y

R

K

N

K

Q

L

M

2

196

Y

R

K

N

K

Q

L

M

R

L

2

197

R

K

N

K

Q

L

M

R

L

Q

2

199

N

K

Q

L

M

R

L

Q

K

Q

2

203

M

R

L

Q

K

Q

A

E

K

N

2

207

K

Q

A

E

K

N

M

K

K

K

2

229

P

R

G

L

G

F

I

F

K

T

2

240

A

P

L

A

A

T

R

A

T

R

2

248

T

R

I

G

H

P

G

G

R

T

2

260

A

G

S

S

A

H

R

P

P

A

2

269

A

L

S

A

R

A

P

V

P

A

2

271

S

A

R

A

P

V

P

A

A

S

2

277

P

A

A

S

P

A

A

W

L

P

2

282

A

A

W

L

P

L

R

T

P

W

2

296

S

C

P

T

S

S

S

T

Y

D

2

304

Y

D

S

L

S

P

Y

G

P

R

2

310

Y

G

P

R

N

P

L

P

N

P

2

328

G

L

K

K

P

A

R

H

C

Q

2

335

H

C

Q

G

Q

K

H

N

V

L

2

343

V

L

A

R

G

K

P

Q

R

K

2

345

A

R

G

K

P

Q

R

K

P

K

2

355

S

E

N

N

S

W

Y

V

E

N

2

368

A

D

L

A

G

S

G

Y

C

G

2

369

D

L

A

G

S

G

Y

C

G

A

2

375

Y

C

G

A

L

W

K

A

I

E

2

387

E

E

G

L

G

G

K

Q

K

D

2

392

G

K

Q

K

D

K

E

R

K

A

2

399

R

K

A

E

N

G

P

H

L

L

2

11

L

R

A

L

H

I

V

V

E

S

1

12

R

A

L

H

I

V

V

E

S

I

1

16

I

V

V

E

S

I

R

D

H

S

1

18

V

E

S

I

R

D

H

S

G

Q

1

23

D

H

S

G

Q

K

M

K

Q

D

1

27

Q

K

M

K

Q

D

K

K

V

D

1

33

K

K

V

D

L

L

V

P

T

K

1

36

D

L

L

V

P

T

K

V

T

G

1

42

K

V

T

G

I

I

T

Q

G

A

1

55

G

H

V

Q

F

V

G

S

Y

K

1

59

F

V

G

S

Y

K

L

A

Y

S

1

60

V

G

S

Y

K

L

A

Y

S

N

1

64

K

L

A

Y

S

N

D

G

E

H

1

65

L

A

Y

S

N

D

G

E

H

W

1

66

A

Y

S

N

D

G

E

H

W

T

1

79

D

E

K

Q

R

K

D

K

V

L

1

85

D

K

V

L

L

G

R

K

A

V

1

86

K

V

L

L

G

R

K

A

V

V

1

89

L

G

R

K

A

V

V

V

S

C

1

90

G

R

K

A

V

V

V

S

C

E

1

93

A

V

V

V

S

C

E

G

I

N

1

95

V

V

S

C

E

G

I

N

I

S

1

99

E

G

I

N

I

S

G

S

F

C

1

102

N

I

S

G

S

F

C

R

N

K

1

115

L

A

F

L

H

K

R

M

N

T

1

116

A

F

L

H

K

R

M

N

T

N

1

119

H

K

R

M

N

T

N

P

S

R

1

129

R

P

Y

H

F

Q

V

P

S

R

1

135

V

P

S

R

I

F

W

R

Q

E

1

140

F

W

R

Q

E

K

A

D

G

G

1

143

Q

E

K

A

D

G

G

S

C

C

1

156

H

A

S

E

A

Y

K

K

V

C

1

160

A

Y

K

K

V

C

L

S

G

A

1

162

K

K

V

C

L

S

G

A

P

H

1

164

V

C

L

S

G

A

P

H

E

V

1

169

A

P

H

E

V

G

W

K

Y

Q

1

171

H

E

V

G

W

K

Y

Q

A

V

1

172

E

V

G

W

K

Y

Q

A

V

T

1

173

V

G

W

K

Y

Q

A

V

T

A

1

174

G

W

K

Y

Q

A

V

T

A

T

1

193

E

I

H

Y

R

K

N

K

Q

L

1

201

Q

L

M

R

L

Q

K

Q

A

E

1

204

R

L

Q

K

Q

A

E

K

N

M

1

205

L

Q

K

Q

A

E

K

N

M

K

1

209

A

E

K

N

M

K

K

K

I

D

1

219

K

Y

T

E

S

P

G

G

G

S

1

231

G

L

G

F

I

F

K

T

I

A

1

236

F

K

T

I

A

P

L

A

A

T

1

241

P

L

A

A

T

R

A

T

R

I

1

245

T

R

A

T

R

I

G

H

P

G

1

249

R

I

G

H

P

G

G

R

T

P

1

251

G

H

P

G

G

R

T

P

R

A

1

252

H

P

G

G

R

T

P

R

A

G

1

253

P

G

G

R

T

P

R

A

G

S

1

258

P

R

A

G

S

S

A

H

R

P

1

267

P

P

A

L

S

A

R

A

P

V

1

268

P

A

L

S

A

R

A

P

V

P

1

276

V

P

A

A

S

P

A

A

W

L

1

284

W

L

P

L

R

T

P

W

T

R

1

286

P

L

R

T

P

W

T

R

P

S

1

315

P

L

P

N

P

R

H

S

P

S

1

319

P

R

H

S

P

S

G

G

G

G

1

325

G

G

G

G

L

K

K

P

A

R

1

333

A

R

H

C

Q

G

Q

K

H

N

1

341

H

N

V

L

A

R

G

K

P

Q

1

351

R

K

P

K

S

E

N

N

S

W

1

356

E

N

N

S

W

Y

V

E

N

G

1

360

W

Y

V

E

N

G

R

P

A

D

1

374

G

Y

C

G

A

L

W

K

A

I

1

388

E

G

L

G

G

K

Q

K

D

K

1

393

K

Q

K

D

K

E

R

K

A

E

1

397

K

E

R

K

A

E

N

G

P

H

1

398

E

R

K

A

E

N

G

P

H

L

1

TABLE XXXVI

151P3D4 v.1: HLA Peptide

Scoring Results A*0201 10-mers SYFPEITHI

SEQ. ID

Pos

1

2

3

4

5

6

7

8

9

0

score

NO.

3

S

L

L

L

L

V

L

I

S

I

28

Portion

40

L

L

V

E

A

E

Q

A

K

V

28

of SEQ

83

K

L

T

S

D

Y

L

K

E

V

25

ID NO:

193

Q

L

Y

D

A

W

R

G

G

L

23

3; each

68

T

A

F

G

S

G

I

H

K

I

22

start

141

V

I

E

G

L

E

D

D

T

V

22

position

280

L

N

D

G

A

Q

I

A

K

V

22

is

144

G

L

E

D

D

T

V

V

V

A

21

specified,

201

G

L

D

W

C

N

A

G

W

L

21

the length

6

L

L

V

L

I

S

I

C

W

A

20

of

9

L

I

S

I

C

W

A

D

H

L

20

peptide is

145

L

E

D

D

T

V

V

V

A

L

20

10 amino

150

V

V

V

A

L

D

L

Q

G

V

20

acids, the

31

H

I

Q

A

E

N

G

P

H

L

19

end

4

L

L

L

L

V

L

I

S

I

C

18

position

23

T

L

D

H

D

R

A

I

H

I

18

for each

103

K

T

Y

G

G

Y

Q

G

R

V

18

peptide is

120

S

D

A

S

L

V

I

T

D

L

18

the start

153

A

L

D

L

Q

G

V

V

F

P

18

position

343

K

L

Y

G

V

Y

C

F

R

A

18

plus nine

32

I

Q

A

E

N

G

P

H

L

L

17

88

Y

L

K

E

V

D

V

F

V

S

17

122

A

S

L

V

I

T

D

L

T

L

17

151

V

V

A

L

D

L

Q

G

V

V

17

263

Y

L

I

H

P

T

K

L

T

Y

17

283

G

A

Q

I

A

K

V

G

Q

I

17

297

K

I

L

G

Y

D

R

C

D

A

17

308

W

L

A

D

G

S

V

R

Y

P

17

309

L

A

D

G

S

V

R

Y

P

I

17

326

S

P

T

E

A

A

V

R

F

V

17

335

V

G

F

P

D

K

K

H

K

L

17

48

K

V

F

S

H

R

G

G

N

V

16

73

G

I

H

K

I

R

I

K

W

T

16

113

F

L

K

G

G

S

D

S

D

A

16

123

S

L

V

I

T

D

L

T

L

E

16

206

N

A

G

W

L

S

D

G

S

V

16

226

C

G

G

Q

N

T

V

P

G

V

16

264

L

I

H

P

T

K

L

T

Y

D

16

8

V

L

I

S

I

C

W

A

D

H

15

15

A

D

H

L

S

D

N

Y

T

L

15

50

F

S

H

R

G

G

N

V

T

L

15

115

K

G

G

S

D

S

D

A

S

L

15

158

G

V

V

F

P

Y

F

P

R

L

15

166

R

L

G

R

Y

N

L

N

F

H

15

181

C

L

D

Q

D

A

V

I

A

S

15

209

W

L

S

D

G

S

V

Q

Y

P

15

269

K

L

T

Y

D

E

A

V

Q

A

15

305

D

A

G

W

L

A

D

G

S

V

15

1

M

K

S

L

L

L

L

V

L

I

14

5

L

L

L

V

L

I

S

I

C

W

14

33

Q

A

E

N

G

P

H

L

L

V

14

75

H

K

I

R

I

K

W

T

K

L

14

136

R

Y

K

C

E

V

I

E

G

L

14

171

N

L

N

F

H

E

A

Q

Q

A

14

173

N

F

H

E

A

Q

Q

A

C

L

14

179

Q

A

C

L

D

Q

D

A

V

I

14

188

I

A

S

F

D

Q

L

Y

D

A

14

255

S

N

F

N

G

R

F

Y

Y

L

14

261

F

Y

Y

L

I

H

P

T

K

L

14

271

T

Y

D

E

A

V

Q

A

C

L

14

277

Q

A

C

L

N

D

G

A

Q

I

14

285

Q

I

A

K

V

G

Q

I

F

A

14

286

I

A

K

V

G

Q

I

F

A

A

14

11

S

I

C

W

A

D

H

L

S

D

13

39

H

L

L

V

E

A

E

Q

A

K

13

78

R

I

K

W

T

K

L

T

S

D

13

87

D

Y

L

K

E

V

D

V

F

V

13

105

Y

G

G

Y

Q

G

R

V

F

L

13

118

S

D

S

D

A

S

L

V

I

T

13

125

V

I

T

D

L

T

L

E

D

Y

13

130

T

L

E

D

Y

G

R

Y

K

C

13

143

E

G

L

E

D

D

T

V

V

V

13

163

Y

F

P

R

L

G

R

Y

N

L

13

178

Q

Q

A

C

L

D

Q

D

A

V

13

185

D

A

V

I

A

S

F

D

Q

L

13

210

L

S

D

G

S

V

Q

Y

P

I

13

223

R

E

P

C

G

G

Q

N

T

V

13

270

L

T

Y

D

E

A

V

Q

A

C

13

279

C

L

N

D

G

A

Q

I

A

K

13

323

R

R

C

S

P

T

E

A

A

V

13

17

H

L

S

D

N

Y

T

L

D

H

12

29

A

I

H

I

Q

A

E

N

G

P

12

76

K

I

R

I

K

W

T

K

L

T

12

116

G

G

S

D

S

D

A

S

L

V

12

132

E

D

Y

G

R

Y

K

C

E

V

12

142

I

E

G

L

E

D

D

T

V

V

12

155

D

L

Q

G

V

V

F

P

Y

F

12

187

V

I

A

S

F

D

Q

L

Y

D

12

256

N

F

N

G

R

F

Y

Y

L

I

12

298

I

L

G

Y

D

R

C

D

A

G

12

338

P

D

K

K

H

K

L

Y

G

V

12

22

Y

T

L

D

H

D

R

A

I

H

11

35

E

N

G

P

H

L

L

V

E

A

11

70

F

G

S

G

I

H

K

I

R

I

11

85

T

S

D

Y

L

K

E

V

D

V

11

124

L

V

I

T

D

L

T

L

E

D

11

180

A

C

L

D

Q

D

A

V

I

A

11

182

L

D

Q

D

A

V

I

A

S

F

11

241

W

D

K

D

K

S

R

Y

D

V

11

267

P

T

K

L

T

Y

D

E

A

V

11

275

A

V

Q

A

C

L

N

D

G

A

11

289

V

G

Q

I

F

A

A

W

K

I

11

290

G

Q

I

F

A

A

W

K

I

L

11

293

F

A

A

W

K

I

L

G

Y

D

11

300

G

Y

D

R

C

D

A

G

W

L

11

34

A

E

N

G

P

H

L

L

V

E

10

57

V

T

L

P

C

K

F

Y

R

D

10

58

T

L

P

C

K

F

Y

R

D

P

10

80

K

W

T

K

L

T

S

D

Y

L

10

95

F

V

S

M

G

Y

H

K

K

T

10

117

G

S

D

S

D

A

S

L

V

I

10

129

L

T

L

E

D

Y

G

R

Y

K

10

152

V

A

L

D

L

Q

G

V

V

F

10

259

G

R

F

Y

Y

L

I

H

P

T

10

292

I

F

A

A

W

K

I

L

G

Y

10

7

L

V

L

I

S

I

C

W

A

D

9

14

W

A

D

H

L

S

D

N

Y

T

9

65

R

D

P

T

A

F

G

S

G

I

9

89

L

K

E

V

D

V

F

V

S

M

9

97

S

M

G

Y

H

K

K

T

Y

G

9

140

E

V

I

E

G

L

E

D

D

T

9

147

D

D

T

V

V

V

A

L

D

L

9

168

G

R

Y

N

L

N

F

H

E

A

9

291

Q

I

F

A

A

W

K

I

L

G

9

2

K

S

L

L

L

L

V

L

I

S

8

21

N

Y

T

L

D

H

D

R

A

I

8

24

L

D

H

D

R

A

I

H

I

Q

8

51

S

H

R

G

G

N

V

T

L

P

8

128

D

L

T

L

E

D

Y

G

R

Y

8

135

G

R

Y

K

C

E

V

I

E

G

8

154

L

D

L

Q

G

V

V

F

P

Y

8

159

V

V

F

P

Y

F

P

R

L

G

8

186

A

V

I

A

S

F

D

Q

L

Y

8

196

D

A

W

R

G

G

L

D

W

C

8

219

I

T

K

P

R

E

P

C

G

G

8

231

T

V

P

G

V

R

N

Y

G

F

8

278

A

C

L

N

D

G

A

Q

I

A

8

294

A

A

W

K

I

L

G

Y

D

R

8

12

I

C

W

A

D

H

L

S

D

N

7

42

V

E

A

E

Q

A

K

V

F

S

7

77

I

R

I

K

W

T

K

L

T

S

7

84

L

T

S

D

Y

L

K

E

V

D

7

86

S

D

Y

L

K

E

V

D

V

F

7

121

D

A

S

L

V

I

T

D

L

T

7

133

D

Y

G

R

Y

K

C

E

V

I

7

148

D

T

V

V

V

A

L

D

L

Q

7

200

G

G

L

D

W

C

N

A

G

W

7

211

S

D

G

S

V

Q

Y

P

I

T

7

213

G

S

V

Q

Y

P

I

T

K

P

7

230

N

T

V

P

G

V

R

N

Y

G

7

262

Y

Y

L

I

H

P

T

K

L

T

7

287

A

K

V

G

Q

I

F

A

A

W

7

288

K

V

G

Q

I

F

A

A

W

K

7

299

L

G

Y

D

R

C

D

A

G

W

7

329

E

A

A

V

R

F

V

G

F

P

7

18

L

S

D

N

Y

T

L

D

H

D

6

28

R

A

I

H

I

Q

A

E

N

G

6

43

E

A

E

Q

A

K

V

F

S

H

6

49

V

F

S

H

R

G

G

N

V

T

6

59

L

P

C

K

F

Y

R

D

P

T

6

64

Y

R

D

P

T

A

F

G

S

G

6

72

S

G

I

H

K

I

R

I

K

W

6

90

K

E

V

D

V

F

V

S

M

G

6

106

G

G

Y

Q

G

R

V

F

L

K

6

107

G

Y

Q

G

R

V

F

L

K

G

6

108

Y

Q

G

R

V

F

L

K

G

G

6

126

I

T

D

L

T

L

E

D

Y

G

6

170

Y

N

L

N

F

H

E

A

Q

Q

6

177

A

Q

Q

A

C

L

D

Q

D

A

6

198

W

R

G

G

L

D

W

C

N

A

6

246

S

R

Y

D

V

F

C

F

T

S

6

274

E

A

V

Q

A

C

L

N

D

G

6

301

Y

D

R

C

D

A

G

W

L

A

6

303

R

C

D

A

G

W

L

A

D

G

6

318

I

S

R

P

R

R

R

C

S

P

6

319

S

R

P

R

R

R

C

S

P

T

6

330

A

A

V

R

F

V

G

F

P

D

6

331

A

V

R

F

V

G

F

P

D

K

6

10

I

S

I

C

W

A

D

H

L

S

5

26

H

D

R

A

I

H

I

Q

A

E

5

27

D

R

A

I

H

I

Q

A

E

N

5

36

N

G

P

H

L

L

V

E

A

E

5

37

G

P

H

L

L

V

E

A

E

Q

5

53

R

G

G

N

V

T

L

P

C

K

5

71

G

S

G

I

H

K

I

R

I

K

5

82

T

K

L

T

S

D

Y

L

K

E

5

93

D

V

F

V

S

M

G

Y

H

K

5

96

V

S

M

G

Y

H

K

K

T

Y

5

111

R

V

F

L

K

G

G

S

D

S

5

112

V

F

L

K

G

G

S

D

S

D

5

114

L

K

G

G

S

D

S

D

A

S

5

119

D

S

D

A

S

L

V

I

T

D

5

149

T

V

V

V

A

L

D

L

Q

G

5

161

F

P

Y

F

P

R

L

G

R

Y

5

176

E

A

Q

Q

A

C

L

D

Q

D

5

189

A

S

F

D

Q

L

Y

D

A

W

5

195

Y

D

A

W

R

G

G

L

D

W

5

204

W

C

N

A

G

W

L

S

D

G

5

205

C

N

A

G

W

L

S

D

G

S

5

208

G

W

L

S

D

G

S

V

Q

Y

5

215

V

Q

Y

P

I

T

K

P

R

E

5

218

P

I

T

K

P

R

E

P

C

G

5

234

G

V

R

N

Y

G

F

W

D

K

5

249

D

V

F

C

F

T

S

N

F

N

5

253

F

T

S

N

F

N

G

R

F

Y

5

266

H

P

T

K

L

T

Y

D

E

A

5

304

C

D

A

G

W

L

A

D

G

S

5

307

G

W

L

A

D

G

S

V

R

Y

5

312

G

S

V

R

Y

P

I

S

R

P

5

313

S

V

R

Y

P

I

S

R

P

R

5

314

V

R

Y

P

I

S

R

P

R

R

5

317

P

I

S

R

P

R

R

R

C

S

5

322

R

R

R

C

S

P

T

E

A

A

5

328

T

E

A

A

V

R

F

V

G

F

5

341

K

H

K

L

Y

G

V

Y

C

F

5

20

D

N

Y

T

L

D

H

D

R

A

4

30

I

H

I

Q

A

E

N

G

P

H

4

41

L

V

E

A

E

Q

A

K

V

F

4

46

Q

A

K

V

F

S

H

R

G

G

4

54

G

G

N

V

T

L

P

C

K

F

4

62

K

F

Y

R

D

P

T

A

F

G

4

81

W

T

K

L

T

S

D

Y

L

K

4

94

V

F

V

S

M

G

Y

H

K

K

4

127

T

D

L

T

L

E

D

Y

G

R

4

137

Y

K

C

E

V

I

E

G

L

E

4

139

C

E

V

I

E

G

L

E

D

D

4

172

L

N

F

H

E

A

Q

Q

A

C

4

190

S

F

D

Q

L

Y

D

A

W

R

4

197

A

W

R

G

G

L

D

W

C

N

4

214

S

V

Q

Y

P

I

T

K

P

R

4

217

Y

P

I

T

K

P

R

E

P

C

4

228

G

Q

N

T

V

P

G

V

R

N

4

238

Y

G

F

W

D

K

D

K

S

R

4

245

K

S

R

Y

D

V

F

C

F

T

4

251

F

C

F

T

S

N

F

N

G

R

4

268

T

K

L

T

Y

D

E

A

V

Q

4

276

V

Q

A

C

L

N

D

G

A

Q

4

282

D

G

A

Q

I

A

K

V

G

Q

4

284

A

Q

I

A

K

V

G

Q

I

F

4

316

Y

P

I

S

R

P

R

R

R

C

4

324

R

C

S

P

T

E

A

A

V

R

4

332

V

R

F

V

G

F

P

D

K

K

4

13

C

W

A

D

H

L

S

D

N

Y

3

19

S

D

N

Y

T

L

D

H

D

R

3

25

D

H

D

R

A

I

H

I

Q

A

3

38

P

H

L

L

V

E

A

E

Q

A

3

52

H

R

G

G

N

V

T

L

P

C

3

56

N

V

T

L

P

C

K

F

Y

R

3

63

F

Y

R

D

P

T

A

F

G

S

3

74

I

H

K

I

R

I

K

W

T

K

3

79

I

K

W

T

K

L

T

S

D

Y

3

98

M

G

Y

H

K

K

T

Y

G

G

3

134

Y

G

R

Y

K

C

E

V

I

E

3

138

K

C

E

V

I

E

G

L

E

D

3

146

E

D

D

T

V

V

V

A

L

D

3

156

L

Q

G

V

V

F

P

Y

F

P

3

175

H

E

A

Q

Q

A

C

L

D

Q

3

202

L

D

W

C

N

A

G

W

L

S

3

207

A

G

W

L

S

D

G

S

V

Q

3

221

K

P

R

E

P

C

G

G

Q

N

3

229

Q

N

T

V

P

G

V

R

N

Y

3

235

V

R

N

Y

G

F

W

D

K

D

3

239

G

F

W

D

K

D

K

S

R

Y

3

244

D

K

S

R

Y

D

V

F

C

F

3

258

N

G

R

F

Y

Y

L

I

H

P

3

260

R

F

Y

Y

L

I

H

P

T

K

3

265

I

H

P

T

K

L

T

Y

D

E

3

306

A

G

W

L

A

D

G

S

V

R

3

310

A

D

G

S

V

R

Y

P

I

S

3

320

R

P

R

R

R

C

S

P

T

E

3

321

P

R

R

R

C

S

P

T

E

A

3

333

R

F

V

G

F

P

D

K

K

H

3

334

F

V

G

F

P

D

K

K

H

K

3

340

K

K

H

K

L

Y

G

V

Y

C

3

344

L

Y

G

V

Y

C

F

R

A

Y

3

345

Y

G

V

Y

C

F

R

A

Y

N

3

44

A

E

Q

A

K

V

F

S

H

R

2

47

A

K

V

F

S

H

R

G

G

N

2

60

P

C

K

F

Y

R

D

P

T

A

2

67

P

T

A

F

G

S

G

I

H

K

2

91

E

V

D

V

F

V

S

M

G

Y

2

99

G

Y

H

K

K

T

Y

G

G

Y

2

104

T

Y

G

G

Y

Q

G

R

V

F

2

110

G

R

V

F

L

K

G

G

S

D

2

160

V

F

P

Y

F

P

R

L

G

R

2

164

F

P

R

L

G

R

Y

N

L

N

2

165

P

R

L

G

R

Y

N

L

N

F

2

169

R

Y

N

L

N

F

H

E

A

Q

2

184

Q

D

A

V

I

A

S

F

D

Q

2

194

L

Y

D

A

W

R

G

G

L

D

2

199

R

G

G

L

D

W

C

N

A

G

2

203

D

W

C

N

A

G

W

L

S

D

2

216

Q

Y

P

I

T

K

P

R

E

P

2

222

P

R

E

P

C

G

G

Q

N

T

2

236

R

N

Y

G

F

W

D

K

D

K

2

243

K

D

K

S

R

Y

D

V

F

C

2

247

R

Y

D

V

F

C

F

T

S

N

2

257

F

N

G

R

F

Y

Y

L

I

H

2

273

D

E

A

V

Q

A

C

L

N

D

2

296

W

K

I

L

G

Y

D

R

C

D

2

302

D

R

C

D

A

G

W

L

A

D

2

325

C

S

P

T

E

A

A

V

R

F

2

337

F

P

D

K

K

H

K

L

Y

G

2

16

D

H

L

S

D

N

Y

T

L

D

1

61

C

K

F

Y

R

D

P

T

A

F

1

69

A

F

G

S

G

I

H

K

I

R

1

100

Y

H

K

K

T

Y

G

G

Y

Q

1

109

Q

G

R

V

F

L

K

G

G

S

1

167

L

G

R

Y

N

L

N

F

H

E

1

191

F

D

Q

L

Y

D

A

W

R

G

1

192

D

Q

L

Y

D

A

W

R

G

G

1

212

D

G

S

V

Q

Y

P

I

T

K

1

220

T

K

P

R

E

P

C

G

G

Q

1

225

P

C

G

G

Q

N

T

V

P

G

1

227

G

G

Q

N

T

V

P

G

V

R

1

232

V

P

G

V

R

N

Y

G

F

W

1

237

N

Y

G

F

W

D

K

D

K

S

1

240

F

W

D

K

D

K

S

R

Y

D

1

248

Y

D

V

F

C

F

T

S

N

F

1

272

Y

D

E

A

V

Q

A

C

L

N

1

295

A

W

K

I

L

G

Y

D

R

C

1

311

D

G

S

V

R

Y

P

I

S

R

1

336

G

F

P

D

K

K

H

K

L

Y

1

342

H

K

L

Y

G

V

Y

C

F

R

1

183

D

Q

D

A

V

I

A

S

F

D

−1

224

E

P

C

G

G

Q

N

T

V

P

−1

242

D

K

D

K

S

R

Y

D

V

F

−1

252

C

F

T

S

N

F

N

G

R

F

−1

281

N

D

G

A

Q

I

A

K

V

G

−1

66

D

P

T

A

F

G

S

G

I

H

−2

339

D

K

K

H

K

L

Y

G

V

Y

−2

233

P

G

V

R

N

Y

G

F

W

D

−3

151P3D4 v.2: HLA Peptide

Scoring Results A*0201 10-mers SYFPEITHI

SEQ. ID

Pos

1

2

3

4

5

6

7

8

9

0

score

NO.

37

L

L

V

P

T

K

V

T

G

I

27

Portion

87

V

L

L

G

R

K

A

V

V

V

27

of SEQ

377

G

A

L

W

K

A

I

E

S

L

23

ID NO:

12

R

A

L

H

I

V

V

E

S

I

20

5; each

28

K

M

K

Q

D

K

K

V

D

L

20

start

381

K

A

I

E

S

L

E

E

G

L

20

position

86

K

V

L

L

G

R

K

A

V

V

19

is

278

A

A

S

P

A

A

W

L

P

L

19

specified,

5

T

T

K

T

F

P

L

R

A

L

18

the length

88

L

L

G

R

K

A

V

V

V

S

18

of

233

G

F

I

F

K

T

I

A

P

L

18

peptide is

269

A

L

S

A

R

A

P

V

P

A

18

10 amino

369

D

L

A

G

S

G

Y

C

G

A

18

acids, the

7

K

T

F

P

L

R

A

L

H

I

17

end

20

S

I

R

D

H

S

G

Q

K

M

17

position

34

K

V

D

L

L

V

P

T

K

V

17

for each

183

T

L

E

E

K

R

K

E

K

A

17

peptide is

241

P

L

A

A

T

R

A

T

R

I

17

the start

361

Y

V

E

N

G

R

P

A

D

L

17

position

370

L

A

G

S

G

Y

C

G

A

L

17

plus nine

56

H

V

Q

F

V

G

S

Y

K

L

16

67

Y

S

N

D

G

E

H

W

T

V

16

164

V

C

L

S

G

A

P

H

E

V

16

238

T

I

A

P

L

A

A

T

R

A

16

8

T

F

P

L

R

A

L

H

I

V

15

29

M

K

Q

D

K

K

V

D

L

L

15

36

D

L

L

V

P

T

K

V

T

G

15

51

A

K

D

F

G

H

V

Q

F

V

15

103

I

S

G

S

F

C

R

N

K

L

15

106

S

F

C

R

N

K

L

K

Y

L

15

109

R

N

K

L

K

Y

L

A

F

L

15

175

W

K

Y

Q

A

V

T

A

T

L

15

196

Y

R

K

N

K

Q

L

M

R

L

15

223

S

P

G

G

G

S

P

R

G

L

15

226

G

G

S

P

R

G

L

G

F

I

15

234

F

I

F

K

T

I

A

P

L

A

15

276

V

P

A

A

S

P

A

A

W

L

15

385

S

L

E

E

G

L

G

G

K

Q

15

389

G

L

G

G

K

Q

K

D

K

E

15

399

R

K

A

E

N

G

P

H

L

L

15

38

L

V

P

T

K

V

T

G

I

I

14

64

K

L

A

Y

S

N

D

G

E

H

14

92

K

A

V

V

V

S

C

E

G

I

14

155

G

H

A

S

E

A

Y

K

K

V

14

202

L

M

R

L

Q

K

Q

A

E

K

14

231

G

L

G

F

I

F

K

T

I

A

14

270

L

S

A

R

A

P

V

P

A

A

14

306

S

L

S

P

Y

G

P

R

N

P

14

9

F

P

L

R

A

L

H

I

V

V

13

10

P

L

R

A

L

H

I

V

V

E

13

94

V

V

V

S

C

E

G

I

N

I

13

114

Y

L

A

F

L

H

K

R

M

N

13

157

A

S

E

A

Y

K

K

V

C

L

13

171

H

E

V

G

W

K

Y

Q

A

V

13

193

E

I

H

Y

R

K

N

K

Q

L

13

204

R

L

Q

K

Q

A

E

K

N

M

13

230

R

G

L

G

F

I

F

K

T

I

13

261

G

S

S

A

H

R

P

P

A

L

13

263

S

A

H

R

P

P

A

L

S

A

13

298

P

T

S

S

S

T

Y

D

S

L

13

320

R

H

S

P

S

G

G

G

G

L

13

335

H

C

Q

G

Q

K

H

N

V

L

13

343

V

L

A

R

G

K

P

Q

R

K

13

373

S

G

Y

C

G

A

L

W

K

A

13

378

A

L

W

K

A

I

E

S

L

E

13

2

L

E

H

T

T

K

T

F

P

L

12

11

L

R

A

L

H

I

V

V

E

S

12

13

A

L

H

I

V

V

E

S

I

R

12

15

H

I

V

V

E

S

I

R

D

H

12

30

K

Q

D

K

K

V

D

L

L

V

12

165

C

L

S

G

A

P

H

E

V

G

12

201

Q

L

M

R

L

Q

K

Q

A

E

12

208

Q

A

E

K

N

M

K

K

K

I

12

284

W

L

P

L

R

T

P

W

T

R

12

307

L

S

P

Y

G

P

R

N

P

L

12

26

G

Q

K

M

K

Q

D

K

K

V

11

42

K

V

T

G

I

I

T

Q

G

A

11

59

F

V

G

S

Y

K

L

A

Y

S

11

78

Q

D

E

K

Q

R

K

D

K

V

11

115

L

A

F

L

H

K

R

M

N

T

11

117

F

L

H

K

R

M

N

T

N

P

11

182

A

T

L

E

E

K

R

K

E

K

11

236

F

K

T

I

A

P

L

A

A

T

11

237

K

T

I

A

P

L

A

A

T

R

11

239

I

A

P

L

A

A

T

R

A

T

11

267

P

P

A

L

S

A

R

A

P

V

11

283

A

W

L

P

L

R

T

P

W

T

11

328

G

L

K

K

P

A

R

H

C

Q

11

334

R

H

C

Q

G

Q

K

H

N

V

11

374

G

Y

C

G

A

L

W

K

A

I

11

45

G

I

I

T

Q

G

A

K

D

F

10

48

T

Q

G

A

K

D

F

G

H

V

10

89

L

G

R

K

A

V

V

V

S

C

10

95

V

V

S

C

E

G

I

N

I

S

10

100

G

I

N

I

S

G

S

F

C

R

10

102

N

I

S

G

S

F

C

R

N

K

10

111

K

L

K

Y

L

A

F

L

H

K

10

112

L

K

Y

L

A

F

L

H

K

R

10

160

A

Y

K

K

V

C

L

S

G

A

10

167

S

G

A

P

H

E

V

G

W

K

10

173

V

G

W

K

Y

Q

A

V

T

A

10

178

Q

A

V

T

A

T

L

E

E

K

10

212

N

M

K

K

K

I

D

K

Y

T

10

244

A

T

R

A

T

R

I

G

H

P

10

249

R

I

G

H

P

G

G

R

T

P

10

272

A

R

A

P

V

P

A

A

S

P

10

274

A

P

V

P

A

A

S

P

A

A

10

344

L

A

R

G

K

P

Q

R

K

P

10

1

M

L

E

H

T

T

K

T

F

P

9

33

K

K

V

D

L

L

V

P

T

K

9

46

I

I

T

Q

G

A

K

D

F

G

9

47

I

T

Q

G

A

K

D

F

G

H

9

80

E

K

Q

R

K

D

K

V

L

L

9

85

D

K

V

L

L

G

R

K

A

V

9

121

R

M

N

T

N

P

S

R

R

P

9

137

S

R

I

F

W

R

Q

E

K

A

9

138

R

I

F

W

R

Q

E

K

A

D

9

216

K

I

D

K

Y

T

E

S

P

G

9

264

A

H

R

P

P

A

L

S

A

R

9

271

S

A

R

A

P

V

P

A

A

S

9

280

S

P

A

A

W

L

P

L

R

T

9

281

P

A

A

W

L

P

L

R

T

P

9

291

W

T

R

P

S

S

C

P

T

S

9

302

S

T

Y

D

S

L

S

P

Y

G

9

353

P

K

S

E

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S

G

G

G

1

333

A

R

H

C

Q

G

Q

K

H

N

1

339

Q

K

H

N

V

L

A

R

G

K

1

345

A

R

G

K

P

Q

R

K

P

K

1

354

K

S

E

N

N

S

W

Y

V

E

1

367

P

A

D

L

A

G

S

G

Y

C

1

372

G

S

G

Y

C

G

A

L

W

K

1

393

K

Q

K

D

K

E

R

K

A

E

1

397

K

E

R

K

A

E

N

G

P

H

1

19

E

S

I

R

D

H

S

G

Q

K

−1

99

E

G

I

N

I

S

G

S

F

C

−1

122

M

N

T

N

P

S

R

R

P

Y

−1

136

P

S

R

I

F

W

R

Q

E

K

−1

143

Q

E

K

A

D

G

G

S

C

C

−1

153

P

Q

G

H

A

S

E

A

Y

K

−1

224

P

G

G

G

S

P

R

G

L

G

−1

341

H

N

V

L

A

R

G

K

P

Q

−1

363

E

N

G

R

P

A

D

L

A

G

−1

387

E

E

G

L

G

G

K

Q

K

D

−1

210

E

K

N

M

K

K

K

I

D

K

−2

317

P

N

P

R

H

S

P

S

G

G

−2

319

P

R

H

S

P

S

G

G

G

G

−2

3

E

H

T

T

K

T

F

P

L

R

−3

186

E

K

R

K

E

K

A

E

I

H

−3

349

P

Q

R

K

P

K

S

E

N

N

−3

TABLE XXXVII

151P3D4 v.1: HLA Peptide

Scoring Results A*0202 10-mers SYFPEITHI

SEQ. ID

Pos

1

2

3

4

5

6

7

8

9

0

score

NO.

293

F

A

A

W

K

I

L

G

Y

D

5

Portion

329

E

A

A

V

R

F

V

G

F

P

5

of SEQ

13

C

W

A

D

H

L

S

D

N

Y

3

ID NO:

27

D

R

A

I

H

I

Q

A

E

N

3

3; each

32

I

Q

A

E

N

G

P

H

L

L

3

start

42

V

E

A

E

Q

A

K

V

F

S

3

position

45

E

Q

A

K

V

F

S

H

R

G

3

is

67

P

T

A

F

G

S

G

I

H

K

3

specified,

120

S

D

A

S

L

V

I

T

D

L

3

the length

151

V

V

A

L

D

L

Q

G

V

V

3

of

175

H

E

A

Q

Q

A

C

L

D

Q

3

peptide is

178

Q

Q

A

C

L

D

Q

D

A

V

3

10 amino

184

Q

D

A

V

I

A

S

F

D

Q

3

acids, the

187

V

I

A

S

F

D

Q

L

Y

D

3

end

195

Y

D

A

W

R

G

G

L

D

W

3

position

205

C

N

A

G

W

L

S

D

G

S

3

for each

273

D

E

A

V

Q

A

C

L

N

D

3

peptide is

276

V

Q

A

C

L

N

D

G

A

Q

3

the start

282

D

G

A

Q

I

A

K

V

G

Q

3

position

285

Q

I

A

K

V

G

Q

I

F

A

3

plus nine

292

I

F

A

A

W

K

I

L

G

Y

3

294

A

A

W

K

I

L

G

Y

D

R

3

304

C

D

A

G

W

L

A

D

G

S

3

308

W

L

A

D

G

S

V

R

Y

P

3

328

T

E

A

A

V

R

F

V

G

F

3

330

A

A

V

R

F

V

G

F

P

D

3

14

W

A

D

H

L

S

D

N

Y

T

2

28

R

A

I

H

I

Q

A

E

N

G

2

33

Q

A

E

N

G

P

H

L

L

V

2

43

E

A

E

Q

A

K

V

F

S

H

2

46

Q

A

K

V

F

S

H

R

G

G

2

68

T

A

F

G

S

G

I

H

K

I

2

121

D

A

S

L

V

I

T

D

L

T

2

152

V

A

L

D

L

Q

G

V

V

F

2

176

E

A

Q

Q

A

C

L

D

Q

D

2

179

Q

A

C

L

D

Q

D

A

V

I

2

185

D

A

V

I

A

S

F

D

Q

L

2

188

I

A

S

F

D

Q

L

Y

D

A

2

196

D

A

W

R

G

G

L

D

W

C

2

206

N

A

G

W

L

S

D

G

S

V

2

274

E

A

V

Q

A

C

L

N

D

G

2

277

Q

A

C

L

N

D

G

A

Q

I

2

283

G

A

Q

I

A

K

V

G

Q

I

2

286

I

A

K

V

G

Q

I

F

A

A

2

305

D

A

G

W

L

A

D

G

S

V

2

309

L

A

D

G

S

V

R

Y

P

I

2

15

A

D

H

L

S

D

N

Y

T

L

1

29

A

I

H

I

Q

A

E

N

G

P

1

34

A

E

N

G

P

H

L

L

V

E

1

44

A

E

Q

A

K

V

F

S

H

R

1

47

A

K

V

F

S

H

R

G

G

N

1

69

A

F

G

S

G

I

H

K

I

R

1

122

A

S

L

V

I

T

D

L

T

L

1

153

A

L

D

L

Q

G

V

V

F

P

1

177

A

Q

Q

A

C

L

D

Q

D

A

1

180

A

C

L

D

Q

D

A

V

I

A

1

186

A

V

I

A

S

F

D

Q

L

Y

1

189

A

S

F

D

Q

L

Y

D

A

W

1

197

A

W

R

G

G

L

D

W

C

N

1

207

A

G

W

L

S

D

G

S

V

Q

1

275

A

V

Q

A

C

L

N

D

G

A

1

278

A

C

L

N

D

G

A

Q

I

A

1

284

A

Q

I

A

K

V

G

Q

I

F

1

287

A

K

V

G

Q

I

F

A

A

W

1

295

A

W

K

I

L

G

Y

D

R

C

1

306

A

G

W

L

A

D

G

S

V

R

1

310

A

D

G

S

V

R

Y

P

I

S

1

331

A

V

R

F

V

G

F

P

D

K

1

151P3D4 v.2: HLA Peptide

Scoring Results A*0202 10-mers SYFPEITHI

SEQ. ID

Pos

1

2

3

4

5

6

7

8

9

0

score

NO.

242

L

A

A

T

R

A

T

R

I

G

5

Portion

277

P

A

A

S

P

A

A

W

L

P

5

of SEQ

281

P

A

A

W

L

P

L

R

T

P

5

ID NO:

272

A

R

A

P

V

P

A

A

S

P

4

5; each

11

L

R

A

L

H

I

V

V

E

S

3

start

49

Q

G

A

K

D

F

G

H

V

Q

3

position

64

K

L

A

Y

S

N

D

G

E

H

3

is

91

R

K

A

V

V

V

S

C

E

G

3

specified,

114

Y

L

A

F

L

H

K

R

M

N

3

the length

144

E

K

A

D

G

G

S

C

C

P

3

of

155

G

H

A

S

E

A

Y

K

K

V

3

peptide is

158

S

E

A

Y

K

K

V

C

L

S

3

10 amino

167

S

G

A

P

H

E

V

G

W

K

3

acids, the

177

Y

Q

A

V

T

A

T

L

E

E

3

end

180

V

T

A

T

L

E

E

K

R

K

3

position

190

E

K

A

E

I

H

Y

R

K

N

3

for each

207

K

Q

A

E

K

N

M

K

K

K

3

peptide is

238

T

I

A

P

L

A

A

T

R

A

3

the start

241

P

L

A

A

T

R

A

T

R

I

3

position

243

A

A

T

R

A

T

R

I

G

H

3

plus nine

245

T

R

A

T

R

I

G

H

P

G

3

258

P

R

A

G

S

S

A

H

R

P

3

262

S

S

A

H

R

P

P

A

L

S

3

267

P

P

A

L

S

A

R

A

P

V

3

270

L

S

A

R

A

P

V

P

A

A

3

276

V

P

A

A

S

P

A

A

W

L

3

278

A

A

S

P

A

A

W

L

P

L

3

280

S

P

A

A

W

L

P

L

R

T

3

282

A

A

W

L

P

L

R

T

P

W

3

331

K

P

A

R

H

C

Q

G

Q

K

3

343

V

L

A

R

G

K

P

Q

R

K

3

366

R

P

A

D

L

A

G

S

G

Y

3

369

D

L

A

G

S

G

Y

C

G

A

3

376

C

G

A

L

W

K

A

I

E

S

3

380

W

K

A

I

E

S

L

E

E

G

3

399

R

K

A

E

N

G

P

H

L

L

3

12

R

A

L

H

I

V

V

E

S

I

2

50

G

A

K

D

F

G

H

V

Q

F

2

65

L

A

Y

S

N

D

G

E

H

W

2

92

K

A

V

V

V

S

C

E

G

I

2

115

L

A

F

L

H

K

R

M

N

T

2

145

K

A

D

G

G

S

C

C

P

Q

2

156

H

A

S

E

A

Y

K

K

V

C

2

159

E

A

Y

K

K

V

C

L

S

G

2

168

G

A

P

H

E

V

G

W

K

Y

2

178

Q

A

V

T

A

T

L

E

E

K

2

181

T

A

T

L

E

E

K

R

K

E

2

191

K

A

E

I

H

Y

R

K

N

K

2

208

Q

A

E

K

N

M

K

K

K

I

2

239

I

A

P

L

A

A

T

R

A

T

2

246

R

A

T

R

I

G

H

P

G

G

2

259

R

A

G

S

S

A

H

R

P

P

2

263

S

A

H

R

P

P

A

L

S

A

2

268

P

A

L

S

A

R

A

P

V

P

2

271

S

A

R

A

P

V

P

A

A

S

2

273

R

A

P

V

P

A

A

S

P

A

2

332

P

A

R

H

C

Q

G

Q

K

H

2

344

L

A

R

G

K

P

Q

R

K

P

2

367

P

A

D

L

A

G

S

G

Y

C

2

370

L

A

G

S

G

Y

C

G

A

L

2

377

G

A

L

W

K

A

I

E

S

L

2

381

K

A

I

E

S

L

E

E

G

L

2

13

A

L

H

I

V

V

E

S

I

R

1

51

A

K

D

F

G

H

V

Q

F

V

1

66

A

Y

S

N

D

G

E

H

W

T

1

93

A

V

V

V

S

C

E

G

I

N

1

116

A

F

L

H

K

R

M

N

T

N

1

146

A

D

G

G

S

C

C

P

Q

G

1

157

A

S

E

A

Y

K

K

V

C

L

1

160

A

Y

K

K

V

C

L

S

G

A

1

169

A

P

H

E

V

G

W

K

Y

Q

1

179

A

V

T

A

T

L

E

E

K

R

1

182

A

T

L

E

E

K

R

K

E

K

1

192

A

E

I

H

Y

R

K

N

K

Q

1

209

A

E

K

N

M

K

K

K

I

D

1

240

A

P

L

A

A

T

R

A

T

R

1

244

A

T

R

A

T

R

I

G

H

P

1

247

A

T

R

I

G

H

P

G

G

R

1

260

A

G

S

S

A

H

R

P

P

A

1

264

A

H

R

P

P

A

L

S

A

R

1

269

A

L

S

A

R

A

P

V

P

A

1

274

A

P

V

P

A

A

S

P

A

A

1

279

A

S

P

A

A

W

L

P

L

R

1

283

A

W

L

P

L

R

T

P

W

T

1

333

A

R

H

C

Q

G

Q

K

H

N

1

345

A

R

G

K

P

Q

R

K

P

K

1

368

A

D

L

A

G

S

G

Y

C

G

1

371

A

G

S

G

Y

C

G

A

L

W

1

378

A

L

W

K

A

I

E

S

L

E

1

382

A

I

E

S

L

E

E

G

L

G

1

TABLE XXXVIII 151P3D4 v.1: HLA Peptide Scoring Results A*0203 10-mers SYFPEITHI SEQ. ID Pos 1 2 3 4 5 6 7 8 9 0 score NO. 286 I A K V G Q I F A A 19 Portion 322 R R R C S P T E A A 19 of SEQ 287 A K V G Q I F A A W 17 ID NO: 323 R R C S P T E A A V 17 3; each 6 L L V L I S I C W A 10 start 20 D N Y T L D H D R A 10 position 25 D H D R A I H I Q A 10 is 35 E N G P H L L V E A 10 specified, 38 P H L L V E A E Q A 10 the length 60 P C K F Y R D P T A 10 of 113 F L K G G S D S D A 10 peptide is 144 G L E D D T V V V A 10 10 amino 168 G R Y N L N F H E A 10 acids, the 171 N L N F H E A Q Q A 10 end 177 A Q Q A C L D Q D A 10 position 180 A C L D Q D A V I A 10 for each 188 I A S F D Q L Y D A 10 peptide is 198 W R G G L D W C N A 10 the start 266 H P T K L T Y D E A 10 position 269 K L T Y D E A V Q A 10 plus nine 275 A V Q A C L N D G A 10 278 A C L N D G A Q I A 10 285 Q I A K V G Q I F A 10 297 K I L G Y D R C D A 10 301 Y D R C D A G W L A 10 321 P R R R C S P T E A 10 343 K L Y G V Y C F R A 10 7 L V L I S I C W A D 9 21 N Y T L D H D R A I 9 26 H D R A I H I Q A E 9 36 N G P H L L V E A E 9 39 H L L V E A E Q A K 9 61 C K F Y R D P T A F 9 114 L K G G S D S D A S 9 145 L E D D T V V V A L 9 169 R Y N L N F H E A Q 9 172 L N F H E A Q Q A C 9 178 Q Q A C L D Q D A V 9 181 C L D Q D A V I A S 9 189 A S F D Q L Y D A W 9 199 R G G L D W C N A G 9 267 P T K L T Y D E A V 9 270 L T Y D E A V Q A C 9 276 V Q A C L N D G A Q 9 279 C L N D G A Q I A K 9 298 I L G Y D R C D A G 9 302 D R C D A G W L A D 9 344 L Y G V Y C F R A Y 9 8 V L I S I C W A D H 8 22 Y T L D H D R A I H 8 27 D R A I H I Q A E N 8 37 G P H L L V E A E Q 8 40 L L V E A E Q A K V 8 62 K F Y R D P T A F G 8 115 K G G S D S D A S L 8 146 E D D T V V V A L D 8 170 Y N L N F H E A Q Q 8 173 N F H E A Q Q A C L 8 179 Q A C L D Q D A V I 8 182 L D Q D A V I A S F 8 190 S F D Q L Y D A W R 8 200 G G L D W C N A G W 8 268 T K L T Y D E A V Q 8 271 T Y D E A V Q A C L 8 277 Q A C L N D G A Q I 8 280 L N D G A Q I A K V 8 288 K V G Q I F A A W K 8 299 L G Y D R C D A G W 8 303 R C D A G W L A D G 8 324 R C S P T E A A V R 8 345 Y G V Y C F R A Y N 8 151P3D4 v.2: HLA Peptide Scoring Results A*0203 10-mers SYFPEITHI SEQ. ID Pos 1 2 3 4 5 6 7 8 9 0 score NO. 235 I F K T I A P L A A 19 Portion 270 L S A R A P V P A A 19 of SEQ 274 A P V P A A S P A A 19 ID NO: 265 H R P P A L S A R A 18 5; each 236 F K T I A P L A A T 17 start 271 S A R A P V P A A S 17 position 275 P V P A A S P A A W 17 is 4 H T T K T F P L R A 10 specified, 42 K V T G I I T Q G A 10 the length 57 V Q F V G S Y K L A 10 of 84 K D K V L L G R K A 10 peptide is 107 F C R N K L K Y L A 10 10 amino 137 S R I F W R Q E K A 10 acids, the 148 G G S C C P Q G H A 10 end 151 C C P Q G H A S E A 10 position 160 A Y K K V C L S G A 10 for each 170 P H E V G W K Y Q A 10 peptide is 173 V G W K Y Q A V T A 10 the start 183 T L E E K R K E K A 10 position 200 K Q L M R L Q K Q A 10 plus nine 231 G L G F I F K T I A 10 234 F I F K T I A P L A 10 238 T I A P L A A T R A 10 251 G H P G G R T P R A 10 255 G R T P R A G S S A 10 260 A G S S A H R P P A 10 263 S A H R P P A L S A 10 269 A L S A R A P V P A 10 273 R A P V P A A S P A 10 324 S G G G G L K K P A 10 336 C Q G Q K H N V L A 10 359 S W Y V E N G R P A 10 362 V E N G R P A D L A 10 369 D L A G S G Y C G A 10 373 S G Y C G A L W K A 10 392 G K Q K D K E R K A 10 5 T T K T F P L R A L 9 43 V T G I I T Q G A K 9 58 Q F V G S Y K L A Y 9 85 D K V L L G R K A V 9 108 C R N K L K Y L A F 9 138 R I F W R Q E K A D 9 149 G S C C P Q G H A S 9 152 C P Q G H A S E A Y 9 161 Y K K V C L S G A P 9 171 H E V G W K Y Q A V 9 174 G W K Y Q A V T A T 9 184 L E E K R K E K A E 9 201 Q L M R L Q K Q A E 9 232 L G F I F K T I A P 9 239 I A P L A A T R A T 9 252 H P G G R T P R A G 9 256 R T P R A G S S A H 9 261 G S S A H R P P A L 9 264 A H R P P A L S A R 9 266 R P P A L S A R A P 9 325 G G G G L K K P A R 9 337 Q G Q K H N V L A R 9 360 W Y V E N G R P A D 9 363 E N G R P A D L A G 9 370 L A G S G Y C G A L 9 374 G Y C G A L W K A I 9 393 K Q K D K E R K A E 9 6 T K T F P L R A L H 8 44 T G I I T Q G A K D 8 59 F V G S Y K L A Y S 8 86 K V L L G R K A V V 8 109 R N K L K Y L A F L 8 139 I F W R Q E K A D G 8 150 S C C P Q G H A S E 8 153 P Q G H A S E A Y K 8 162 K K V C L S G A P H 8 172 E V G W K Y Q A V T 8 175 W K Y Q A V T A T L 8 185 E E K R K E K A E I 8 202 L M R L Q K Q A E K 8 233 G F I F K T I A P L 8 237 K T I A P L A A T R 8 240 A P L A A T R A T R 8 253 P G G R T P R A G S 8 257 T P R A G S S A H R 8 262 S S A H R P P A L S 8 267 P P A L S A R A P V 8 272 A R A P V P A A S P 8 276 V P A A S P A A W L 8 326 G G G L K K P A R H 8 338 G Q K H N V L A R G 8 361 Y V E N G R P A D L 8 364 N G R P A D L A G S 8 371 A G S G Y C G A L W 8 375 Y C G A L W K A I E 8 394 Q K D K E R K A E N 8

TABLE XXXIX

151P3D4 v.1: HLA Peptide

Scoring Results A3 10-mers SYFPEITHI

SEQ. ID

Pos

1

2

3

4

5

6

7

8

9

0

score

NO.

288

K

V

G

Q

I

F

A

A

W

K

30

Portion

263

Y

L

I

H

P

T

K

L

T

Y

26

of SEQ

331

A

V

R

F

V

G

F

P

D

K

26

ID NO:

186

A

V

I

A

S

F

D

Q

L

Y

24

3; each

234

G

V

R

N

Y

G

F

W

D

K

24

start

39

H

L

L

V

E

A

E

Q

A

K

23

position

41

L

V

E

A

E

Q

A

K

V

F

23

is

93

D

V

F

V

S

M

G

Y

H

K

23

specified,

269

K

L

T

Y

D

E

A

V

Q

A

23

the length

260

R

F

Y

Y

L

I

H

P

T

K

22

of

279

C

L

N

D

G

A

Q

I

A

K

22

peptide is

111

R

V

F

L

K

G

G

S

D

S

21

10 amino

166

R

L

G

R

Y

N

L

N

F

H

21

acids, the

324

R

C

S

P

T

E

A

A

V

R

21

end

8

V

L

I

S

I

C

W

A

D

H

20

position

236

R

N

Y

G

F

W

D

K

D

K

20

for each

334

F

V

G

F

P

D

K

K

H

K

20

peptide is

144

G

L

E

D

D

T

V

V

V

A

19

the start

193

Q

L

Y

D

A

W

R

G

G

L

19

position

343

K

L

Y

G

V

Y

C

F

R

A

19

plus nine

17

H

L

S

D

N

Y

T

L

D

H

18

74

I

H

K

I

R

I

K

W

T

K

18

128

D

L

T

L

E

D

Y

G

R

Y

18

152

V

A

L

D

L

Q

G

V

V

F

18

153

A

L

D

L

Q

G

V

V

F

P

18

306

A

G

W

L

A

D

G

S

V

R

18

313

S

V

R

Y

P

I

S

R

P

R

18

48

K

V

F

S

H

R

G

G

N

V

17

91

E

V

D

V

F

V

S

M

G

Y

17

151

V

V

A

L

D

L

Q

G

V

V

17

3

S

L

L

L

L

V

L

I

S

I

16

4

L

L

L

L

V

L

I

S

I

C

16

78

R

I

K

W

T

K

L

T

S

D

16

88

Y

L

K

E

V

D

V

F

V

S

16

113

F

L

K

G

G

S

D

S

D

A

16

124

L

V

I

T

D

L

T

L

E

D

16

129

L

T

L

E

D

Y

G

R

Y

K

16

149

T

V

V

V

A

L

D

L

Q

G

16

155

D

L

Q

G

V

V

F

P

Y

F

16

171

N

L

N

F

H

E

A

Q

Q

A

16

231

T

V

P

G

V

R

N

Y

G

F

16

297

K

I

L

G

Y

D

R

C

D

A

16

53

R

G

G

N

V

T

L

P

C

K

15

56

N

V

T

L

P

C

K

F

Y

R

15

76

K

I

R

I

K

W

T

K

L

T

15

125

V

I

T

D

L

T

L

E

D

Y

15

201

G

L

D

W

C

N

A

G

W

L

15

208

G

W

L

S

D

G

S

V

Q

Y

15

212

D

G

S

V

Q

Y

P

I

T

K

15

214

S

V

Q

Y

P

I

T

K

P

R

15

275

A

V

Q

A

C

L

N

D

G

A

15

284

A

Q

I

A

K

V

G

Q

I

F

15

7

L

V

L

I

S

I

C

W

A

D

14

11

S

I

C

W

A

D

H

L

S

D

14

40

L

L

V

E

A

E

Q

A

K

V

14

67

P

T

A

F

G

S

G

I

H

K

14

86

S

D

Y

L

K

E

V

D

V

F

14

106

G

G

Y

Q

G

R

V

F

L

K

14

140

E

V

I

E

G

L

E

D

D

T

14

141

V

I

E

G

L

E

D

D

T

V

14

159

V

V

F

P

Y

F

P

R

L

G

14

207

A

G

W

L

S

D

G

S

V

Q

14

221

K

P

R

E

P

C

G

G

Q

N

14

292

I

F

A

A

W

K

I

L

G

Y

14

307

G

W

L

A

D

G

S

V

R

Y

14

320

R

P

R

R

R

C

S

P

T

E

14

23

T

L

D

H

D

R

A

I

H

I

13

31

H

I

Q

A

E

N

G

P

H

L

13

62

K

F

Y

R

D

P

T

A

F

G

13

83

K

L

T

S

D

Y

L

K

E

V

13

104

T

Y

G

G

Y

Q

G

R

V

F

13

123

S

L

V

I

T

D

L

T

L

E

13

180

A

C

L

D

Q

D

A

V

I

A

13

298

I

L

G

Y

D

R

C

D

A

G

13

5

L

L

L

V

L

I

S

I

C

W

12

6

L

L

V

L

I

S

I

C

W

A

12

9

L

I

S

I

C

W

A

D

H

L

12

29

A

I

H

I

Q

A

E

N

G

P

12

34

A

E

N

G

P

H

L

L

V

E

12

44

A

E

Q

A

K

V

F

S

H

R

12

77

I

R

I

K

W

T

K

L

T

S

12

81

W

T

K

L

T

S

D

Y

L

K

12

96

V

S

M

G

Y

H

K

K

T

Y

12

122

A

S

L

V

I

T

D

L

T

L

12

130

T

L

E

D

Y

G

R

Y

K

C

12

150

V

V

V

A

L

D

L

Q

G

V

12

187

V

I

A

S

F

D

Q

L

Y

D

12

264

L

I

H

P

T

K

L

T

Y

D

12

277

Q

A

C

L

N

D

G

A

Q

I

12

291

Q

I

F

A

A

W

K

I

L

G

12

308

W

L

A

D

G

S

V

R

Y

P

12

314

V

R

Y

P

I

S

R

P

R

R

12

317

P

I

S

R

P

R

R

R

C

S

12

339

D

K

K

H

K

L

Y

G

V

Y

12

22

Y

T

L

D

H

D

R

A

I

H

11

50

F

S

H

R

G

G

N

V

T

L

11

71

G

S

G

I

H

K

I

R

I

K

11

79

I

K

W

T

K

L

T

S

D

Y

11

143

E

G

L

E

D

D

T

V

V

V

11

161

F

P

Y

F

P

R

L

G

R

Y

11

165

P

R

L

G

R

Y

N

L

N

F

11

181

C

L

D

Q

D

A

V

I

A

S

11

209

W

L

S

D

G

S

V

Q

Y

P

11

227

G

G

Q

N

T

V

P

G

V

R

11

285

Q

I

A

K

V

G

Q

I

F

A

11

318

I

S

R

P

R

R

R

C

S

P

11

325

C

S

P

T

E

A

A

V

R

F

11

328

T

E

A

A

V

R

F

V

G

F

11

332

V

R

F

V

G

F

P

D

K

K

11

28

R

A

I

H

I

Q

A

E

N

G

10

30

I

H

I

Q

A

E

N

G

P

H

10

58

T

L

P

C

K

F

Y

R

D

P

10

65

R

D

P

T

A

F

G

S

G

I

10

94

V

F

V

S

M

G

Y

H

K

K

10

95

F

V

S

M

G

Y

H

K

K

T

10

103

K

T

Y

G

G

Y

Q

G

R

V

10

158

G

V

V

F

P

Y

F

P

R

L

10

179

Q

A

C

L

D

Q

D

A

V

I

10

182

L

D

Q

D

A

V

I

A

S

F

10

239

G

F

W

D

K

D

K

S

R

Y

10

246

S

R

Y

D

V

F

C

F

T

S

10

249

D

V

F

C

F

T

S

N

F

N

10

253

F

T

S

N

F

N

G

R

F

Y

10

257

F

N

G

R

F

Y

Y

L

I

H

10

294

A

A

W

K

I

L

G

Y

D

R

10

315

R

Y

P

I

S

R

P

R

R

R

10

333

R

F

V

G

F

P

D

K

K

H

10

340

K

K

H

K

L

Y

G

V

Y

C

10

2

K

S

L

L

L

L

V

L

I

S

9

38

P

H

L

L

V

E

A

E

Q

A

9

73

G

I

H

K

I

R

I

K

W

T

9

138

K

C

E

V

I

E

G

L

E

D

9

170

Y

N

L

N

F

H

E

A

Q

Q

9

190

S

F

D

Q

L

Y

D

A

W

R

9

268

T

K

L

T

Y

D

E

A

V

Q

9

278

A

C

L

N

D

G

A

Q

I

A

9

281

N

D

G

A

Q

I

A

K

V

G

9

287

A

K

V

G

Q

I

F

A

A

W

9

303

R

C

D

A

G

W

L

A

D

G

9

330

A

A

V

R

F

V

G

F

P

D

9

341

K

H

K

L

Y

G

V

Y

C

F

9

13

C

W

A

D

H

L

S

D

N

Y

8

15

A

D

H

L

S

D

N

Y

T

L

8

90

K

E

V

D

V

F

V

S

M

G

8

115

K

G

G

S

D

S

D

A

S

L

8

142

I

E

G

L

E

D

D

T

V

V

8

154

L

D

L

Q

G

V

V

F

P

Y

8

160

V

F

P

Y

F

P

R

L

G

R

8

183

D

Q

D

A

V

I

A

S

F

D

8

197

A

W

R

G

G

L

D

W

C

N

8

218

P

I

T

K

P

R

E

P

C

G

8

223

R

E

P

C

G

G

Q

N

T

V

8

229

Q

N

T

V

P

G

V

R

N

Y

8

242

D

K

D

K

S

R

Y

D

V

F

8

243

K

D

K

S

R

Y

D

V

F

C

8

299

L

G

Y

D

R

C

D

A

G

W

8

300

G

Y

D

R

C

D

A

G

W

L

8

321

P

R

R

R

C

S

P

T

E

A

8

322

R

R

R

C

S

P

T

E

A

A

8

323

R

R

C

S

P

T

E

A

A

V

8

12

I

C

W

A

D

H

L

S

D

N

7

35

E

N

G

P

H

L

L

V

E

A

7

49

V

F

S

H

R

G

G

N

V

T

7

51

S

H

R

G

G

N

V

T

L

P

7

61

C

K

F

Y

R

D

P

T

A

F

7

63

F

Y

R

D

P

T

A

F

G

S

7

66

D

P

T

A

F

G

S

G

I

H

7

69

A

F

G

S

G

I

H

K

I

R

7

75

H

K

I

R

I

K

W

T

K

L

7

99

G

Y

H

K

K

T

Y

G

G

Y

7

101

H

K

K

T

Y

G

G

Y

Q

G

7

102

K

K

T

Y

G

G

Y

Q

G

R

7

116

G

G

S

D

S

D

A

S

L

V

7

117

G

S

D

S

D

A

S

L

V

I

7

133

D

Y

G

R

Y

K

C

E

V

I

7

134

Y

G

R

Y

K

C

E

V

I

E

7

195

Y

D

A

W

R

G

G

L

D

W

7

215

V

Q

Y

P

I

T

K

P

R

E

7

219

I

T

K

P

R

E

P

C

G

G

7

224

E

P

C

G

G

Q

N

T

V

P

7

228

G

Q

N

T

V

P

G

V

R

N

7

233

P

G

V

R

N

Y

G

F

W

D

7

244

D

K

S

R

Y

D

V

F

C

F

7

247

R

Y

D

V

F

C

F

T

S

N

7

248

Y

D

V

F

C

F

T

S

N

F

7

254

T

S

N

F

N

G

R

F

Y

Y

7

261

F

Y

Y

L

I

H

P

T

K

L

7

311

D

G

S

V

R

Y

P

I

S

R

7

319

S

R

P

R

R

R

C

S

P

T

7

327

P

T

E

A

A

V

R

F

V

G

7

336

G

F

P

D

K

K

H

K

L

Y

7

344

L

Y

G

V

Y

C

F

R

A

Y

7

25

D

H

D

R

A

I

H

I

Q

A

6

26

H

D

R

A

I

H

I

Q

A

E

6

33

Q

A

E

N

G

P

H

L

L

V

6

42

V

E

A

E

Q

A

K

V

F

S

6

43

E

A

E

Q

A

K

V

F

S

H

6

55

G

N

V

T

L

P

C

K

F

Y

6

64

Y

R

D

P

T

A

F

G

S

G

6

87

D

Y

L

K

E

V

D

V

F

V

6

89

L

K

E

V

D

V

F

V

S

M

6

109

Q

G

R

V

F

L

K

G

G

S

6

110

G

R

V

F

L

K

G

G

S

D

6

118

S

D

S

D

A

S

L

V

I

T

6

119

D

S

D

A

S

L

V

I

T

D

6

127

T

D

L

T

L

E

D

Y

G

R

6

132

E

D

Y

G

R

Y

K

C

E

V

6

145

L

E

D

D

T

V

V

V

A

L

6

147

D

D

T

V

V

V

A

L

D

L

6

157

Q

G

V

V

F

P

Y

F

P

R

6

162

P

Y

F

P

R

L

G

R

Y

N

6

169

R

Y

N

L

N

F

H

E

A

Q

6

194

L

Y

D

A

W

R

G

G

L

D

6

199

R

G

G

L

D

W

C

N

A

G

6

200

G

G

L

D

W

C

N

A

G

W

6

203

D

W

C

N

A

G

W

L

S

D

6

222

P

R

E

P

C

G

G

Q

N

T

6

225

P

C

G

G

Q

N

T

V

P

G

6

238

Y

G

F

W

D

K

D

K

S

R

6

245

K

S

R

Y

D

V

F

C

F

T

6

270

L

T

Y

D

E

A

V

Q

A

C

6

301

Y

D

R

C

D

A

G

W

L

A

6

304

C

D

A

G

W

L

A

D

G

S

6

312

G

S

V

R

Y

P

I

S

R

P

6

342

H

K

L

Y

G

V

Y

C

F

R

6

1

M

K

S

L

L

L

L

V

L

I

5

10

I

S

I

C

W

A

D

H

L

S

5

19

S

D

N

Y

T

L

D

H

D

R

5

27

D

R

A

I

H

I

Q

A

E

N

5

32

I

Q

A

E

N

G

P

H

L

L

5

47

A

K

V

F

S

H

R

G

G

N

5

52

H

R

G

G

N

V

T

L

P

C

5

54

G

G

N

V

T

L

P

C

K

F

5

57

V

T

L

P

C

K

F

Y

R

D

5

60

P

C

K

F

Y

R

D

P

T

A

5

72

S

G

I

H

K

I

R

I

K

W

5

82

T

K

L

T

S

D

Y

L

K

E

5

84

L

T

S

D

Y

L

K

E

V

D

5

92

V

D

V

F

V

S

M

G

Y

H

5

100

Y

H

K

K

T

Y

G

G

Y

Q

5

105

Y

G

G

Y

Q

G

R

V

F

L

5

107

G

Y

Q

G

R

V

F

L

K

G

5

136

R

Y

K

C

E

V

I

E

G

L

5

168

G

R

Y

N

L

N

F

H

E

A

5

174

F

H

E

A

Q

Q

A

C

L

D

5

177

A

Q

Q

A

C

L

D

Q

D

A

5

189

A

S

F

D

Q

L

Y

D

A

W

5

204

W

C

N

A

G

W

L

S

D

G

5

252

C

F

T

S

N

F

N

G

R

F

5

272

Y

D

E

A

V

Q

A

C

L

N

5

280

L

N

D

G

A

Q

I

A

K

V

5

282

D

G

A

Q

I

A

K

V

G

Q

5

283

G

A

Q

I

A

K

V

G

Q

I

5

295

A

W

K

I

L

G

Y

D

R

C

5

302

D

R

C

D

A

G

W

L

A

D

5

20

D

N

Y

T

L

D

H

D

R

A

4

37

G

P

H

L

L

V

E

A

E

Q

4

85

T

S

D

Y

L

K

E

V

D

V

4

98

M

G

Y

H

K

K

T

Y

G

G

4

112

V

F

L

K

G

G

S

D

S

D

4

135

G

R

Y

K

C

E

V

I

E

G

4

163

Y

F

P

R

L

G

R

Y

N

L

4

164

F

P

R

L

G

R

Y

N

L

N

4

173

N

F

H

E

A

Q

Q

A

C

L

4

175

H

E

A

Q

Q

A

C

L

D

Q

4

178

Q

Q

A

C

L

D

Q

D

A

V

4

185

D

A

V

I

A

S

F

D

Q

L

4

191

F

D

Q

L

Y

D

A

W

R

G

4

196

D

A

W

R

G

G

L

D

W

C

4

216

Q

Y

P

I

T

K

P

R

E

P

4

217

Y

P

I

T

K

P

R

E

P

C

4

220

T

K

P

R

E

P

C

G

G

Q

4

230

N

T

V

P

G

V

R

N

Y

G

4

251

F

C

F

T

S

N

F

N

G

R

4

271

T

Y

D

E

A

V

Q

A

C

L

4

273

D

E

A

V

Q

A

C

L

N

D

4

286

I

A

K

V

G

Q

I

F

A

A

4

289

V

G

Q

I

F

A

A

W

K

I

4

296

W

K

I

L

G

Y

D

R

C

D

4

316

Y

P

I

S

R

P

R

R

R

C

4

345

Y

G

V

Y

C

F

R

A

Y

N

4

16

D

H

L

S

D

N

Y

T

L

D

3

46

Q

A

K

V

F

S

H

R

G

G

3

80

K

W

T

K

L

T

S

D

Y

L

3

108

Y

Q

G

R

V

F

L

K

G

G

3

114

L

K

G

G

S

D

S

D

A

S

3

120

S

D

A

S

L

V

I

T

D

L

3

126

I

T

D

L

T

L

E

D

Y

G

3

146

E

D

D

T

V

V

V

A

L

D

3

167

L

G

R

Y

N

L

N

F

H

E

3

176

E

A

Q

Q

A

C

L

D

Q

D

3

184

Q

D

A

V

I

A

S

F

D

Q

3

202

L

D

W

C

N

A

G

W

L

S

3

205

C

N

A

G

W

L

S

D

G

S

3

206

N

A

G

W

L

S

D

G

S

V

3

241

W

D

K

D

K

S

R

Y

D

V

3

258

N

G

R

F

Y

Y

L

I

H

P

3

262

Y

Y

L

I

H

P

T

K

L

T

3

267

P

T

K

L

T

Y

D

E

A

V

3

276

V

Q

A

C

L

N

D

G

A

Q

3

290

G

Q

I

F

A

A

W

K

I

L

3

305

D

A

G

W

L

A

D

G

S

V

3

309

L

A

D

G

S

V

R

Y

P

I

3

310

A

D

G

S

V

R

Y

P

I

S

3

335

V

G

F

P

D

K

K

H

K

L

3

337

F

P

D

K

K

H

K

L

Y

G

3

21

N

Y

T

L

D

H

D

R

A

I

2

68

T

A

F

G

S

G

I

H

K

I

2

70

F

G

S

G

I

H

K

I

R

I

2

97

S

M

G

Y

H

K

K

T

Y

G

2

137

Y

K

C

E

V

I

E

G

L

E

2

188

I

A

S

F

D

Q

L

Y

D

A

2

192

D

Q

L

Y

D

A

W

R

G

G

2

198

W

R

G

G

L

D

W

C

N

A

2

210

L

S

D

G

S

V

Q

Y

P

I

2

255

S

N

F

N

G

R

F

Y

Y

L

2

256

N

F

N

G

R

F

Y

Y

L

I

2

265

I

H

P

T

K

L

T

Y

D

E

2

293

F

A

A

W

K

I

L

G

Y

D

2

326

S

P

T

E

A

A

V

R

F

V

2

329

E

A

A

V

R

F

V

G

F

P

2

18

L

S

D

N

Y

T

L

D

H

D

1

24

L

D

H

D

R

A

I

H

I

Q

1

36

N

G

P

H

L

L

V

E

A

E

1

45

E

Q

A

K

V

F

S

H

R

G

1

59

L

P

C

K

F

Y

R

D

P

T

1

121

D

A

S

L

V

I

T

D

L

T

1

139

C

E

V

I

E

G

L

E

D

D

1

156

L

Q

G

V

V

F

P

Y

F

P

1

172

L

N

F

H

E

A

Q

Q

A

C

1

211

S

D

G

S

V

Q

Y

P

I

T

1

213

G

S

V

Q

Y

P

I

T

K

P

1

232

V

P

G

V

R

N

Y

G

F

W

1

338

P

D

K

K

H

K

L

Y

G

V

1

151P3D4 v.2: HLA Peptide

Scoring Results A3 10-mers SYFPEITHI

SEQ. ID

Pos

1

2

3

4

5

6

7

8

9

0

score

NO.

111

K

L

K

Y

L

A

F

L

H

K

27

Portion

87

V

L

L

G

R

K

A

V

V

V

25

of SEQ

343

V

L

A

R

G

K

P

Q

R

K

25

ID NO:

75

T

V

Y

Q

D

E

K

Q

R

K

24

5; each

10

P

L

R

A

L

H

I

V

V

E

23

start

86

K

V

L

L

G

R

K

A

V

V

23

position

237

K

T

I

A

P

L

A

A

T

R

22

is

13

A

L

H

I

V

V

E

S

I

R

21

specified,

88

L

L

G

R

K

A

V

V

V

S

21

the length

198

K

N

K

Q

L

M

R

L

Q

K

21

of

331

K

P

A

R

H

C

Q

G

Q

K

21

peptide is

342

N

V

L

A

R

G

K

P

Q

R

21

10 amino

19

E

S

I

R

D

H

S

G

Q

K

20

acids, the

36

D

L

L

V

P

T

K

V

T

G

20

end

102

N

I

S

G

S

F

C

R

N

K

20

position

269

A

L

S

A

R

A

P

V

P

A

20

for each

284

W

L

P

L

R

T

P

W

T

R

20

peptide is

64

K

L

A

Y

S

N

D

G

E

H

19

the start

179

A

V

T

A

T

L

E

E

K

R

19

position

240

A

P

L

A

A

T

R

A

T

R

19

plus nine

249

R

I

G

H

P

G

G

R

T

P

19

322

S

P

S

G

G

G

G

L

K

K

19

33

K

K

V

D

L

L

V

P

T

K

18

45

G

I

I

T

Q

G

A

K

D

F

18

366

R

P

A

D

L

A

G

S

G

Y

18

386

L

E

E

G

L

G

G

K

Q

K

18

154

Q

G

H

A

S

E

A

Y

K

K

17

163

K

V

C

L

S

G

A

P

H

E

17

167

S

G

A

P

H

E

V

G

W

K

17

172

E

V

G

W

K

Y

Q

A

V

T

17

182

A

T

L

E

E

K

R

K

E

K

17

202

L

M

R

L

Q

K

Q

A

E

K

17

241

P

L

A

A

T

R

A

T

R

I

17

264

A

H

R

P

P

A

L

S

A

R

17

275

P

V

P

A

A

S

P

A

A

W

17

295

S

S

C

P

T

S

S

S

T

Y

17

372

G

S

G

Y

C

G

A

L

W

K

17

20

S

I

R

D

H

S

G

Q

K

M

16

34

K

V

D

L

L

V

P

T

K

V

16

55

G

H

V

Q

F

V

G

S

Y

K

16

165

C

L

S

G

A

P

H

E

V

G

16

189

K

E

K

A

E

I

H

Y

R

K

16

201

Q

L

M

R

L

Q

K

Q

A

E

16

228

S

P

R

G

L

G

F

I

F

K

16

238

T

I

A

P

L

A

A

T

R

A

16

339

Q

K

H

N

V

L

A

R

G

K

16

378

A

L

W

K

A

I

E

S

L

E

16

385

S

L

E

E

G

L

G

G

K

Q

16

42

K

V

T

G

I

I

T

Q

G

A

15

83

R

K

D

K

V

L

L

G

R

K

15

136

P

S

R

I

F

W

R

Q

E

K

15

191

K

A

E

I

H

Y

R

K

N

K

15

206

Q

K

Q

A

E

K

N

M

K

K

15

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S

L

S

P

Y

G

P

R

N

5

316

L

P

N

P

R

H

S

P

S

G

5

327

G

G

L

K

K

P

A

R

H

C

5

330

K

K

P

A

R

H

C

Q

G

Q

5

340

K

H

N

V

L

A

R

G

K

P

5

344

L

A

R

G

K

P

Q

R

K

P

5

362

V

E

N

G

R

P

A

D

L

A

5

373

S

G

Y

C

G

A

L

W

K

A

5

375

Y

C

G

A

L

W

K

A

I

E

5

376

C

G

A

L

W

K

A

I

E

S

5

394

Q

K

D

K

E

R

K

A

E

N

5

3

E

H

T

T

K

T

F

P

L

R

4

4

H

T

T

K

T

F

P

L

R

A

4

18

V

E

S

I

R

D

H

S

G

Q

4

41

T

K

V

T

G

I

I

T

Q

G

4

53

D

F

G

H

V

Q

F

V

G

S

4

63

Y

K

L

A

Y

S

N

D

G

E

4

106

S

F

C

R

N

K

L

K

Y

L

4

107

F

C

R

N

K

L

K

Y

L

A

4

118

L

H

K

R

M

N

T

N

P

S

4

121

R

M

N

T

N

P

S

R

R

P

4

130

P

Y

H

F

Q

V

P

S

R

I

4

131

Y

H

F

Q

V

P

S

R

I

F

4

137

S

R

I

F

W

R

Q

E

K

A

4

149

G

S

C

C

P

Q

G

H

A

S

4

169

A

P

H

E

V

G

W

K

Y

Q

4

177

Y

Q

A

V

T

A

T

L

E

E

4

197

R

K

N

K

Q

L

M

R

L

Q

4

223

S

P

G

G

G

S

P

R

G

L

4

224

P

G

G

G

S

P

R

G

L

G

4

226

G

G

S

P

R

G

L

G

F

I

4

239

I

A

P

L

A

A

T

R

A

T

4

245

T

R

A

T

R

I

G

H

P

G

4

252

H

P

G

G

R

T

P

R

A

G

4

259

R

A

G

S

S

A

H

R

P

P

4

260

A

G

S

S

A

H

R

P

P

A

4

261

G

S

S

A

H

R

P

P

A

L

4

277

P

A

A

S

P

A

A

W

L

P

4

292

T

R

P

S

S

C

P

T

S

S

4

318

N

P

R

H

S

P

S

G

G

G

4

319

P

R

H

S

P

S

G

G

G

G

4

334

R

H

C

Q

G

Q

K

H

N

V

4

336

C

Q

G

Q

K

H

N

V

L

A

4

338

G

Q

K

H

N

V

L

A

R

G

4

341

H

N

V

L

A

R

G

K

P

Q

4

357

N

N

S

W

Y

V

E

N

G

R

4

377

G

A

L

W

K

A

I

E

S

L

4

390

L

G

G

K

Q

K

D

K

E

R

4

14

L

H

I

V

V

E

S

I

R

D

3

39

V

P

T

K

V

T

G

I

I

T

3

48

T

Q

G

A

K

D

F

G

H

V

3

51

A

K

D

F

G

H

V

Q

F

V

3

62

S

Y

K

L

A

Y

S

N

D

G

3

70

D

G

E

H

W

T

V

Y

Q

D

3

85

D

K

V

L

L

G

R

K

A

V

3

92

K

A

V

V

V

S

C

E

G

I

3

96

V

S

C

E

G

I

N

I

S

G

3

103

I

S

G

S

F

C

R

N

K

L

3

115

L

A

F

L

H

K

R

M

N

T

3

125

N

P

S

R

R

P

Y

H

F

Q

3

161

Y

K

K

V

C

L

S

G

A

P

3

164

V

C

L

S

G

A

P

H

E

V

3

170

P

H

E

V

G

W

K

Y

Q

A

3

171

H

E

V

G

W

K

Y

Q

A

V

3

174

G

W

K

Y

Q

A

V

T

A

T

3

196

Y

R

K

N

K

Q

L

M

R

L

3

217

I

D

K

Y

T

E

S

P

G

G

3

289

T

P

W

T

R

P

S

S

C

P

3

290

P

W

T

R

P

S

S

C

P

T

3

299

T

S

S

S

T

Y

D

S

L

S

3

310

Y

G

P

R

N

P

L

P

N

P

3

324

S

G

G

G

G

L

K

K

P

A

3

333

A

R

H

C

Q

G

Q

K

H

N

3

347

G

K

P

Q

R

K

P

K

S

E

3

349

P

Q

R

K

P

K

S

E

N

N

3

360

W

Y

V

E

N

G

R

P

A

D

3

374

G

Y

C

G

A

L

W

K

A

I

3

396

D

K

E

R

K

A

E

N

G

P

3

5

T

T

K

T

F

P

L

R

A

L

2

78

Q

D

E

K

Q

R

K

D

K

V

2

141

W

R

Q

E

K

A

D

G

G

S

2

144

E

K

A

D

G

G

S

C

C

P

2

158

S

E

A

Y

K

K

V

C

L

S

2

190

E

K

A

E

I

H

Y

R

K

N

2

208

Q

A

E

K

N

M

K

K

K

I

2

222

E

S

P

G

G

G

S

P

R

G

2

232

L

G

F

I

F

K

T

I

A

P

2

251

G

H

P

G

G

R

T

P

R

A

2

296

S

C

P

T

S

S

S

T

Y

D

2

298

P

T

S

S

S

T

Y

D

S

L

2

323

P

S

G

G

G

G

L

K

K

P

2

367

P

A

D

L

A

G

S

G

Y

C

2

370

L

A

G

S

G

Y

C

G

A

L

2

380

W

K

A

I

E

S

L

E

E

G

2

8

T

F

P

L

R

A

L

H

I

V

1

26

G

Q

K

M

K

Q

D

K

K

V

1

29

M

K

Q

D

K

K

V

D

L

L

1

76

V

Y

Q

D

E

K

Q

R

K

D

1

132

H

F

Q

V

P

S

R

I

F

W

1

148

G

G

S

C

C

P

Q

G

H

A

1

155

G

H

A

S

E

A

Y

K

K

V

1

181

T

A

T

L

E

E

K

R

K

E

1

184

L

E

E

K

R

K

E

K

A

E

1

199

N

K

Q

L

M

R

L

Q

K

Q

1

212

N

M

K

K

K

I

D

K

Y

T

1

229

P

R

G

L

G

F

I

F

K

T

1

242

L

A

A

T

R

A

T

R

I

G

1

303

T

Y

D

S

L

S

P

Y

G

P

1

307

L

S

P

Y

G

P

R

N

P

L

1

353

P

K

S

E

N

N

S

W

Y

V

1

358

N

S

W

Y

V

E

N

G

R

P

1

387

E

E

G

L

G

G

K

Q

K

D

1

TABLE XL

151P3D4 v.1: HLA Peptide Scoring

Results A26 10-mers SYFPEITHI

SEQ. ID

Pos

1

2

3

4

5

6

7

8

9

0

score

NO.

155

D

L

Q

G

V

V

F

P

Y

F

31

Portion

91

E

V

D

V

F

V

S

M

G

Y

29

of SEQ

128

D

L

T

L

E

D

Y

G

R

Y

29

ID NO:

125

V

I

T

D

L

T

L

E

D

Y

25

3; each

158

G

V

V

F

P

Y

F

P

R

L

24

start

231

T

V

P

G

V

R

N

Y

G

F

24

position

186

A

V

I

A

S

F

D

Q

L

Y

23

is

242

D

K

D

K

S

R

Y

D

V

F

22

specified,

292

I

F

A

A

W

K

I

L

G

Y

22

the length

339

D

K

K

H

K

L

Y

G

V

Y

21

of

31

H

I

Q

A

E

N

G

P

H

L

20

peptide is

41

L

V

E

A

E

Q

A

K

V

F

20

10 amino

140

E

V

I

E

G

L

E

D

D

T

20

acids, the

148

D

T

V

V

V

A

L

D

L

Q

20

end

244

D

K

S

R

Y

D

V

F

C

F

20

position

253

F

T

S

N

F

N

G

R

F

Y

20

for each

263

Y

L

I

H

P

T

K

L

T

Y

20

peptide is

9

L

I

S

I

C

W

A

D

H

L

19

the start

93

D

V

F

V

S

M

G

Y

H

K

19

position

185

D

A

V

I

A

S

F

D

Q

L

19

plus nine

239

G

F

W

D

K

D

K

S

R

Y

19

193

Q

L

Y

D

A

W

R

G

G

L

18

249

D

V

F

C

F

T

S

N

F

N

18

252

C

F

T

S

N

F

N

G

R

F

18

336

G

F

P

D

K

K

H

K

L

Y

18

57

V

T

L

P

C

K

F

Y

R

D

17

173

N

F

H

E

A

Q

Q

A

C

L

17

182

L

D

Q

D

A

V

I

A

S

F

17

201

G

L

D

W

C

N

A

G

W

L

17

270

L

T

Y

D

E

A

V

Q

A

C

17

328

T

E

A

A

V

R

F

V

G

F

17

78

R

I

K

W

T

K

L

T

S

D

16

99

G

Y

H

K

K

T

Y

G

G

Y

16

145

L

E

D

D

T

V

V

V

A

L

16

150

V

V

V

A

L

D

L

Q

G

V

16

163

Y

F

P

R

L

G

R

Y

N

L

16

264

L

I

H

P

T

K

L

T

Y

D

16

73

G

I

H

K

I

R

I

K

W

T

15

88

Y

L

K

E

V

D

V

F

V

S

15

154

L

D

L

Q

G

V

V

F

P

Y

15

161

F

P

Y

F

P

R

L

G

R

Y

15

181

C

L

D

Q

D

A

V

I

A

S

15

229

Q

N

T

V

P

G

V

R

N

Y

15

331

A

V

R

F

V

G

F

P

D

K

15

341

K

H

K

L

Y

G

V

Y

C

F

15

344

L

Y

G

V

Y

C

F

R

A

Y

15

35

E

N

G

P

H

L

L

V

E

A

14

48

K

V

F

S

H

R

G

G

N

V

14

83

K

L

T

S

D

Y

L

K

E

V

14

86

S

D

Y

L

K

E

V

D

V

F

14

89

L

K

E

V

D

V

F

V

S

M

14

120

S

D

A

S

L

V

I

T

D

L

14

136

R

Y

K

C

E

V

I

E

G

L

14

144

G

L

E

D

D

T

V

V

V

A

14

147

D

D

T

V

V

V

A

L

D

L

14

153

A

L

D

L

Q

G

V

V

F

P

14

159

V

V

F

P

Y

F

P

R

L

G

14

209

W

L

S

D

G

S

V

Q

Y

P

14

219

I

T

K

P

R

E

P

C

G

G

14

234

G

V

R

N

Y

G

F

W

D

K

14

255

S

N

F

N

G

R

F

Y

Y

L

14

308

W

L

A

D

G

S

V

R

Y

P

14

3

S

L

L

L

L

V

L

I

S

I

13

4

L

L

L

L

V

L

I

S

I

C

13

13

C

W

A

D

H

L

S

D

N

Y

13

58

T

L

P

C

K

F

Y

R

D

P

13

61

C

K

F

Y

R

D

P

T

A

F

13

103

K

T

Y

G

G

Y

Q

G

R

V

13

111

R

V

F

L

K

G

G

S

D

S

13

124

L

V

I

T

D

L

T

L

E

D

13

165

P

R

L

G

R

Y

N

L

N

F

13

208

G

W

L

S

D

G

S

V

Q

Y

13

284

A

Q

I

A

K

V

G

Q

I

F

13

325

C

S

P

T

E

A

A

V

R

F

13

335

V

G

F

P

D

K

K

H

K

L

13

6

L

L

V

L

I

S

I

C

W

A

12

8

V

L

I

S

I

C

W

A

D

H

12

22

Y

T

L

D

H

D

R

A

I

H

12

40

L

L

V

E

A

E

Q

A

K

V

12

43

E

A

E

Q

A

K

V

F

S

H

12

67

P

T

A

F

G

S

G

I

H

K

12

94

V

F

V

S

M

G

Y

H

K

K

12

96

V

S

M

G

Y

H

K

K

T

Y

12

104

T

Y

G

G

Y

Q

G

R

V

F

12

113

F

L

K

G

G

S

D

S

D

A

12

123

S

L

V

I

T

D

L

T

L

E

12

129

L

T

L

E

D

Y

G

R

Y

K

12

141

V

I

E

G

L

E

D

D

T

V

12

146

E

D

D

T

V

V

V

A

L

D

12

152

V

A

L

D

L

Q

G

V

V

F

12

166

R

L

G

R

Y

N

L

N

F

H

12

176

E

A

Q

Q

A

C

L

D

Q

D

12

187

V

I

A

S

F

D

Q

L

Y

D

12

218

P

I

T

K

P

R

E

P

C

G

12

230

N

T

V

P

G

V

R

N

Y

G

12

248

Y

D

V

F

C

F

T

S

N

F

12

256

N

F

N

G

R

F

Y

Y

L

I

12

267

P

T

K

L

T

Y

D

E

A

V

12

271

T

Y

D

E

A

V

Q

A

C

L

12

285

Q

I

A

K

V

G

Q

I

F

A

12

288

K

V

G

Q

I

F

A

A

W

K

12

291

Q

I

F

A

A

W

K

I

L

G

12

297

K

I

L

G

Y

D

R

C

D

A

12

307

G

W

L

A

D

G

S

V

R

Y

12

7

L

V

L

I

S

I

C

W

A

D

11

11

S

I

C

W

A

D

H

L

S

D

11

16

D

H

L

S

D

N

Y

T

L

D

11

29

A

I

H

I

Q

A

E

N

G

P

11

32

I

Q

A

E

N

G

P

H

L

L

11

54

G

G

N

V

T

L

P

C

K

F

11

75

H

K

I

R

I

K

W

T

K

L

11

79

I

K

W

T

K

L

T

S

D

Y

11

81

W

T

K

L

T

S

D

Y

L

K

11

84

L

T

S

D

Y

L

K

E

V

D

11

95

F

V

S

M

G

Y

H

K

K

T

11

115

K

G

G

S

D

S

D

A

S

L

11

119

D

S

D

A

S

L

V

I

T

D

11

126

I

T

D

L

T

L

E

D

Y

G

11

149

T

V

V

V

A

L

D

L

Q

G

11

151

V

V

A

L

D

L

Q

G

V

V

11

274

E

A

V

Q

A

C

L

N

D

G

11

275

A

V

Q

A

C

L

N

D

G

A

11

329

E

A

A

V

R

F

V

G

F

P

11

334

F

V

G

F

P

D

K

K

H

K

11

343

K

L

Y

G

V

Y

C

F

R

A

11

23

T

L

D

H

D

R

A

I

H

I

10

39

H

L

L

V

E

A

E

Q

A

K

10

55

G

N

V

T

L

P

C

K

F

Y

10

56

N

V

T

L

P

C

K

F

Y

R

10

76

K

I

R

I

K

W

T

K

L

T

10

130

T

L

E

D

Y

G

R

Y

K

C

10

171

N

L

N

F

H

E

A

Q

Q

A

10

196

D

A

W

R

G

G

L

D

W

C

10

214

S

V

Q

Y

P

I

T

K

P

R

10

254

T

S

N

F

N

G

R

F

Y

Y

10

269

K

L

T

Y

D

E

A

V

Q

A

10

279

C

L

N

D

G

A

Q

I

A

K

10

282

D

G

A

Q

I

A

K

V

G

Q

10

290

G

Q

I

F

A

A

W

K

I

L

10

313

S

V

R

Y

P

I

S

R

P

R

10

317

P

I

S

R

P

R

R

R

C

S

10

327

P

T

E

A

A

V

R

F

V

G

10

17

H

L

S

D

N

Y

T

L

D

H

9

27

D

R

A

I

H

I

Q

A

E

N

9

45

E

Q

A

K

V

F

S

H

R

G

9

50

F

S

H

R

G

G

N

V

T

L

9

68

T

A

F

G

S

G

I

H

K

I

9

80

K

W

T

K

L

T

S

D

Y

L

9

105

Y

G

G

Y

Q

G

R

V

F

L

9

132

E

D

Y

G

R

Y

K

C

E

V

9

143

E

G

L

E

D

D

T

V

V

V

9

190

S

F

D

Q

L

Y

D

A

W

R

9

261

F

Y

Y

L

I

H

P

T

K

L

9

280

L

N

D

G

A

Q

I

A

K

V

9

298

I

L

G

Y

D

R

C

D

A

G

9

300

G

Y

D

R

C

D

A

G

W

L

9

333

R

F

V

G

F

P

D

K

K

H

9

5

L

L

L

V

L

I

S

I

C

W

8

15

A

D

H

L

S

D

N

Y

T

L

8

25

D

H

D

R

A

I

H

I

Q

A

8

64

Y

R

D

P

T

A

F

G

S

G

8

87

D

Y

L

K

E

V

D

V

F

V

8

112

V

F

L

K

G

G

S

D

S

D

8

122

A

S

L

V

I

T

D

L

T

L

8

160

V

F

P

Y

F

P

R

L

G

R

8

183

D

Q

D

A

V

I

A

S

F

D

8

189

A

S

F

D

Q

L

Y

D

A

W

8

224

E

P

C

G

G

Q

N

T

V

P

8

273

D

E

A

V

Q

A

C

L

N

D

8

287

A

K

V

G

Q

I

F

A

A

W

8

302

D

R

C

D

A

G

W

L

A

D

8

20

D

N

Y

T

L

D

H

D

R

A

7

62

K

F

Y

R

D

P

T

A

F

G

7

69

A

F

G

S

G

I

H

K

I

R

7

90

K

E

V

D

V

F

V

S

M

G

7

107

G

Y

Q

G

R

V

F

L

K

G

7

192

D

Q

L

Y

D

A

W

R

G

G

7

203

D

W

C

N

A

G

W

L

S

D

7

226

C

G

G

Q

N

T

V

P

G

V

7

250

V

F

C

F

T

S

N

F

N

G

7

251

F

C

F

T

S

N

F

N

G

R

7

260

R

F

Y

Y

L

I

H

P

T

K

7

305

D

A

G

W

L

A

D

G

S

V

7

311

D

G

S

V

R

Y

P

I

S

R

7

338

P

D

K

K

H

K

L

Y

G

V

7

18

L

S

D

N

Y

T

L

D

H

D

6

26

H

D

R

A

I

H

I

Q

A

E

6

34

A

E

N

G

P

H

L

L

V

E

6

36

N

G

P

H

L

L

V

E

A

E

6

44

A

E

Q

A

K

V

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S

H

R

6

49

V

F

S

H

R

G

G

N

V

T

6

51

S

H

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G

G

N

V

T

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6

66

D

P

T

A

F

G

S

G

I

H

6

102

K

K

T

Y

G

G

Y

Q

G

R

6

118

S

D

S

D

A

S

L

V

I

T

6

121

D

A

S

L

V

I

T

D

L

T

6

133

D

Y

G

R

Y

K

C

E

V

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6

135

G

R

Y

K

C

E

V

I

E

G

6

211

S

D

G

S

V

Q

Y

P

I

T

6

212

D

G

S

V

Q

Y

P

I

T

K

6

213

G

S

V

Q

Y

P

I

T

K

P

6

247

R

Y

D

V

F

C

F

T

S

N

6

259

G

R

F

Y

Y

L

I

H

P

T

6

266

H

P

T

K

L

T

Y

D

E

A

6

286

I

A

K

V

G

Q

I

F

A

A

6

295

A

W

K

I

L

G

Y

D

R

C

6

303

R

C

D

A

G

W

L

A

D

G

6

310

A

D

G

S

V

R

Y

P

I

S

6

312

G

S

V

R

Y

P

I

S

R

P

6

326

S

P

T

E

A

A

V

R

F

V

6

1

M

K

S

L

L

L

L

V

L

I

5

12

I

C

W

A

D

H

L

S

D

N

5

24

L

D

H

D

R

A

I

H

I

Q

5

53

R

G

G

N

V

T

L

P

C

K

5

82

T

K

L

T

S

D

Y

L

K

E

5

106

G

G

Y

Q

G

R

V

F

L

K

5

108

Y

Q

G

R

V

F

L

K

G

G

5

131

L

E

D

Y

G

R

Y

K

C

E

5

168

G

R

Y

N

L

N

F

H

E

A

5

204

W

C

N

A

G

W

L

S

D

G

5

258

N

G

R

F

Y

Y

L

I

H

P

5

283

G

A

Q

I

A

K

V

G

Q

I

5

293

F

A

A

W

K

I

L

G

Y

D

5

2

K

S

L

L

L

L

V

L

I

S

4

42

V

E

A

E

Q

A

K

V

F

S

4

71

G

S

G

I

H

K

I

R

I

K

4

92

V

D

V

F

V

S

M

G

Y

H

4

139

C

E

V

I

E

G

L

E

D

D

4

157

Q

G

V

V

F

P

Y

F

P

R

4

162

P

Y

F

P

R

L

G

R

Y

N

4

164

F

P

R

L

G

R

Y

N

L

N

4

172

L

N

F

H

E

A

Q

Q

A

C

4

188

I

A

S

F

D

Q

L

Y

D

A

4

205

C

N

A

G

W

L

S

D

G

S

4

215

V

Q

Y

P

I

T

K

P

R

E

4

222

P

R

E

P

C

G

G

Q

N

T

4

232

V

P

G

V

R

N

Y

G

F

W

4

245

K

S

R

Y

D

V

F

C

F

T

4

257

F

N

G

R

F

Y

Y

L

I

H

4

304

C

D

A

G

W

L

A

D

G

S

4

314

V

R

Y

P

I

S

R

P

R

R

4

316

Y

P

I

S

R

P

R

R

R

C

4

342

H

K

L

Y

G

V

Y

C

F

R

4

28

R

A

I

H

I

Q

A

E

N

G

3

30

I

H

I

Q

A

E

N

G

P

H

3

65

R

D

P

T

A

F

G

S

G

I

3

70

F

G

S

G

I

H

K

I

R

I

3

72

S

G

I

H

K

I

R

I

K

W

3

77

I

R

I

K

W

T

K

L

T

S

3

114

L

K

G

G

S

D

S

D

A

S

3

198

W

R

G

G

L

D

W

C

N

A

3

200

G

G

L

D

W

C

N

A

G

W

3

210

L

S

D

G

S

V

Q

Y

P

I

3

221

K

P

R

E

P

C

G

G

Q

N

3

225

P

C

G

G

Q

N

T

V

P

G

3

238

Y

G

F

W

D

K

D

K

S

R

3

243

K

D

K

S

R

Y

D

V

F

C

3

299

L

G

Y

D

R

C

D

A

G

W

3

309

L

A

D

G

S

V

R

Y

P

I

3

318

I

S

R

P

R

R

R

C

S

P

3

323

R

R

C

S

P

T

E

A

A

V

3

324

R

C

S

P

T

E

A

A

V

R

3

332

V

R

F

V

G

F

P

D

K

K

3

10

I

S

I

C

W

A

D

H

L

S

2

37

G

P

H

L

L

V

E

A

E

Q

2

46

Q

A

K

V

F

S

H

R

G

G

2

52

H

R

G

G

N

V

T

L

P

C

2

60

P

C

K

F

Y

R

D

P

T

A

2

63

F

Y

R

D

P

T

A

F

G

S

2

85

T

S

D

Y

L

K

E

V

D

V

2

100

Y

H

K

K

T

Y

G

G

Y

Q

2

101

H

K

K

T

Y

G

G

Y

Q

G

2

116

G

G

S

D

S

D

A

S

L

V

2

117

G

S

D

S

D

A

S

L

V

I

2

137

Y

K

C

E

V

I

E

G

L

E

2

170

Y

N

L

N

F

H

E

A

Q

Q

2

175

H

E

A

Q

Q

A

C

L

D

Q

2

178

Q

Q

A

C

L

D

Q

D

A

V

2

180

A

C

L

D

Q

D

A

V

I

A

2

197

A

W

R

G

G

L

D

W

C

N

2

216

Q

Y

P

I

T

K

P

R

E

P

2

217

Y

P

I

T

K

P

R

E

P

C

2

220

T

K

P

R

E

P

C

G

G

Q

2

228

G

Q

N

T

V

P

G

V

R

N

2

236

R

N

Y

G

F

W

D

K

D

K

2

240

F

W

D

K

D

K

S

R

Y

D

2

241

W

D

K

D

K

S

R

Y

D

V

2

276

V

Q

A

C

L

N

D

G

A

Q

2

277

Q

A

C

L

N

D

G

A

Q

I

2

296

W

K

I

L

G

Y

D

R

C

D

2

315

R

Y

P

I

S

R

P

R

R

R

2

319

S

R

P

R

R

R

C

S

P

T

2

337

F

P

D

K

K

H

K

L

Y

G

2

340

K

K

H

K

L

Y

G

V

Y

C

2

14

W

A

D

H

L

S

D

N

Y

T

1

21

N

Y

T

L

D

H

D

R

A

I

1

38

P

H

L

L

V

E

A

E

Q

A

1

47

A

K

V

F

S

H

R

G

G

N

1

59

L

P

C

K

F

Y

R

D

P

T

1

74

I

H

K

I

R

I

K

W

T

K

1

98

M

G

Y

H

K

K

T

Y

G

G

1

109

Q

G

R

V

F

L

K

G

G

S

1

110

G

R

V

F

L

K

G

G

S

D

1

127

T

D

L

T

L

E

D

Y

G

R

1

134

Y

G

R

Y

K

C

E

V

I

E

1

138

K

C

E

V

I

E

G

L

E

D

1

167

L

G

R

Y

N

L

N

F

H

E

1

169

R

Y

N

L

N

F

H

E

A

Q

1

177

A

Q

Q

A

C

L

D

Q

D

A

1

179

Q

A

C

L

D

Q

D

A

V

I

1

184

Q

D

A

V

I

A

S

F

D

Q

1

191

F

D

Q

L

Y

D

A

W

R

G

1

194

L

Y

D

A

W

R

G

G

L

D

1

195

Y

D

A

W

R

G

G

L

D

W

1

199

R

G

G

L

D

W

C

N

A

G

1

206

N

A

G

W

L

S

D

G

S

V

1

207

A

G

W

L

S

D

G

S

V

Q

1

223

R

E

P

C

G

G

Q

N

T

V

1

235

V

R

N

Y

G

F

W

D

K

D

1

237

N

Y

G

F

W

D

K

D

K

S

1

246

S

R

Y

D

V

F

C

F

T

S

1

265

I

H

P

T

K

L

T

Y

D

E

1

268

T

K

L

T

Y

D

E

A

V

Q

1

278

A

C

L

N

D

G

A

Q

I

A

1

289

V

G

Q

I

F

A

A

W

K

I

1

294

A

A

W

K

I

L

G

Y

D

R

1

306

A

G

W

L

A

D

G

S

V

R

1

320

R

P

R

R

R

C

S

P

T

E

1

321

P

R

R

R

C

S

P

T

E

A

1

322

R

R

R

C

S

P

T

E

A

A

1

345

Y

G

V

Y

C

F

R

A

Y

N

1

151P3D4 v.2: HLA Peptide Scoring

Results A26 10-mers SYFPEITHI

SEQ. ID

Pos

1

2

3

4

5

6

7

8

9

0

score

NO.

193

E

I

H

Y

R

K

N

K

Q

L

25

Portion

5

T

T

K

T

F

P

L

R

A

L

24

of SEQ

298

P

T

S

S

S

T

Y

D

S

L

24

ID NO:

45

G

I

I

T

Q

G

A

K

D

F

22

5; each

369

D

L

A

G

S

G

Y

C

G

A

22

start

20

S

I

R

D

H

S

G

Q

K

M

21

position

233

G

F

I

F

K

T

I

A

P

L

21

is

56

H

V

Q

F

V

G

S

Y

K

L

19

specified,

58

Q

F

V

G

S

Y

K

L

A

Y

19

the length

361

Y

V

E

N

G

R

P

A

D

L

19

of

53

D

F

G

H

V

Q

F

V

G

S

18

peptide is

106

S

F

C

R

N

K

L

K

Y

L

18

10 amino

204

R

L

Q

K

Q

A

E

K

N

M

18

acids, the

134

Q

V

P

S

R

I

F

W

R

Q

17

end

172

E

V

G

W

K

Y

Q

A

V

T

17

position

398

E

R

K

A

E

N

G

P

H

L

17

for each

59

F

V

G

S

Y

K

L

A

Y

S

16

peptide is

79

D

E

K

Q

R

K

D

K

V

L

16

the start

108

C

R

N

K

L

K

Y

L

A

F

16

position

211

K

N

M

K

K

K

I

D

K

Y

16

plus nine

7

K

T

F

P

L

R

A

L

H

I

15

36

D

L

L

V

P

T

K

V

T

G

15

37

L

L

V

P

T

K

V

T

G

I

15

40

P

T

K

V

T

G

I

I

T

Q

15

54

F

G

H

V

Q

F

V

G

S

Y

15

80

E

K

Q

R

K

D

K

V

L

L

15

196

Y

R

K

N

K

Q

L

M

R

L

15

244

A

T

R

A

T

R

I

G

H

P

15

301

S

S

T

Y

D

S

L

S

P

Y

15

15

H

I

V

V

E

S

I

R

D

H

14

42

K

V

T

G

I

I

T

Q

G

A

14

50

G

A

K

D

F

G

H

V

Q

F

14

95

V

V

S

C

E

G

I

N

I

S

14

109

R

N

K

L

K

Y

L

A

F

L

14

111

K

L

K

Y

L

A

F

L

H

K

14

187

K

R

K

E

K

A

E

I

H

Y

14

190

E

K

A

E

I

H

Y

R

K

N

14

234

F

I

F

K

T

I

A

P

L

A

14

238

T

I

A

P

L

A

A

T

R

A

14

366

R

P

A

D

L

A

G

S

G

Y

14

10

P

L

R

A

L

H

I

V

V

E

13

16

I

V

V

E

S

I

R

D

H

S

13

23

D

H

S

G

Q

K

M

K

Q

D

13

29

M

K

Q

D

K

K

V

D

L

L

13

47

I

T

Q

G

A

K

D

F

G

H

13

68

S

N

D

G

E

H

W

T

V

Y

13

75

T

V

Y

Q

D

E

K

Q

R

K

13

88

L

L

G

R

K

A

V

V

V

S

13

102

N

I

S

G

S

F

C

R

N

K

13

105

G

S

F

C

R

N

K

L

K

Y

13

123

N

T

N

P

S

R

R

P

Y

H

13

124

T

N

P

S

R

R

P

Y

H

F

13

131

Y

H

F

Q

V

P

S

R

I

F

13

138

R

I

F

W

R

Q

E

K

A

D

13

152

C

P

Q

G

H

A

S

E

A

Y

13

182

A

T

L

E

E

K

R

K

E

K

13

216

K

I

D

K

Y

T

E

S

P

G

13

237

K

T

I

A

P

L

A

A

T

R

13

256

R

T

P

R

A

G

S

S

A

H

13

275

P

V

P

A

A

S

P

A

A

W

13

288

R

T

P

W

T

R

P

S

S

C

13

291

W

T

R

P

S

S

C

P

T

S

13

295

S

S

C

P

T

S

S

S

T

Y

13

352

K

P

K

S

E

N

N

S

W

Y

13

377

G

A

L

W

K

A

I

E

S

L

13

381

K

A

I

E

S

L

E

E

G

L

13

384

E

S

L

E

E

G

L

G

G

K

13

4

H

T

T

K

T

F

P

L

R

A

12

17

V

V

E

S

I

R

D

H

S

G

12

32

D

K

K

V

D

L

L

V

P

T

12

34

K

V

D

L

L

V

P

T

K

V

12

94

V

V

V

S

C

E

G

I

N

I

12

163

K

V

C

L

S

G

A

P

H

E

12

168

G

A

P

H

E

V

G

W

K

Y

12

180

V

T

A

T

L

E

E

K

R

K

12

220

Y

T

E

S

P

G

G

G

S

P

12

225

G

G

G

S

P

R

G

L

G

F

12

302

S

T

Y

D

S

L

S

P

Y

G

12

342

N

V

L

A

R

G

K

P

Q

R

12

356

E

N

N

S

W

Y

V

E

N

G

12

3

E

H

T

T

K

T

F

P

L

R

11

8

T

F

P

L

R

A

L

H

I

V

11

28

K

M

K

Q

D

K

K

V

D

L

11

38

L

V

P

T

K

V

T

G

I

I

11

43

V

T

G

I

I

T

Q

G

A

K

11

46

I

I

T

Q

G

A

K

D

F

G

11

70

D

G

E

H

W

T

V

Y

Q

D

11

74

W

T

V

Y

Q

D

E

K

Q

R

11

86

K

V

L

L

G

R

K

A

V

V

11

87

V

L

L

G

R

K

A

V

V

V

11

98

C

E

G

I

N

I

S

G

S

F

11

179

A

V

T

A

T

L

E

E

K

R

11

183

T

L

E

E

K

R

K

E

K

A

11

222

E

S

P

G

G

G

S

P

R

G

11

223

S

P

G

G

G

S

P

R

G

L

11

227

G

S

P

R

G

L

G

F

I

F

11

247

A

T

R

I

G

H

P

G

G

R

11

306

S

L

S

P

Y

G

P

R

N

P

11

320

R

H

S

P

S

G

G

G

G

L

11

343

V

L

A

R

G

K

P

Q

R

K

11

382

A

I

E

S

L

E

E

G

L

G

11

385

S

L

E

E

G

L

G

G

K

Q

11

389

G

L

G

G

K

Q

K

D

K

E

11

399

R

K

A

E

N

G

P

H

L

L

11

64

K

L

A

Y

S

N

D

G

E

H

10

93

A

V

V

V

S

C

E

G

I

N

10

100

G

I

N

I

S

G

S

F

C

R

10

103

I

S

G

S

F

C

R

N

K

L

10

114

Y

L

A

F

L

H

K

R

M

N

10

116

A

F

L

H

K

R

M

N

T

N

10

117

F

L

H

K

R

M

N

T

N

P

10

122

M

N

T

N

P

S

R

R

P

Y

10

165

C

L

S

G

A

P

H

E

V

G

10

175

W

K

Y

Q

A

V

T

A

T

L

10

201

Q

L

M

R

L

Q

K

Q

A

E

10

241

P

L

A

A

T

R

A

T

R

I

10

249

R

I

G

H

P

G

G

R

T

P

10

261

G

S

S

A

H

R

P

P

A

L

10

276

V

P

A

A

S

P

A

A

W

L

10

278

A

A

S

P

A

A

W

L

P

L

10

315

P

L

P

N

P

R

H

S

P

S

10

328

G

L

K

K

P

A

R

H

C

Q

10

335

H

C

Q

G

Q

K

H

N

V

L

10

370

L

A

G

S

G

Y

C

G

A

L

10

378

A

L

W

K

A

I

E

S

L

E

10

13

A

L

H

I

V

V

E

S

I

R

9

19

E

S

I

R

D

H

S

G

Q

K

9

99

E

G

I

N

I

S

G

S

F

C

9

113

K

Y

L

A

F

L

H

K

R

M

9

147

D

G

G

S

C

C

P

Q

G

H

9

157

A

S

E

A

Y

K

K

V

C

L

9

185

E

E

K

R

K

E

K

A

E

I

9

194

I

H

Y

R

K

N

K

Q

L

M

9

269

A

L

S

A

R

A

P

V

P

A

9

284

W

L

P

L

R

T

P

W

T

R

9

305

D

S

L

S

P

Y

G

P

R

N

9

307

L

S

P

Y

G

P

R

N

P

L

9

1

M

L

E

H

T

T

K

T

F

P

8

2

L

E

H

T

T

K

T

F

P

L

8

97

S

C

E

G

I

N

I

S

G

S

8

101

I

N

I

S

G

S

F

C

R

N

8

144

E

K

A

D

G

G

S

C

C

P

8

159

E

A

Y

K

K

V

C

L

S

G

8

160

A

Y

K

K

V

C

L

S

G

A

8

171

H

E

V

G

W

K

Y

Q

A

V

8

207

K

Q

A

E

K

N

M

K

K

K

8

231

G

L

G

F

I

F

K

T

I

A

8

235

I

F

K

T

I

A

P

L

A

A

8

264

A

H

R

P

P

A

L

S

A

R

8

286

P

L

R

T

P

W

T

R

P

S

8

364

N

G

R

P

A

D

L

A

G

S

8

387

E

E

G

L

G

G

K

Q

K

D

8

388

E

G

L

G

G

K

Q

K

D

K

8

11

L

R

A

L

H

I

V

V

E

S

7

61

G

S

Y

K

L

A

Y

S

N

D

7

72

E

H

W

T

V

Y

Q

D

E

K

7

82

Q

R

K

D

K

V

L

L

G

R

7

83

R

K

D

K

V

L

L

G

R

K

7

85

D

K

V

L

L

G

R

K

A

V

7

89

L

G

R

K

A

V

V

V

S

C

7

127

S

R

R

P

Y

H

F

Q

V

P

7

139

I

F

W

R

Q

E

K

A

D

G

7

155

G

H

A

S

E

A

Y

K

K

V

7

167

S

G

A

P

H

E

V

G

W

K

7

186

E

K

R

K

E

K

A

E

I

H

7

218

D

K

Y

T

E

S

P

G

G

G

7

270

L

S

A

R

A

P

V

P

A

A

7

310

Y

G

P

R

N

P

L

P

N

P

7

323

P

S

G

G

G

G

L

K

K

P

7

338

G

Q

K

H

N

V

L

A

R

G

7

363

E

N

G

R

P

A

D

L

A

G

7

396

D

K

E

R

K

A

E

N

G

P

7

31

Q

D

K

K

V

D

L

L

V

P

6

33

K

K

V

D

L

L

V

P

T

K

6

51

A

K

D

F

G

H

V

Q

F

V

6

57

V

Q

F

V

G

S

Y

K

L

A

6

90

G

R

K

A

V

V

V

S

C

E

6

129

R

P

Y

H

F

Q

V

P

S

R

6

132

H

F

Q

V

P

S

R

I

F

W

6

133

F

Q

V

P

S

R

I

F

W

R

6

174

G

W

K

Y

Q

A

V

T

A

T

6

199

N

K

Q

L

M

R

L

Q

K

Q

6

210

E

K

N

M

K

K

K

I

D

K

6

214

K

K

K

I

D

K

Y

T

E

S

6

226

G

G

S

P

R

G

L

G

F

I

6

228

S

P

R

G

L

G

F

I

F

K

6

230

R

G

L

G

F

I

F

K

T

I

6

236

F

K

T

I

A

P

L

A

A

T

6

279

A

S

P

A

A

W

L

P

L

R

6

337

Q

G

Q

K

H

N

V

L

A

R

6

355

S

E

N

N

S

W

Y

V

E

N

6

380

W

K

A

I

E

S

L

E

E

G

6

12

R

A

L

H

I

V

V

E

S

I

5

41

T

K

V

T

G

I

I

T

Q

G

5

48

T

Q

G

A

K

D

F

G

H

V

5

71

G

E

H

W

T

V

Y

Q

D

E

5

81

K

Q

R

K

D

K

V

L

L

G

5

112

L

K

Y

L

A

F

L

H

K

R

5

158

S

E

A

Y

K

K

V

C

L

S

5

178

Q

A

V

T

A

T

L

E

E

K

5

188

R

K

E

K

A

E

I

H

Y

R

5

197

R

K

N

K

Q

L

M

R

L

Q

5

229

P

R

G

L

G

F

I

F

K

T

5

248

T

R

I

G

H

P

G

G

R

T

5

251

G

H

P

G

G

R

T

P

R

A

5

265

H

R

P

P

A

L

S

A

R

A

5

272

A

R

A

P

V

P

A

A

S

P

5

281

P

A

A

W

L

P

L

R

T

P

5

346

R

G

K

P

Q

R

K

P

K

S

5

373

S

G

Y

C

G

A

L

W

K

A

5

44

T

G

I

I

T

Q

G

A

K

D

4

52

K

D

F

G

H

V

Q

F

V

G

4

115

L

A

F

L

H

K

R

M

N

T

4

125

N

P

S

R

R

P

Y

H

F

Q

4

146

A

D

G

G

S

C

C

P

Q

G

4

150

S

C

C

P

Q

G

H

A

S

E

4

151

C

C

P

Q

G

H

A

S

E

A

4

215

K

K

I

D

K

Y

T

E

S

P

4

255

G

R

T

P

R

A

G

S

S

A

4

258

P

R

A

G

S

S

A

H

R

P

4

274

A

P

V

P

A

A

S

P

A

A

4

287

L

R

T

P

W

T

R

P

S

S

4

304

Y

D

S

L

S

P

Y

G

P

R

4

312

P

R

N

P

L

P

N

P

R

H

4

316

L

P

N

P

R

H

S

P

S

G

4

325

G

G

G

G

L

K

K

P

A

R

4

329

L

K

K

P

A

R

H

C

Q

G

4

350

Q

R

K

P

K

S

E

N

N

S

4

360

W

Y

V

E

N

G

R

P

A

D

4

394

Q

K

D

K

E

R

K

A

E

N

4

395

K

D

K

E

R

K

A

E

N

G

4

14

L

H

I

V

V

E

S

I

R

D

3

22

R

D

H

S

G

Q

K

M

K

Q

3

69

N

D

G

E

H

W

T

V

Y

Q

3

77

Y

Q

D

E

K

Q

R

K

D

K

3

96

V

S

C

E

G

I

N

I

S

G

3

137

S

R

I

F

W

R

Q

E

K

A

3

141

W

R

Q

E

K

A

D

G

G

S

3

145

K

A

D

G

G

S

C

C

P

Q

3

192

A

E

I

H

Y

R

K

N

K

Q

3

198

K

N

K

Q

L

M

R

L

Q

K

3

205

L

Q

K

Q

A

E

K

N

M

K

3

217

I

D

K

Y

T

E

S

P

G

G

3

219

K

Y

T

E

S

P

G

G

G

S

3

221

T

E

S

P

G

G

G

S

P

R

3

232

L

G

F

I

F

K

T

I

A

P

3

252

H

P

G

G

R

T

P

R

A

G

3

283

A

W

L

P

L

R

T

P

W

T

3

292

T

R

P

S

S

C

P

T

S

S

3

293

R

P

S

S

C

P

T

S

S

S

3

303

T

Y

D

S

L

S

P

Y

G

P

3

308

S

P

Y

G

P

R

N

P

L

P

3

314

N

P

L

P

N

P

R

H

S

P

3

317

P

N

P

R

H

S

P

S

G

G

3

322

S

P

S

G

G

G

G

L

K

K

3

330

K

K

P

A

R

H

C

Q

G

Q

3

344

L

A

R

G

K

P

Q

R

K

P

3

347

G

K

P

Q

R

K

P

K

S

E

3

351

R

K

P

K

S

E

N

N

S

W

3

371

A

G

S

G

Y

C

G

A

L

W

3

374

G

Y

C

G

A

L

W

K

A

I

3

386

L

E

E

G

L

G

G

K

Q

K

3

391

G

G

K

Q

K

D

K

E

R

K

3

393

K

Q

K

D

K

E

R

K

A

E

3

18

V

E

S

I

R

D

H

S

G

Q

2

21

I

R

D

H

S

G

Q

K

M

K

2

24

H

S

G

Q

K

M

K

Q

D

K

2

25

S

G

Q

K

M

K

Q

D

K

K

2

26

G

Q

K

M

K

Q

D

K

K

V

2

30

K

Q

D

K

K

V

D

L

L

V

2

49

Q

G

A

K

D

F

G

H

V

Q

2

55

G

H

V

Q

F

V

G

S

Y

K

2

65

L

A

Y

S

N

D

G

E

H

W

2

76

V

Y

Q

D

E

K

Q

R

K

D

2

78

Q

D

E

K

Q

R

K

D

K

V

2

84

K

D

K

V

L

L

G

R

K

A

2

91

R

K

A

V

V

V

S

C

E

G

2

119

H

K

R

M

N

T

N

P

S

R

2

120

K

R

M

N

T

N

P

S

R

R

2

128

R

R

P

Y

H

F

Q

V

P

S

2

130

P

Y

H

F

Q

V

P

S

R

I

2

136

P

S

R

I

F

W

R

Q

E

K

2

140

F

W

R

Q

E

K

A

D

G

G

2

142

R

Q

E

K

A

D

G

G

S

C

2

143

Q

E

K

A

D

G

G

S

C

C

2

156

H

A

S

E

A

Y

K

K

V

C

2

161

Y

K

K

V

C

L

S

G

A

P

2

164

V

C

L

S

G

A

P

H

E

V

2

166

L

S

G

A

P

H

E

V

G

W

2

169

A

P

H

E

V

G

W

K

Y

Q

2

173

V

G

W

K

Y

Q

A

V

T

A

2

177

Y

Q

A

V

T

A

T

L

E

E

2

184

L

E

E

K

R

K

E

K

A

E

2

189

K

E

K

A

E

I

H

Y

R

K

2

195

H

Y

R

K

N

K

Q

L

M

R

2

202

L

M

R

L

Q

K

Q

A

E

K

2

203

M

R

L

Q

K

Q

A

E

K

N

2

206

Q

K

Q

A

E

K

N

M

K

K

2

208

Q

A

E

K

N

M

K

K

K

I

2

212

N

M

K

K

K

I

D

K

Y

T

2

213

M

K

K

K

I

D

K

Y

T

E

2

224

P

G

G

G

S

P

R

G

L

G

2

239

I

A

P

L

A

A

T

R

A

T

2

246

R

A

T

R

I

G

H

P

G

G

2

250

I

G

H

P

G

G

R

T

P

R

2

253

P

G

G

R

T

P

R

A

G

S

2

257

T

P

R

A

G

S

S

A

H

R

2

260

A

G

S

S

A

H

R

P

P

A

2

262

S

S

A

H

R

P

P

A

L

S

2

266

R

P

P

A

L

S

A

R

A

P

2

267

P

P

A

L

S

A

R

A

P

V

2

268

P

A

L

S

A

R

A

P

V

P

2

271

S

A

R

A

P

V

P

A

A

S

2

273

R

A

P

V

P

A

A

S

P

A

2

277

P

A

A

S

P

A

A

W

L

P

2

280

S

P

A

A

W

L

P

L

R

T

2

294

P

S

S

C

P

T

S

S

S

T

2

299

T

S

S

S

T

Y

D

S

L

S

2

309

P

Y

G

P

R

N

P

L

P

N

2

313

R

N

P

L

P

N

P

R

H

S

2

319

P

R

H

S

P

S

G

G

G

G

2

321

H

S

P

S

G

G

G

G

L

K

2

324

S

G

G

G

G

L

K

K

P

A

2

326

G

G

G

L

K

K

P

A

R

H

2

327

G

G

L

K

K

P

A

R

H

C

2

331

K

P

A

R

H

C

Q

G

Q

K

2

332

P

A

R

H

C

Q

G

Q

K

H

2

334

R

H

C

Q

G

Q

K

H

N

V

2

336

C

Q

G

Q

K

H

N

V

L

A

2

348

K

P

Q

R

K

P

K

S

E

N

2

349

P

Q

R

K

P

K

S

E

N

N

2

353

P

K

S

E

N

N

S

W

Y

V

2

362

V

E

N

G

R

P

A

D

L

A

2

365

G

R

P

A

D

L

A

G

S

G

2

376

C

G

A

L

W

K

A

I

E

S

2

379

L

W

K

A

I

E

S

L

E

E

2

390

L

G

G

K

Q

K

D

K

E

R

2

392

G

K

Q

K

D

K

E

R

K

A

2

6

T

K

T

F

P

L

R

A

L

H

1

27

Q

K

M

K

Q

D

K

K

V

D

1

39

V

P

T

K

V

T

G

I

I

T

1

60

V

G

S

Y

K

L

A

Y

S

N

1

62

S

Y

K

L

A

Y

S

N

D

G

1

63

Y

K

L

A

Y

S

N

D

G

E

1

67

Y

S

N

D

G

E

H

W

T

V

1

73

H

W

T

V

Y

Q

D

E

K

Q

1

92

K

A

V

V

V

S

C

E

G

I

1

110

N

K

L

K

Y

L

A

F

L

H

1

118

L

H

K

R

M

N

T

N

P

S

1

121

R

M

N

T

N

P

S

R

R

P

1

126

P

S

R

R

P

Y

H

F

Q

V

1

135

V

P

S

R

I

F

W

R

Q

E

1

148

G

G

S

C

C

P

Q

G

H

A

1

149

G

S

C

C

P

Q

G

H

A

S

1

153

P

Q

G

H

A

S

E

A

Y

K

1

154

Q

G

H

A

S

E

A

Y

K

K

1

162

K

K

V

C

L

S

G

A

P

H

1

170

P

H

E

V

G

W

K

Y

Q

A

1

181

T

A

T

L

E

E

K

R

K

E

1

191

K

A

E

I

H

Y

R

K

N

K

1

200

K

Q

L

M

R

L

Q

K

Q

A

1

209

A

E

K

N

M

K

K

K

I

D

1

240

A

P

L

A

A

T

R

A

T

R

1

242

L

A

A

T

R

A

T

R

I

G

1

243

A

A

T

R

A

T

R

I

G

H

1

245

T

R

A

T

R

I

G

H

P

G

1

254

G

G

R

T

P

R

A

G

S

S

1

259

R

A

G

S

S

A

H

R

P

P

1

263

S

A

H

R

P

P

A

L

S

A

1

285

L

P

L

R

T

P

W

T

R

P

1

289

T

P

W

T

R

P

S

S

C

P

1

296

S

C

P

T

S

S

S

T

Y

D

1

297

C

P

T

S

S

S

T

Y

D

S

1

300

S

S

S

T

Y

D

S

L

S

P

1

318

N

P

R

H

S

P

S

G

G

G

1

333

A

R

H

C

Q

G

Q

K

H

N

1

339

Q

K

H

N

V

L

A

R

G

K

1

340

K

H

N

V

L

A

R

G

K

P

1

345

A

R

G

K

P

Q

R

K

P

K

1

357

N

N

S

W

Y

V

E

N

G

R

1

358

N

S

W

Y

V

E

N

G

R

P

1

367

P

A

D

L

A

G

S

G

Y

C

1

375

Y

C

G

A

L

W

K

A

I

E

1

383

I

E

S

L

E

E

G

L

G

G

1

397

K

E

R

K

A

E

N

G

P

H

1

TABLE XLI

SEQ. ID

Pos

1

2

3

4

5

6

7

8

9

0

score

NO.

151P3D4 v.1

HLA Peptide Scoring

Results B*0702 10-mers SYFPEITHI

59

L

P

C

K

F

Y

R

D

P

T

19

Portion

326

S

P

T

E

A

A

V

R

F

V

18

of SEQ

266

H

P

T

K

L

T

Y

D

E

A

17

ID NO:

105

Y

G

G

Y

Q

G

R

V

F

L

15

3; each

145

L

E

D

D

T

V

V

V

A

L

15

start

224

E

P

C

G

G

Q

N

T

V

P

15

position

122

A

S

L

V

I

T

D

L

T

L

14

is

320

R

P

R

R

R

C

S

P

T

E

14

specified,

337

F

P

D

K

K

H

K

L

Y

G

14

the length

115

K

G

G

S

D

S

D

A

S

L

13

of

221

K

P

R

E

P

C

G

G

Q

N

13

peptide is

9

L

I

S

I

C

W

A

D

H

L

12

10 amino

15

A

D

H

L

S

D

N

Y

T

L

12

acids, the

31

H

I

Q

A

E

N

G

P

H

L

12

end

32

I

Q

A

E

N

G

P

H

L

L

12

position

50

F

S

H

R

G

G

N

V

T

L

12

for each

80

K

W

T

K

L

T

S

D

Y

L

12

peptide is

120

S

D

A

S

L

V

I

T

D

L

12

the start

147

D

D

T

V

V

V

A

L

D

L

12

position

158

G

V

V

F

P

Y

F

P

R

L

12

plus nine

164

F

P

R

L

G

R

Y

N

L

N

12

217

Y

P

I

T

K

P

R

E

P

C

12

232

V

P

G

V

R

N

Y

G

F

W

12

271

T

Y

D

E

A

V

Q

A

C

L

12

35

E

N

G

P

H

L

L

V

E

A

11

37

G

P

H

L

L

V

E

A

E

Q

11

66

D

P

T

A

F

G

S

G

I

H

11

75

H

K

I

R

I

K

W

T

K

L

11

136

R

Y

K

C

E

V

I

E

G

L

11

143

E

G

L

E

D

D

T

V

V

V

11

163

Y

F

P

R

L

G

R

Y

N

L

11

173

N

F

H

E

A

Q

Q

A

C

L

11

185

D

A

V

I

A

S

F

D

Q

L

11

193

Q

L

Y

D

A

W

R

G

G

L

11

201

G

L

D

W

C

N

A

G

W

L

11

245

K

S

R

Y

D

V

F

C

F

T

11

255

S

N

F

N

G

R

F

Y

Y

L

11

261

F

Y

Y

L

I

H

P

T

K

L

11

300

G

Y

D

R

C

D

A

G

W

L

11

309

L

A

D

G

S

V

R

Y

P

I

11

316

Y

P

I

S

R

P

R

R

R

C

11

322

R

R

R

C

S

P

T

E

A

A

11

328

T

E

A

A

V

R

F

V

G

F

11

335

V

G

F

P

D

K

K

H

K

L

11

1

M

K

S

L

L

L

L

V

L

I

10

70

F

G

S

G

I

H

K

I

R

I

10

76

K

I

R

I

K

W

T

K

L

T

10

87

D

Y

L

K

E

V

D

V

F

V

10

104

T

Y

G

G

Y

Q

G

R

V

F

10

117

G

S

D

S

D

A

S

L

V

I

10

118

S

D

S

D

A

S

L

V

I

T

10

142

I

E

G

L

E

D

D

T

V

V

10

144

G

L

E

D

D

T

V

V

V

A

10

155

D

L

Q

G

V

V

F

P

Y

F

10

161

F

P

Y

F

P

R

L

G

R

Y

10

165

P

R

L

G

R

Y

N

L

N

F

10

180

A

C

L

D

Q

D

A

V

I

A

10

210

L

S

D

G

S

V

Q

Y

P

I

10

280

L

N

D

G

A

Q

I

A

K

V

10

290

G

Q

I

F

A

A

W

K

I

L

10

297

K

I

L

G

Y

D

R

C

D

A

10

49

V

F

S

H

R

G

G

N

V

T

9

85

T

S

D

Y

L

K

E

V

D

V

9

89

L

K

E

V

D

V

F

V

S

M

9

103

K

T

Y

G

G

Y

Q

G

R

V

9

121

D

A

S

L

V

I

T

D

L

T

9

132

E

D

Y

G

R

Y

K

C

E

V

9

152

V

A

L

D

L

Q

G

V

V

F

9

177

A

Q

Q

A

C

L

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S

1

249

D

V

F

C

F

T

S

N

F

N

1

251

F

C

F

T

S

N

F

N

G

R

1

254

T

S

N

F

N

G

R

F

Y

Y

1

272

Y

D

E

A

V

Q

A

C

L

N

1

274

E

A

V

Q

A

C

L

N

D

G

1

279

C

L

N

D

G

A

Q

I

A

K

1

291

Q

I

F

A

A

W

K

I

L

G

1

293

F

A

A

W

K

I

L

G

Y

D

1

299

L

G

Y

D

R

C

D

A

G

W

1

315

R

Y

P

I

S

R

P

R

R

R

1

334

F

V

G

F

P

D

K

K

H

K

1

339

D

K

K

H

K

L

Y

G

V

Y

1

342

H

K

L

Y

G

V

Y

C

F

R

1

151P3D4 v.2

HLA Peptide Scoring

Results B*0702 10-mers SYFPEITHI

223

S

P

G

G

G

S

P

R

G

L

23

Portion

276

V

P

A

A

S

P

A

A

W

L

23

of SEQ

274

A

P

V

P

A

A

S

P

A

A

21

ID NO:

267

P

P

A

L

S

A

R

A

P

V

20

5; each

280

S

P

A

A

W

L

P

L

R

T

20

start

278

A

A

S

P

A

A

W

L

P

L

18

position

9

F

P

L

R

A

L

H

I

V

V

17

is

39

V

P

T

K

V

T

G

I

I

T

17

specified,

228

S

P

R

G

L

G

F

I

F

K

16

the length

322

S

P

S

G

G

G

G

L

K

K

16

of

157

A

S

E

A

Y

K

K

V

C

L

15

peptide is

240

A

P

L

A

A

T

R

A

T

R

15

10 amino

261

G

S

S

A

H

R

P

P

A

L

15

acids, the

252

H

P

G

G

R

T

P

R

A

G

14

end

257

T

P

R

A

G

S

S

A

H

R

14

position

269

A

L

S

A

R

A

P

V

P

A

14

for each

293

R

P

S

S

C

P

T

S

S

S

14

peptide is

320

R

H

S

P

S

G

G

G

G

L

14

the start

28

K

M

K

Q

D

K

K

V

D

L

13

position

80

E

K

Q

R

K

D

K

V

L

L

13

plus nine

103

I

S

G

S

F

C

R

N

K

L

13

109

R

N

K

L

K

Y

L

A

F

L

13

125

N

P

S

R

R

P

Y

H

F

Q

13

129

R

P

Y

H

F

Q

V

P

S

R

13

152

C

P

Q

G

H

A

S

E

A

Y

13

260

A

G

S

S

A

H

R

P

P

A

13

266

R

P

P

A

L

S

A

R

A

P

13

308

S

P

Y

G

P

R

N

P

L

P

13

311

G

P

R

N

P

L

P

N

P

R

13

335

H

C

Q

G

Q

K

H

N

V

L

13

398

E

R

K

A

E

N

G

P

H

L

13

2

L

E

H

T

T

K

T

F

P

L

12

135

V

P

S

R

I

F

W

R

Q

E

12

169

A

P

H

E

V

G

W

K

Y

Q

12

175

W

K

Y

Q

A

V

T

A

T

L

12

233

G

F

I

F

K

T

I

A

P

L

12

298

P

T

S

S

S

T

Y

D

S

L

12

307

L

S

P

Y

G

P

R

N

P

L

12

314

N

P

L

P

N

P

R

H

S

P

12

316

L

P

N

P

R

H

S

P

S

G

12

318

N

P

R

H

S

P

S

G

G

G

12

331

K

P

A

R

H

C

Q

G

Q

K

12

366

R

P

A

D

L

A

G

S

G

Y

12

370

L

A

G

S

G

Y

C

G

A

L

12

399

R

K

A

E

N

G

P

H

L

L

12

5

T

T

K

T

F

P

L

R

A

L

11

29

M

K

Q

D

K

K

V

D

L

L

11

30

K

Q

D

K

K

V

D

L

L

V

11

51

A

K

D

F

G

H

V

Q

F

V

11

79

D

E

K

Q

R

K

D

K

V

L

11

87

V

L

L

G

R

K

A

V

V

V

11

193

E

I

H

Y

R

K

N

K

Q

L

11

283

A

W

L

P

L

R

T

P

W

T

11

285

L

P

L

R

T

P

W

T

R

P

11

297

C

P

T

S

S

S

T

Y

D

S

11

348

K

P

Q

R

K

P

K

S

E

N

11

352

K

P

K

S

E

N

N

S

W

Y

11

361

Y

V

E

N

G

R

P

A

D

L

11

381

K

A

I

E

S

L

E

E

G

L

11

7

K

T

F

P

L

R

A

L

H

I

10

42

K

V

T

G

I

I

T

Q

G

A

10

56

H

V

Q

F

V

G

S

Y

K

L

10

66

A

Y

S

N

D

G

E

H

W

T

10

106

S

F

C

R

N

K

L

K

Y

L

10

108

C

R

N

K

L

K

Y

L

A

F

10

172

E

V

G

W

K

Y

Q

A

V

T

10

196

Y

R

K

N

K

Q

L

M

R

L

10

226

G

G

S

P

R

G

L

G

F

I

10

230

R

G

L

G

F

I

F

K

T

I

10

235

I

F

K

T

I

A

P

L

A

A

10

251

G

H

P

G

G

R

T

P

R

A

10

270

L

S

A

R

A

P

V

P

A

A

10

289

T

P

W

T

R

P

S

S

C

P

10

324

S

G

G

G

G

L

K

K

P

A

10

377

G

A

L

W

K

A

I

E

S

L

10

4

H

T

T

K

T

F

P

L

R

A

9

32

D

K

K

V

D

L

L

V

P

T

9

34

K

V

D

L

L

V

P

T

K

V

9

37

L

L

V

P

T

K

V

T

G

I

9

48

T

Q

G

A

K

D

F

G

H

V

9

86

K

V

L

L

G

R

K

A

V

V

9

160

A

Y

K

K

V

C

L

S

G

A

9

171

H

E

V

G

W

K

Y

Q

A

V

9

173

V

G

W

K

Y

Q

A

V

T

A

9

174

G

W

K

Y

Q

A

V

T

A

T

9

225

G

G

G

S

P

R

G

L

G

F

9

238

T

I

A

P

L

A

A

T

R

A

9

239

I

A

P

L

A

A

T

R

A

T

9

241

P

L

A

A

T

R

A

T

R

I

9

336

C

Q

G

Q

K

H

N

V

L

A

9

369

D

L

A

G

S

G

Y

C

G

A

9

374

G

Y

C

G

A

L

W

K

A

I

9

12

R

A

L

H

I

V

V

E

S

I

8

20

S

I

R

D

H

S

G

Q

K

M

8

35

V

D

L

L

V

P

T

K

V

T

8

50

G

A

K

D

F

G

H

V

Q

F

8

85

D

K

V

L

L

G

R

K

A

V

8

107

F

C

R

N

K

L

K

Y

L

A

8

113

K

Y

L

A

F

L

H

K

R

M

8

126

P

S

R

R

P

Y

H

F

Q

V

8

148

G

G

S

C

C

P

Q

G

H

A

8

185

E

E

K

R

K

E

K

A

E

I

8

204

R

L

Q

K

Q

A

E

K

N

M

8

231

G

L

G

F

I

F

K

T

I

A

8

234

F

I

F

K

T

I

A

P

L

A

8

236

F

K

T

I

A

P

L

A

A

T

8

248

T

R

I

G

H

P

G

G

R

T

8

263

S

A

H

R

P

P

A

L

S

A

8

265

H

R

P

P

A

L

S

A

R

A

8

273

R

A

P

V

P

A

A

S

P

A

8

294

P

S

S

C

P

T

S

S

S

T

8

353

P

K

S

E

N

N

S

W

Y

V

8

362

V

E

N

G

R

P

A

D

L

A

8

38

L

V

P

T

K

V

T

G

I

I

7

78

Q

D

E

K

Q

R

K

D

K

V

7

81

K

Q

R

K

D

K

V

L

L

G

7

84

K

D

K

V

L

L

G

R

K

A

7

92

K

A

V

V

V

S

C

E

G

I

7

98

C

E

G

I

N

I

S

G

S

F

7

115

L

A

F

L

H

K

R

M

N

T

7

155

G

H

A

S

E

A

Y

K

K

V

7

194

I

H

Y

R

K

N

K

Q

L

M

7

200

K

Q

L

M

R

L

Q

K

Q

A

7

208

Q

A

E

K

N

M

K

K

K

I

7

212

N

M

K

K

K

I

D

K

Y

T

7

229

P

R

G

L

G

F

I

F

K

T

7

255

G

R

T

P

R

A

G

S

S

A

7

290

P

W

T

R

P

S

S

C

P

T

7

334

R

H

C

Q

G

Q

K

H

N

V

7

359

S

W

Y

V

E

N

G

R

P

A

7

371

A

G

S

G

Y

C

G

A

L

W

7

392

G

K

Q

K

D

K

E

R

K

A

7

8

T

F

P

L

R

A

L

H

I

V

6

10

P

L

R

A

L

H

I

V

V

E

6

26

G

Q

K

M

K

Q

D

K

K

V

6

45

G

I

I

T

Q

G

A

K

D

F

6

57

V

Q

F

V

G

S

Y

K

L

A

6

67

Y

S

N

D

G

E

H

W

T

V

6

89

L

G

R

K

A

V

V

V

S

C

6

94

V

V

V

S

C

E

G

I

N

I

6

124

T

N

P

S

R

R

P

Y

H

F

6

130

P

Y

H

F

Q

V

P

S

R

I

6

131

Y

H

F

Q

V

P

S

R

I

F

6

137

S

R

I

F

W

R

Q

E

K

A

6

146

A

D

G

G

S

C

C

P

Q

G

6

151

C

C

P

Q

G

H

A

S

E

A

6

164

V

C

L

S

G

A

P

H

E

V

6

170

P

H

E

V

G

W

K

Y

Q

A

6

183

T

L

E

E

K

R

K

E

K

A

6

227

G

S

P

R

G

L

G

F

I

F

6

264

A

H

R

P

P

A

L

S

A

R

6

345

A

R

G

K

P

Q

R

K

P

K

6

373

S

G

Y

C

G

A

L

W

K

A

6

58

Q

F

V

G

S

Y

K

L

A

Y

5

68

S

N

D

G

E

H

W

T

V

Y

5

88

L

L

G

R

K

A

V

V

V

S

5

127

S

R

R

P

Y

H

F

Q

V

P

5

145

K

A

D

G

G

S

C

C

P

Q

5

165

C

L

S

G

A

P

H

E

V

G

5

195

H

Y

R

K

N

K

Q

L

M

R

5

244

A

T

R

A

T

R

I

G

H

P

5

250

I

G

H

P

G

G

R

T

P

R

5

271

S

A

R

A

P

V

P

A

A

S

5

272

A

R

A

P

V

P

A

A

S

P

5

282

A

A

W

L

P

L

R

T

P

W

5

309

P

Y

G

P

R

N

P

L

P

N

5

325

G

G

G

G

L

K

K

P

A

R

5

337

Q

G

Q

K

H

N

V

L

A

R

5

363

E

N

G

R

P

A

D

L

A

G

5

383

I

E

S

L

E

E

G

L

G

G

5

397

K

E

R

K

A

E

N

G

P

H

5

11

L

R

A

L

H

I

V

V

E

S

4

23

D

H

S

G

Q

K

M

K

Q

D

4

31

Q

D

K

K

V

D

L

L

V

P

4

52

K

D

F

G

H

V

Q

F

V

G

4

53

D

F

G

H

V

Q

F

V

G

S

4

69

N

D

G

E

H

W

T

V

Y

Q

4

102

N

I

S

G

S

F

C

R

N

K

4

111

K

L

K

Y

L

A

F

L

H

K

4

128

R

R

P

Y

H

F

Q

V

P

S

4

159

E

A

Y

K

K

V

C

L

S

G

4

166

L

S

G

A

P

H

E

V

G

W

4

177

Y

Q

A

V

T

A

T

L

E

E

4

186

E

K

R

K

E

K

A

E

I

H

4

198

K

N

K

Q

L

M

R

L

Q

K

4

216

K

I

D

K

Y

T

E

S

P

G

4

221

T

E

S

P

G

G

G

S

P

R

4

222

E

S

P

G

G

G

S

P

R

G

4

224

P

G

G

G

S

P

R

G

L

G

4

247

A

T

R

I

G

H

P

G

G

R

4

279

A

S

P

A

A

W

L

P

L

R

4

286

P

L

R

T

P

W

T

R

P

S

4

291

W

T

R

P

S

S

C

P

T

S

4

300

S

S

S

T

Y

D

S

L

S

P

4

344

L

A

R

G

K

P

Q

R

K

P

4

364

N

G

R

P

A

D

L

A

G

S

4

3

E

H

T

T

K

T

F

P

L

R

3

27

Q

K

M

K

Q

D

K

K

V

D

3

33

K

K

V

D

L

L

V

P

T

K

3

47

I

T

Q

G

A

K

D

F

G

H

3

49

Q

G

A

K

D

F

G

H

V

Q

3

83

R

K

D

K

V

L

L

G

R

K

3

119

H

K

R

M

N

T

N

P

S

R

3

123

N

T

N

P

S

R

R

P

Y

H

3

136

P

S

R

I

F

W

R

Q

E

K

3

156

H

A

S

E

A

Y

K

K

V

C

3

162

K

K

V

C

L

S

G

A

P

H

3

167

S

G

A

P

H

E

V

G

W

K

3

176

K

Y

Q

A

V

T

A

T

L

E

3

179

A

V

T

A

T

L

E

E

K

R

3

182

A

T

L

E

E

K

R

K

E

K

3

202

L

M

R

L

Q

K

Q

A

E

K

3

211

K

N

M

K

K

K

I

D

K

Y

3

237

K

T

I

A

P

L

A

A

T

R

3

243

A

A

T

R

A

T

R

I

G

H

3

253

P

G

G

R

T

P

R

A

G

S

3

258

P

R

A

G

S

S

A

H

R

P

3

259

R

A

G

S

S

A

H

R

P

P

3

275

P

V

P

A

A

S

P

A

A

W

3

287

L

R

T

P

W

T

R

P

S

S

3

304

Y

D

S

L

S

P

Y

G

P

R

3

306

S

L

S

P

Y

G

P

R

N

P

3

323

P

S

G

G

G

G

L

K

K

P

3

346

R

G

K

P

Q

R

K

P

K

S

3

349

P

Q

R

K

P

K

S

E

N

N

3

360

W

Y

V

E

N

G

R

P

A

D

3

368

A

D

L

A

G

S

G

Y

C

G

3

372

G

S

G

Y

C

G

A

L

W

K

3

375

Y

C

G

A

L

W

K

A

I

E

3

378

A

L

W

K

A

I

E

S

L

E

3

379

L

W

K

A

I

E

S

L

E

E

3

388

E

G

L

G

G

K

Q

K

D

K

3

389

G

L

G

G

K

Q

K

D

K

E

3

393

K

Q

K

D

K

E

R

K

A

E

3

394

Q

K

D

K

E

R

K

A

E

N

3

1

M

L

E

H

T

T

K

T

F

P

2

6

T

K

T

F

P

L

R

A

L

H

2

13

A

L

H

I

V

V

E

S

I

R

2

16

I

V

V

E

S

I

R

D

H

S

2

18

V

E

S

I

R

D

H

S

G

Q

2

21

I

R

D

H

S

G

Q

K

M

K

2

36

D

L

L

V

P

T

K

V

T

G

2

43

V

T

G

I

I

T

Q

G

A

K

2

46

I

I

T

Q

G

A

K

D

F

G

2

59

F

V

G

S

Y

K

L

A

Y

S

2

60

V

G

S

Y

K

L

A

Y

S

N

2

64

K

L

A

Y

S

N

D

G

E

H

2

77

Y

Q

D

E

K

Q

R

K

D

K

2

82

Q

R

K

D

K

V

L

L

G

R

2

90

G

R

K

A

V

V

V

S

C

E

2

91

R

K

A

V

V

V

S

C

E

G

2

93

A

V

V

V

S

C

E

G

I

N

2

95

V

V

S

C

E

G

I

N

I

S

2

97

S

C

E

G

I

N

I

S

G

S

2

99

E

G

I

N

I

S

G

S

F

C

2

101

I

N

I

S

G

S

F

C

R

N

2

104

S

G

S

F

C

R

N

K

L

K

2

105

G

S

F

C

R

N

K

L

K

Y

2

116

A

F

L

H

K

R

M

N

T

N

2

117

F

L

H

K

R

M

N

T

N

P

2

118

L

H

K

R

M

N

T

N

P

S

2

120

K

R

M

N

T

N

P

S

R

R

2

122

M

N

T

N

P

S

R

R

P

Y

2

132

H

F

Q

V

P

S

R

I

F

W

2

138

R

I

F

W

R

Q

E

K

A

D

2

139

I

F

W

R

Q

E

K

A

D

G

2

140

F

W

R

Q

E

K

A

D

G

G

2

142

R

Q

E

K

A

D

G

G

S

C

2

144

E

K

A

D

G

G

S

C

C

P

2

150

S

C

C

P

Q

G

H

A

S

E

2

153

P

Q

G

H

A

S

E

A

Y

K

2

158

S

E

A

Y

K

K

V

C

L

S

2

163

K

V

C

L

S

G

A

P

H

E

2

184

L

E

E

K

R

K

E

K

A

E

2

188

R

K

E

K

A

E

I

H

Y

R

2

189

K

E

K

A

E

I

H

Y

R

K

2

190

E

K

A

E

I

H

Y

R

K

N

2

191

K

A

E

I

H

Y

R

K

N

K

2

192

A

E

I

H

Y

R

K

N

K

Q

2

197

R

K

N

K

Q

L

M

R

L

Q

2

201

Q

L

M

R

L

Q

K

Q

A

E

2

207

K

Q

A

E

K

N

M

K

K

K

2

209

A

E

K

N

M

K

K

K

I

D

2

214

K

K

K

I

D

K

Y

T

E

S

2

215

K

K

I

D

K

Y

T

E

S

P

2

217

I

D

K

Y

T

E

S

P

G

G

2

232

L

G

F

I

F

K

T

I

A

P

2

242

L

A

A

T

R

A

T

R

I

G

2

245

T

R

A

T

R

I

G

H

P

G

2

246

R

A

T

R

I

G

H

P

G

G

2

249

R

I

G

H

P

G

G

R

T

P

2

254

G

G

R

T

P

R

A

G

S

S

2

256

R

T

P

R

A

G

S

S

A

H

2

262

S

S

A

H

R

P

P

A

L

S

2

268

P

A

L

S

A

R

A

P

V

P

2

299

T

S

S

S

T

Y

D

S

L

S

2

312

P

R

N

P

L

P

N

P

R

H

2

326

G

G

G

L

K

K

P

A

R

H

2

328

G

L

K

K

P

A

R

H

C

Q

2

330

K

K

P

A

R

H

C

Q

G

Q

2

332

P

A

R

H

C

Q

G

Q

K

H

2

333

A

R

H

C

Q

G

Q

K

H

N

2

340

K

H

N

V

L

A

R

G

K

P

2

342

N

V

L

A

R

G

K

P

Q

R

2

351

R

K

P

K

S

E

N

N

S

W

2

354

K

S

E

N

N

S

W

Y

V

E

2

355

S

E

N

N

S

W

Y

V

E

N

2

356

E

N

N

S

W

Y

V

E

N

G

2

357

N

N

S

W

Y

V

E

N

G

R

2

382

A

I

E

S

L

E

E

G

L

G

2

386

L

E

E

G

L

G

G

K

Q

K

2

387

E

E

G

L

G

G

K

Q

K

D

2

390

L

G

G

K

Q

K

D

K

E

R

2

19

E

S

I

R

D

H

S

G

Q

K

1

22

R

D

H

S

G

Q

K

M

K

Q

1

24

H

S

G

Q

K

M

K

Q

D

K

1

25

S

G

Q

K

M

K

Q

D

K

K

1

41

T

K

V

T

G

I

I

T

Q

G

1

44

T

G

I

I

T

Q

G

A

K

D

1

54

F

G

H

V

Q

F

V

G

S

Y

1

61

G

S

Y

K

L

A

Y

S

N

D

1

63

Y

K

L

A

Y

S

N

D

G

E

1

70

D

G

E

H

W

T

V

Y

Q

D

1

72

E

H

W

T

V

Y

Q

D

E

K

1

110

N

K

L

K

Y

L

A

F

L

H

1

114

Y

L

A

F

L

H

K

R

M

N

1

121

R

M

N

T

N

P

S

R

R

P

1

133

F

Q

V

P

S

R

I

F

W

R

1

134

Q

V

P

S

R

I

F

W

R

Q

1

143

Q

E

K

A

D

G

G

S

C

C

1

147

D

G

G

S

C

C

P

Q

G

H

1

149

G

S

C

C

P

Q

G

H

A

S

1

154

Q

G

H

A

S

E

A

Y

K

K

1

161

Y

K

K

V

C

L

S

G

A

P

1

180

V

T

A

T

L

E

E

K

R

K

1

187

K

R

K

E

K

A

E

I

H

Y

1

206

Q

K

Q

A

E

K

N

M

K

K

1

210

E

K

N

M

K

K

K

I

D

K

1

213

M

K

K

K

I

D

K

Y

T

E

1

219

K

Y

T

E

S

P

G

G

G

S

1

277

P

A

A

S

P

A

A

W

L

P

1

281

P

A

A

W

L

P

L

R

T

P

1

288

R

T

P

W

T

R

P

S

S

C

1

292

T

R

P

S

S

C

P

T

S

S

1

295

S

S

C

P

T

S

S

S

T

Y

1

296

S

C

P

T

S

S

S

T

Y

D

1

301

S

S

T

Y

D

S

L

S

P

Y

1

302

S

T

Y

D

S

L

S

P

Y

G

1

303

T

Y

D

S

L

S

P

Y

G

P

1

305

D

S

L

S

P

Y

G

P

R

N

1

310

Y

G

P

R

N

P

L

P

N

P

1

313

R

N

P

L

P

N

P

R

H

S

1

315

P

L

P

N

P

R

H

S

P

S

1

327

G

G

L

K

K

P

A

R

H

C

1

329

L

K

K

P

A

R

H

C

Q

G

1

338

G

Q

K

H

N

V

L

A

R

G

1

341

H

N

V

L

A

R

G

K

P

Q

1

343

V

L

A

R

G

K

P

Q

R

K

1

350

Q

R

K

P

K

S

E

N

N

S

1

365

G

R

P

A

D

L

A

G

S

G

1

367

P

A

D

L

A

G

S

G

Y

C

1

376

C

G

A

L

W

K

A

I

E

S

1

380

W

K

A

I

E

S

L

E

E

G

1

384

E

S

L

E

E

G

L

G

G

K

1

395

K

D

K

E

R

K

A

E

N

G

1

TABLE XLII
151P3D4
HLA Peptide Scoring
Results B*08 10-mers SYFPEITHI
												SEQ.
Pos	1	2	3	4	5	6	7	8	9	0	score	ID NO.
	NO DATA

TABLE XLIII
151P3D4
HLA Peptide Scoring
Results B*1510 10-mers SYFPEITHI
												SEQ.
Pos	1	2	3	4	5	6	7	8	9	0	score	ID NO.
	NO DATA

TABLE XLIV
151P3D4
HLA Peptide Scoring
Results B*2705 10-mers SYFPEITHI
												SEQ.
Pos	1	2	3	4	5	6	7	8	9	0	score	ID NO.
	NO DATA

TABLE XLV
151P3D4
HLA Peptide Scoring
Results B*2709 10-mers SYFPEITHI
												SEQ.
Pos	1	2	3	4	5	6	7	8	9	0	score	ID NO.
	NO DATA

TABLE XLVI

SEQ. ID

Pos

1

2

3

4

5

6

7

8

9

0

score

NO.

151P3D4 v.1

HLA Peptide

Scoring Results B*4402 10-mers SYFPEITHI

145

L

E

D

D

T

V

V

V

A

L

26

Portion

328

T

E

A

A

V

R

F

V

G

F

22

of SEQ

189

A

S

F

D

Q

L

Y

D

A

W

18

ID NO:

34

A

E

N

G

P

H

L

L

V

E

17

3; each

72

S

G

I

H

K

I

R

I

K

W

17

start

186

A

V

I

A

S

F

D

Q

L

Y

17

position

287

A

K

V

G

Q

I

F

A

A

W

17

is

335

V

G

F

P

D

K

K

H

K

L

17

specified,

68

T

A

F

G

S

G

I

H

K

I

16

the length

122

A

S

L

V

I

T

D

L

T

L

16

of

284

A

Q

I

A

K

V

G

Q

I

F

16

peptide is

15

A

D

H

L

S

D

N

Y

T

L

15

10 amino

61

C

K

F

Y

R

D

P

T

A

F

15

acids, the

75

H

K

I

R

I

K

W

T

K

L

15

end

96

V

S

M

G

Y

H

K

K

T

Y

15

position

255

S

N

F

N

G

R

F

Y

Y

L

15

for each

263

Y

L

I

H

P

T

K

L

T

Y

15

peptide is

290

G

Q

I

F

A

A

W

K

I

L

15

the start

336

G

F

P

D

K

K

H

K

L

Y

15

position

41

L

V

E

A

E

Q

A

K

V

F

14

plus nine

44

A

E

Q

A

K

V

F

S

H

R

14

86

S

D

Y

L

K

E

V

D

V

F

14

120

S

D

A

S

L

V

I

T

D

L

14

152

V

A

L

D

L

Q

G

V

V

F

14

182

L

D

Q

D

A

V

I

A

S

F

14

292

I

F

A

A

W

K

I

L

G

Y

14

325

C

S

P

T

E

A

A

V

R

F

14

344

L

Y

G

V

Y

C

F

R

A

Y

14

1

M

K

S

L

L

L

L

V

L

I

13

3

S

L

L

L

L

V

L

I

S

I

13

21

N

Y

T

L

D

H

D

R

A

I

13

32

I

Q

A

E

N

G

P

H

L

L

13

50

F

S

H

R

G

G

N

V

T

L

13

55

G

N

V

T

L

P

C

K

F

Y

13

90

K

E

V

D

V

F

V

S

M

G

13

91

E

V

D

V

F

V

S

M

G

Y

13

104

T

Y

G

G

Y

Q

G

R

V

F

13

131

L

E

D

Y

G

R

Y

K

C

E

13

136

R

Y

K

C

E

V

I

E

G

L

13

163

Y

F

P

R

L

G

R

Y

N

L

13

165

P

R

L

G

R

Y

N

L

N

F

13

208

G

W

L

S

D

G

S

V

Q

Y

13

223

R

E

P

C

G

G

Q

N

T

V

13

244

D

K

S

R

Y

D

V

F

C

F

13

253

F

T

S

N

F

N

G

R

F

Y

13

261

F

Y

Y

L

I

H

P

T

K

L

13

300

G

Y

D

R

C

D

A

G

W

L

13

341

K

H

K

L

Y

G

V

Y

C

F

13

5

L

L

L

V

L

I

S

I

C

W

12

9

L

I

S

I

C

W

A

D

H

L

12

54

G

G

N

V

T

L

P

C

K

F

12

79

I

K

W

T

K

L

T

S

D

Y

12

105

Y

G

G

Y

Q

G

R

V

F

L

12

125

V

I

T

D

L

T

L

E

D

Y

12

142

I

E

G

L

E

D

D

T

V

V

12

147

D

D

T

V

V

V

A

L

D

L

12

154

L

D

L

Q

G

V

V

F

P

Y

12

155

D

L

Q

G

V

V

F

P

Y

F

12

185

D

A

V

I

A

S

F

D

Q

L

12

193

Q

L

Y

D

A

W

R

G

G

L

12

200

G

G

L

D

W

C

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2

321

P

R

R

R

C

S

P

T

E

A

2

323

R

R

C

S

P

T

E

A

A

V

2

327

P

T

E

A

A

V

R

F

V

G

2

334

F

V

G

F

P

D

K

K

H

K

2

337

F

P

D

K

K

H

K

L

Y

G

2

340

K

K

H

K

L

Y

G

V

Y

C

2

343

K

L

Y

G

V

Y

C

F

R

A

2

12

I

C

W

A

D

H

L

S

D

N

1

20

D

N

Y

T

L

D

H

D

R

A

1

37

G

P

H

L

L

V

E

A

E

Q

1

40

L

L

V

E

A

E

Q

A

K

V

1

46

Q

A

K

V

F

S

H

R

G

G

1

59

L

P

C

K

F

Y

R

D

P

T

1

60

P

C

K

F

Y

R

D

P

T

A

1

67

P

T

A

F

G

S

G

I

H

K

1

74

I

H

K

I

R

I

K

W

T

K

1

78

R

I

K

W

T

K

L

T

S

D

1

97

S

M

G

Y

H

K

K

T

Y

G

1

98

M

G

Y

H

K

K

T

Y

G

G

1

102

K

K

T

Y

G

G

Y

Q

G

R

1

112

V

F

L

K

G

G

S

D

S

D

1

113

F

L

K

G

G

S

D

S

D

A

1

134

Y

G

R

Y

K

C

E

V

I

E

1

137

Y

K

C

E

V

I

E

G

L

E

1

150

V

V

V

A

L

D

L

Q

G

V

1

156

L

Q

G

V

V

F

P

Y

F

P

1

187

V

I

A

S

F

D

Q

L

Y

D

1

198

W

R

G

G

L

D

W

C

N

A

1

202

L

D

W

C

N

A

G

W

L

S

1

204

W

C

N

A

G

W

L

S

D

G

1

205

C

N

A

G

W

L

S

D

G

S

1

206

N

A

G

W

L

S

D

G

S

V

1

211

S

D

G

S

V

Q

Y

P

I

T

1

226

C

G

G

Q

N

T

V

P

G

V

1

233

P

G

V

R

N

Y

G

F

W

D

1

235

V

R

N

Y

G

F

W

D

K

D

1

260

R

F

Y

Y

L

I

H

P

T

K

1

282

D

G

A

Q

I

A

K

V

G

Q

1

285

Q

I

A

K

V

G

Q

I

F

A

1

293

F

A

A

W

K

I

L

G

Y

D

1

301

Y

D

R

C

D

A

G

W

L

A

1

338

P

D

K

K

H

K

L

Y

G

V

1

342

H

K

L

Y

G

V

Y

C

F

R

1

345

Y

G

V

Y

C

F

R

A

Y

N

1

151P3D4 v.2

HLA Peptide

Scoring Results B*4402 10-mers SYFPEITHI

79

D

E

K

Q

R

K

D

K

V

L

23

Portion

2

L

E

H

T

T

K

T

F

P

L

22

of SEQ

185

E

E

K

R

K

E

K

A

E

I

21

ID NO:

98

C

E

G

I

N

I

S

G

S

F

20

5; each

192

A

E

I

H

Y

R

K

N

K

Q

18

start

278

A

A

S

P

A

A

W

L

P

L

18

position

45

G

I

I

T

Q

G

A

K

D

F

17

is

7

K

T

F

P

L

R

A

L

H

I

16

specified,

209

A

E

K

N

M

K

K

K

I

D

16

the length

211

K

N

M

K

K

K

I

D

K

Y

16

of

233

G

F

I

F

K

T

I

A

P

L

16

peptide is

371

A

G

S

G

Y

C

G

A

L

W

16

10 amino

5

T

T

K

T

F

P

L

R

A

L

15

acids, the

80

E

K

Q

R

K

D

K

V

L

L

15

end

106

S

F

C

R

N

K

L

K

Y

L

15

position

193

E

I

H

Y

R

K

N

K

Q

L

15

for each

282

A

A

W

L

P

L

R

T

P

W

15

peptide is

295

S

S

C

P

T

S

S

S

T

Y

15

the start

58

Q

F

V

G

S

Y

K

L

A

Y

14

position

68

S

N

D

G

E

H

W

T

V

Y

14

plus nine

105

G

S

F

C

R

N

K

L

K

Y

14

157

A

S

E

A

Y

K

K

V

C

L

14

184

L

E

E

K

R

K

E

K

A

E

14

221

T

E

S

P

G

G

G

S

P

R

14

223

S

P

G

G

G

S

P

R

G

L

14

230

R

G

L

G

F

I

F

K

T

I

14

261

G

S

S

A

H

R

P

P

A

L

14

275

P

V

P

A

A

S

P

A

A

W

14

320

R

H

S

P

S

G

G

G

G

L

14

377

G

A

L

W

K

A

I

E

S

L

14

381

K

A

I

E

S

L

E

E

G

L

14

386

L

E

E

G

L

G

G

K

Q

K

14

387

E

E

G

L

G

G

K

Q

K

D

14

29

M

K

Q

D

K

K

V

D

L

L

13

50

G

A

K

D

F

G

H

V

Q

F

13

103

I

S

G

S

F

C

R

N

K

L

13

108

C

R

N

K

L

K

Y

L

A

F

13

122

M

N

T

N

P

S

R

R

P

Y

13

131

Y

H

F

Q

V

P

S

R

I

F

13

152

C

P

Q

G

H

A

S

E

A

Y

13

158

S

E

A

Y

K

K

V

C

L

S

13

171

H

E

V

G

W

K

Y

Q

A

V

13

226

G

G

S

P

R

G

L

G

F

I

13

307

L

S

P

Y

G

P

R

N

P

L

13

335

H

C

Q

G

Q

K

H

N

V

L

13

355

S

E

N

N

S

W

Y

V

E

N

13

362

V

E

N

G

R

P

A

D

L

A

13

374

G

Y

C

G

A

L

W

K

A

I

13

383

I

E

S

L

E

E

G

L

G

G

13

399

R

K

A

E

N

G

P

H

L

L

13

28

K

M

K

Q

D

K

K

V

D

L

12

37

L

L

V

P

T

K

V

T

G

I

12

109

R

N

K

L

K

Y

L

A

F

L

12

124

T

N

P

S

R

R

P

Y

H

F

12

132

H

F

Q

V

P

S

R

I

F

W

12

168

G

A

P

H

E

V

G

W

K

Y

12

175

W

K

Y

Q

A

V

T

A

T

L

12

187

K

R

K

E

K

A

E

I

H

Y

12

196

Y

R

K

N

K

Q

L

M

R

L

12

227

G

S

P

R

G

L

G

F

I

F

12

301

S

S

T

Y

D

S

L

S

P

Y

12

351

R

K

P

K

S

E

N

N

S

W

12

361

Y

V

E

N

G

R

P

A

D

L

12

370

L

A

G

S

G

Y

C

G

A

L

12

398

E

R

K

A

E

N

G

P

H

L

12

18

V

E

S

I

R

D

H

S

G

Q

11

38

L

V

P

T

K

V

T

G

I

I

11

54

F

G

H

V

Q

F

V

G

S

Y

11

56

H

V

Q

F

V

G

S

Y

K

L

11

166

L

S

G

A

P

H

E

V

G

W

11

189

K

E

K

A

E

I

H

Y

R

K

11

208

Q

A

E

K

N

M

K

K

K

I

11

225

G

G

G

S

P

R

G

L

G

F

11

276

V

P

A

A

S

P

A

A

W

L

11

298

P

T

S

S

S

T

Y

D

S

L

11

352

K

P

K

S

E

N

N

S

W

Y

11

366

R

P

A

D

L

A

G

S

G

Y

11

397

K

E

R

K

A

E

N

G

P

H

11

12

R

A

L

H

I

V

V

E

S

I

10

65

L

A

Y

S

N

D

G

E

H

W

10

71

G

E

H

W

T

V

Y

Q

D

E

10

143

Q

E

K

A

D

G

G

S

C

C

10

92

K

A

V

V

V

S

C

E

G

I

9

94

V

V

V

S

C

E

G

I

N

I

9

130

P

Y

H

F

Q

V

P

S

R

I

9

241

P

L

A

A

T

R

A

T

R

I

9

264

A

H

R

P

P

A

L

S

A

R

9

274

A

P

V

P

A

A

S

P

A

A

8

283

A

W

L

P

L

R

T

P

W

T

8

19

E

S

I

R

D

H

S

G

Q

K

7

182

A

T

L

E

E

K

R

K

E

K

7

272

A

R

A

P

V

P

A

A

S

P

7

306

S

L

S

P

Y

G

P

R

N

P

7

314

N

P

L

P

N

P

R

H

S

P

7

393

K

Q

K

D

K

E

R

K

A

E

7

35

V

D

L

L

V

P

T

K

V

T

6

66

A

Y

S

N

D

G

E

H

W

T

6

85

D

K

V

L

L

G

R

K

A

V

6

99

E

G

I

N

I

S

G

S

F

C

6

116

A

F

L

H

K

R

M

N

T

N

6

127

S

R

R

P

Y

H

F

Q

V

P

6

133

F

Q

V

P

S

R

I

F

W

R

6

138

R

I

F

W

R

Q

E

K

A

D

6

215

K

K

I

D

K

Y

T

E

S

P

6

232

L

G

F

I

F

K

T

I

A

P

6

237

K

T

I

A

P

L

A

A

T

R

6

239

I

A

P

L

A

A

T

R

A

T

6

240

A

P

L

A

A

T

R

A

T

R

6

243

A

A

T

R

A

T

R

I

G

H

6

244

A

T

R

A

T

R

I

G

H

P

6

269

A

L

S

A

R

A

P

V

P

A

6

279

A

S

P

A

A

W

L

P

L

R

6

345

A

R

G

K

P

Q

R

K

P

K

6

363

E

N

G

R

P

A

D

L

A

G

6

388

E

G

L

G

G

K

Q

K

D

K

6

3

E

H

T

T

K

T

F

P

L

R

5

10

P

L

R

A

L

H

I

V

V

E

5

23

D

H

S

G

Q

K

M

K

Q

D

5

34

K

V

D

L

L

V

P

T

K

V

5

40

P

T

K

V

T

G

I

I

T

Q

5

41

T

K

V

T

G

I

I

T

Q

G

5

51

A

K

D

F

G

H

V

Q

F

V

5

52

K

D

F

G

H

V

Q

F

V

G

5

57

V

Q

F

V

G

S

Y

K

L

A

5

87

V

L

L

G

R

K

A

V

V

V

5

95

V

V

S

C

E

G

I

N

I

S

5

97

S

C

E

G

I

N

I

S

G

S

5

104

S

G

S

F

C

R

N

K

L

K

5

123

N

T

N

P

S

R

R

P

Y

H

5

137

S

R

I

F

W

R

Q

E

K

A

5

146

A

D

G

G

S

C

C

P

Q

G

5

167

S

G

A

P

H

E

V

G

W

K

5

169

A

P

H

E

V

G

W

K

Y

Q

5

200

K

Q

L

M

R

L

Q

K

Q

A

5

229

P

R

G

L

G

F

I

F

K

T

5

235

I

F

K

T

I

A

P

L

A

A

5

252

H

P

G

G

R

T

P

R

A

G

5

260

A

G

S

S

A

H

R

P

P

A

5

266

R

P

P

A

L

S

A

R

A

P

5

309

P

Y

G

P

R

N

P

L

P

N

5

322

S

P

S

G

G

G

G

L

K

K

5

323

P

S

G

G

G

G

L

K

K

P

5

333

A

R

H

C

Q

G

Q

K

H

N

5

364

N

G

R

P

A

D

L

A

G

S

5

8

T

F

P

L

R

A

L

H

I

V

4

9

F

P

L

R

A

L

H

I

V

V

4

14

L

H

I

V

V

E

S

I

R

D

4

15

H

I

V

V

E

S

I

R

D

H

4

27

Q

K

M

K

Q

D

K

K

V

D

4

30

K

Q

D

K

K

V

D

L

L

V

4

33

K

K

V

D

L

L

V

P

T

K

4

44

T

G

I

I

T

Q

G

A

K

D

4

77

Y

Q

D

E

K

Q

R

K

D

K

4

81

K

Q

R

K

D

K

V

L

L

G

4

86

K

V

L

L

G

R

K

A

V

V

4

88

L

L

G

R

K

A

V

V

V

S

4

101

I

N

I

S

G

S

F

C

R

N

4

102

N

I

S

G

S

F

C

R

N

K

4

110

N

K

L

K

Y

L

A

F

L

H

4

112

L

K

Y

L

A

F

L

H

K

R

4

113

K

Y

L

A

F

L

H

K

R

M

4

115

L

A

F

L

H

K

R

M

N

T

4

120

K

R

M

N

T

N

P

S

R

R

4

125

N

P

S

R

R

P

Y

H

F

Q

4

135

V

P

S

R

I

F

W

R

Q

E

4

150

S

C

C

P

Q

G

H

A

S

E

4

156

H

A

S

E

A

Y

K

K

V

C

4

160

A

Y

K

K

V

C

L

S

G

A

4

179

A

V

T

A

T

L

E

E

K

R

4

188

R

K

E

K

A

E

I

H

Y

R

4

190

E

K

A

E

I

H

Y

R

K

N

4

191

K

A

E

I

H

Y

R

K

N

K

4

198

K

N

K

Q

L

M

R

L

Q

K

4

199

N

K

Q

L

M

R

L

Q

K

Q

4

201

Q

L

M

R

L

Q

K

Q

A

E

4

207

K

Q

A

E

K

N

M

K

K

K

4

222

E

S

P

G

G

G

S

P

R

G

4

228

S

P

R

G

L

G

F

I

F

K

4

234

F

I

F

K

T

I

A

P

L

A

4

238

T

I

A

P

L

A

A

T

R

A

4

247

A

T

R

I

G

H

P

G

G

R

4

248

T

R

I

G

H

P

G

G

R

T

4

250

I

G

H

P

G

G

R

T

P

R

4

256

R

T

P

R

A

G

S

S

A

H

4

263

S

A

H

R

P

P

A

L

S

A

4

265

H

R

P

P

A

L

S

A

R

A

4

270

L

S

A

R

A

P

V

P

A

A

4

271

S

A

R

A

P

V

P

A

A

S

4

284

W

L

P

L

R

T

P

W

T

R

4

287

L

R

T

P

W

T

R

P

S

S

4

291

W

T

R

P

S

S

C

P

T

S

4

300

S

S

S

T

Y

D

S

L

S

P

4

313

R

N

P

L

P

N

P

R

H

S

4

324

S

G

G

G

G

L

K

K

P

A

4

329

L

K

K

P

A

R

H

C

Q

G

4

337

Q

G

Q

K

H

N

V

L

A

R

4

346

R

G

K

P

Q

R

K

P

K

S

4

347

G

K

P

Q

R

K

P

K

S

E

4

350

Q

R

K

P

K

S

E

N

N

S

4

368

A

D

L

A

G

S

G

Y

C

G

4

378

A

L

W

K

A

I

E

S

L

E

4

382

A

I

E

S

L

E

E

G

L

G

4

384

E

S

L

E

E

G

L

G

G

K

4

11

L

R

A

L

H

I

V

V

E

S

3

13

A

L

H

I

V

V

E

S

I

R

3

20

S

I

R

D

H

S

G

Q

K

M

3

21

I

R

D

H

S

G

Q

K

M

K

3

26

G

Q

K

M

K

Q

D

K

K

V

3

31

Q

D

K

K

V

D

L

L

V

P

3

36

D

L

L

V

P

T

K

V

T

G

3

42

K

V

T

G

I

I

T

Q

G

A

3

62

S

Y

K

L

A

Y

S

N

D

G

3

69

N

D

G

E

H

W

T

V

Y

Q

3

72

E

H

W

T

V

Y

Q

D

E

K

3

74

W

T

V

Y

Q

D

E

K

Q

R

3

76

V

Y

Q

D

E

K

Q

R

K

D

3

82

Q

R

K

D

K

V

L

L

G

R

3

84

K

D

K

V

L

L

G

R

K

A

3

93

A

V

V

V

S

C

E

G

I

N

3

111

K

L

K

Y

L

A

F

L

H

K

3

118

L

H

K

R

M

N

T

N

P

S

3

144

E

K

A

D

G

G

S

C

C

P

3

145

K

A

D

G

G

S

C

C

P

Q

3

149

G

S

C

C

P

Q

G

H

A

S

3

155

G

H

A

S

E

A

Y

K

K

V

3

159

E

A

Y

K

K

V

C

L

S

G

3

163

K

V

C

L

S

G

A

P

H

E

3

164

V

C

L

S

G

A

P

H

E

V

3

165

C

L

S

G

A

P

H

E

V

G

3

172

E

V

G

W

K

Y

Q

A

V

T

3

173

V

G

W

K

Y

Q

A

V

T

A

3

174

G

W

K

Y

Q

A

V

T

A

T

3

176

K

Y

Q

A

V

T

A

T

L

E

3

180

V

T

A

T

L

E

E

K

R

K

3

181

T

A

T

L

E

E

K

R

K

E

3

186

E

K

R

K

E

K

A

E

I

H

3

203

M

R

L

Q

K

Q

A

E

K

N

3

210

E

K

N

M

K

K

K

I

D

K

3

212

N

M

K

K

K

I

D

K

Y

T

3

224

P

G

G

G

S

P

R

G

L

G

3

236

F

K

T

I

A

P

L

A

A

T

3

242

L

A

A

T

R

A

T

R

I

G

3

251

G

H

P

G

G

R

T

P

R

A

3

255

G

R

T

P

R

A

G

S

S

A

3

258

P

R

A

G

S

S

A

H

R

P

3

262

S

S

A

H

R

P

P

A

L

S

3

268

P

A

L

S

A

R

A

P

V

P

3

280

S

P

A

A

W

L

P

L

R

T

3

281

P

A

A

W

L

P

L

R

T

P

3

286

P

L

R

T

P

W

T

R

P

S

3

296

S

C

P

T

S

S

S

T

Y

D

3

308

S

P

Y

G

P

R

N

P

L

P

3

310

Y

G

P

R

N

P

L

P

N

P

3

311

G

P

R

N

P

L

P

N

P

R

3

312

P

R

N

P

L

P

N

P

R

H

3

316

L

P

N

P

R

H

S

P

S

G

3

317

P

N

P

R

H

S

P

S

G

G

3

325

G

G

G

G

L

K

K

P

A

R

3

327

G

G

L

K

K

P

A

R

H

C

3

331

K

P

A

R

H

C

Q

G

Q

K

3

339

Q

K

H

N

V

L

A

R

G

K

3

340

K

H

N

V

L

A

R

G

K

P

3

341

H

N

V

L

A

R

G

K

P

Q

3

342

N

V

L

A

R

G

K

P

Q

R

3

344

L

A

R

G

K

P

Q

R

K

P

3

354

K

S

E

N

N

S

W

Y

V

E

3

356

E

N

N

S

W

Y

V

E

N

G

3

357

N

N

S

W

Y

V

E

N

G

R

3

360

W

Y

V

E

N

G

R

P

A

D

3

373

S

G

Y

C

G

A

L

W

K

A

3

376

C

G

A

L

W

K

A

I

E

S

3

4

H

T

T

K

T

F

P

L

R

A

2

6

T

K

T

F

P

L

R

A

L

H

2

25

S

G

Q

K

M

K

Q

D

K

K

2

32

D

K

K

V

D

L

L

V

P

T

2

43

V

T

G

I

I

T

Q

G

A

K

2

49

Q

G

A

K

D

F

G

H

V

Q

2

53

D

F

G

H

V

Q

F

V

G

S

2

60

V

G

S

Y

K

L

A

Y

S

N

2

67

Y

S

N

D

G

E

H

W

T

V

2

70

D

G

E

H

W

T

V

Y

Q

D

2

83

R

K

D

K

V

L

L

G

R

K

2

89

L

G

R

K

A

V

V

V

S

C

2

107

F

C

R

N

K

L

K

Y

L

A

2

121

R

M

N

T

N

P

S

R

R

P

2

126

P

S

R

R

P

Y

H

F

Q

V

2

128

R

R

P

Y

H

F

Q

V

P

S

2

134

Q

V

P

S

R

I

F

W

R

Q

2

151

C

C

P

Q

G

H

A

S

E

A

2

154

Q

G

H

A

S

E

A

Y

K

K

2

161

Y

K

K

V

C

L

S

G

A

P

2

177

Y

Q

A

V

T

A

T

L

E

E

2

178

Q

A

V

T

A

T

L

E

E

K

2

194

I

H

Y

R

K

N

K

Q

L

M

2

197

R

K

N

K

Q

L

M

R

L

Q

2

204

R

L

Q

K

Q

A

E

K

N

M

2

216

K

I

D

K

Y

T

E

S

P

G

2

218

D

K

Y

T

E

S

P

G

G

G

2

245

T

R

A

T

R

I

G

H

P

G

2

249

R

I

G

H

P

G

G

R

T

P

2

253

P

G

G

R

T

P

R

A

G

S

2

254

G

G

R

T

P

R

A

G

S

S

2

267

P

P

A

L

S

A

R

A

P

V

2

273

R

A

P

V

P

A

A

S

P

A

2

277

P

A

A

S

P

A

A

W

L

P

2

285

L

P

L

R

T

P

W

T

R

P

2

288

R

T

P

W

T

R

P

S

S

C

2

292

T

R

P

S

S

C

P

T

S

S

2

293

R

P

S

S

C

P

T

S

S

S

2

299

T

S

S

S

T

Y

D

S

L

S

2

302

S

T

Y

D

S

L

S

P

Y

G

2

303

T

Y

D

S

L

S

P

Y

G

P

2

304

Y

D

S

L

S

P

Y

G

P

R

2

315

P

L

P

N

P

R

H

S

P

S

2

321

H

S

P

S

G

G

G

G

L

K

2

326

G

G

G

L

K

K

P

A

R

H

2

328

G

L

K

K

P

A

R

H

C

Q

2

330

K

K

P

A

R

H

C

Q

G

Q

2

336

C

Q

G

Q

K

H

N

V

L

A

2

343

V

L

A

R

G

K

P

Q

R

K

2

348

K

P

Q

R

K

P

K

S

E

N

2

359

S

W

Y

V

E

N

G

R

P

A

2

365

G

R

P

A

D

L

A

G

S

G

2

367

P

A

D

L

A

G

S

G

Y

C

2

372

G

S

G

Y

C

G

A

L

W

K

2

385

S

L

E

E

G

L

G

G

K

Q

2

389

G

L

G

G

K

Q

K

D

K

E

2

390

L

G

G

K

Q

K

D

K

E

R

2

392

G

K

Q

K

D

K

E

R

K

A

2

395

K

D

K

E

R

K

A

E

N

G

2

396

D

K

E

R

K

A

E

N

G

P

2

16

I

V

V

E

S

I

R

D

H

S

1

17

V

V

E

S

I

R

D

H

S

G

1

22

R

D

H

S

G

Q

K

M

K

Q

1

39

V

P

T

K

V

T

G

I

I

T

1

47

I

T

Q

G

A

K

D

F

G

H

1

48

T

Q

G

A

K

D

F

G

H

V

1

59

F

V

G

S

Y

K

L

A

Y

S

1

63

Y

K

L

A

Y

S

N

D

G

E

1

64

K

L

A

Y

S

N

D

G

E

H

1

73

H

W

T

V

Y

Q

D

E

K

Q

1

78

Q

D

E

K

Q

R

K

D

K

V

1

90

G

R

K

A

V

V

V

S

C

E

1

96

V

S

C

E

G

I

N

I

S

G

1

114

Y

L

A

F

L

H

K

R

M

N

1

129

R

P

Y

H

F

Q

V

P

S

R

1

136

P

S

R

I

F

W

R

Q

E

K

1

139

I

F

W

R

Q

E

K

A

D

G

1

140

F

W

R

Q

E

K

A

D

G

G

1

147

D

G

G

S

C

C

P

Q

G

H

1

148

G

G

S

C

C

P

Q

G

H

A

1

162

K

K

V

C

L

S

G

A

P

H

1

170

P

H

E

V

G

W

K

Y

Q

A

1

183

T

L

E

E

K

R

K

E

K

A

1

195

H

Y

R

K

N

K

Q

L

M

R

1

202

L

M

R

L

Q

K

Q

A

E

K

1

205

L

Q

K

Q

A

E

K

N

M

K

1

206

Q

K

Q

A

E

K

N

M

K

K

1

213

M

K

K

K

I

D

K

Y

T

E

1

214

K

K

K

I

D

K

Y

T

E

S

1

219

K

Y

T

E

S

P

G

G

G

S

1

246

R

A

T

R

I

G

H

P

G

G

1

259

R

A

G

S

S

A

H

R

P

P

1

289

T

P

W

T

R

P

S

S

C

P

1

290

P

W

T

R

P

S

S

C

P

T

1

294

P

S

S

C

P

T

S

S

S

T

1

297

C

P

T

S

S

S

T

Y

D

S

1

305

D

S

L

S

P

Y

G

P

R

N

1

318

N

P

R

H

S

P

S

G

G

G

1

332

P

A

R

H

C

Q

G

Q

K

H

1

334

R

H

C

Q

G

Q

K

H

N

V

1

338

G

Q

K

H

N

V

L

A

R

G

1

353

P

K

S

E

N

N

S

W

Y

V

1

358

N

S

W

Y

V

E

N

G

R

P

1

369

D

L

A

G

S

G

Y

C

G

A

1

379

L

W

K

A

I

E

S

L

E

E

1

380

W

K

A

I

E

S

L

E

E

G

1

394

Q

K

D

K

E

R

K

A

E

N

1

TABLE XLVII
151P3D4
HLA Peptide Scoring
Results B*5101 10-mers SYFPEITHI
												SEQ.
Pos	1	2	3	4	5	6	7	8	9	0	score	ID NO.
	NO DATA

TABLE XLVIII

SEQ. ID

Pos

1

2

3

4

5

6

7

8

9

0

1

2

3

4

5

score

NO.

151P3D4 v.1

HLA Peptide Scoring Results DRB1*0101

15 - mers SYFPEITHI

78

R

I

K

W

T

K

L

T

S

D

Y

L

K

E

V

35

Portion of

259

G

R

F

Y

Y

L

I

H

P

T

K

L

T

Y

D

33

SEQ ID NO:

61

C

K

F

Y

R

D

P

T

A

F

G

S

G

I

H

30

3; each start

214

S

V

Q

Y

P

I

T

K

P

R

E

P

C

G

G

28

position is

7

L

V

L

I

S

I

C

W

A

D

H

L

S

D

N

27

specified, the

27

D

R

A

I

H

I

Q

A

E

N

G

P

H

L

L

27

length of

102

K

K

T

Y

G

G

Y

Q

G

R

V

F

L

K

G

27

peptide is 15

148

D

T

V

V

V

A

L

D

L

Q

G

V

V

F

P

27

amino acids,

161

F

P

Y

F

P

R

L

G

R

Y

N

L

N

F

H

27

the end

169

R

Y

N

L

N

F

H

E

A

Q

Q

A

C

L

D

27

position for

109

Q

G

R

V

F

L

K

G

G

S

D

S

D

A

S

26

each peptide

267

P

T

K

L

T

Y

D

E

A

V

Q

A

C

L

N

26

is the start

298

I

L

G

Y

D

R

C

D

A

G

W

L

A

D

G

26

position plus

1

M

K

S

L

L

L

L

V

L

I

S

I

C

W

A

25

fourteen

39

H

L

L

V

E

A

E

Q

A

K

V

F

S

H

R

25

139

C

E

V

I

E

G

L

E

D

D

T

V

V

V

A

25

283

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G

G

Q

N

T

V

P

10

224

E

P

C

G

G

Q

N

T

V

P

G

V

R

N

Y

10

237

N

Y

G

F

W

D

K

D

K

S

R

Y

D

V

F

10

240

F

W

D

K

D

K

S

R

Y

D

V

F

C

F

T

10

265

I

H

P

T

K

L

T

Y

D

E

A

V

Q

A

C

10

288

K

V

G

Q

I

F

A

A

W

K

I

L

G

Y

D

10

316

Y

P

I

S

R

P

R

R

R

C

S

P

T

E

A

10

324

R

C

S

P

T

E

A

A

V

R

F

V

G

F

P

10

332

V

R

F

V

G

F

P

D

K

K

H

K

L

Y

G

10

13

C

W

A

D

H

L

S

D

N

Y

T

L

D

H

D

9

35

E

N

G

P

H

L

L

V

E

A

E

Q

A

K

V

9

48

K

V

F

S

H

R

G

G

N

V

T

L

P

C

K

9

65

R

D

P

T

A

F

G

S

G

I

H

K

I

R

I

9

95

F

V

S

M

G

Y

H

K

K

T

Y

G

G

Y

Q

9

106

G

G

Y

Q

G

R

V

F

L

K

G

G

S

D

S

9

127

T

D

L

T

L

E

D

Y

G

R

Y

K

C

E

V

9

147

D

D

T

V

V

V

A

L

D

L

Q

G

V

V

F

9

177

A

Q

Q

A

C

L

D

Q

D

A

V

I

A

S

F

9

186

A

V

I

A

S

F

D

Q

L

Y

D

A

W

R

G

9

189

A

S

F

D

Q

L

Y

D

A

W

R

G

G

L

D

9

193

Q

L

Y

D

A

W

R

G

G

L

D

W

C

N

A

9

205

C

N

A

G

W

L

S

D

G

S

V

Q

Y

P

I

9

220

T

K

P

R

E

P

C

G

G

Q

N

T

V

P

G

9

221

K

P

R

E

P

C

G

G

Q

N

T

V

P

G

V

9

222

P

R

E

P

C

G

G

Q

N

T

V

P

G

V

R

9

231

T

V

P

G

V

R

N

Y

G

F

W

D

K

D

K

9

239

G

F

W

D

K

D

K

S

R

Y

D

V

F

C

F

9

251

F

C

F

T

S

N

F

N

G

R

F

Y

Y

L

I

9

262

Y

Y

L

I

H

P

T

K

L

T

Y

D

E

A

V

9

277

Q

A

C

L

N

D

G

A

Q

I

A

K

V

G

Q

9

278

A

C

L

N

D

G

A

Q

I

A

K

V

G

Q

I

9

284

A

Q

I

A

K

V

G

Q

I

F

A

A

W

K

I

9

304

C

D

A

G

W

L

A

D

G

S

V

R

Y

P

I

9

310

A

D

G

S

V

R

Y

P

I

S

R

P

R

R

R

9

322

R

R

R

C

S

P

T

E

A

A

V

R

F

V

G

9

328

T

E

A

A

V

R

F

V

G

F

P

D

K

K

H

9

333

R

F

V

G

F

P

D

K

K

H

K

L

Y

G

V

9

8

V

L

I

S

I

C

W

A

D

H

L

S

D

N

Y

8

9

L

I

S

I

C

W

A

D

H

L

S

D

N

Y

T

8

12

I

C

W

A

D

H

L

S

D

N

Y

T

L

D

H

8

23

T

L

D

H

D

R

A

I

H

I

Q

A

E

N

G

8

24

L

D

H

D

R

A

I

H

I

Q

A

E

N

G

P

8

31

H

I

Q

A

E

N

G

P

H

L

L

V

E

A

E

8

33

Q

A

E

N

G

P

H

L

L

V

E

A

E

Q

A

8

34

A

E

N

G

P

H

L

L

V

E

A

E

Q

A

K

8

37

G

P

H

L

L

V

E

A

E

Q

A

K

V

F

S

8

64

Y

R

D

P

T

A

F

G

S

G

I

H

K

I

R

8

87

D

Y

L

K

E

V

D

V

F

V

S

M

G

Y

H

8

90

K

E

V

D

V

F

V

S

M

G

Y

H

K

K

T

8

96

V

S

M

G

Y

H

K

K

T

Y

G

G

Y

Q

G

8

101

H

K

K

T

Y

G

G

Y

Q

G

R

V

F

L

K

8

113

F

L

K

G

G

S

D

S

D

A

S

L

V

I

T

8

130

T

L

E

D

Y

G

R

Y

K

C

E

V

I

E

G

8

138

K

C

E

V

I

E

G

L

E

D

D

T

V

V

V

8

143

E

G

L

E

D

D

T

V

V

V

A

L

D

L

Q

8

163

Y

F

P

R

L

G

R

Y

N

L

N

F

H

E

A

8

164

F

P

R

L

G

R

Y

N

L

N

F

H

E

A

Q

8

175

H

E

A

Q

Q

A

C

L

D

Q

D

A

V

I

A

8

180

A

C

L

D

Q

D

A

V

I

A

S

F

D

Q

L

8

184

Q

D

A

V

I

A

S

F

D

Q

L

Y

D

A

W

8

185

D

A

V

I

A

S

F

D

Q

L

Y

D

A

W

R

8

208

G

W

L

S

D

G

S

V

Q

Y

P

I

T

K

P

8

242

D

K

D

K

S

R

Y

D

V

F

C

F

T

S

N

8

253

F

T

S

N

F

N

G

R

F

Y

Y

L

I

H

P

8

261

F

Y

Y

L

I

H

P

T

K

L

T

Y

D

E

A

8

274

E

A

V

Q

A

C

L

N

D

G

A

Q

I

A

K

8

280

L

N

D

G

A

Q

I

A

K

V

G

Q

I

F

A

8

289

V

G

Q

I

F

A

A

W

K

I

L

G

Y

D

R

8

296

W

K

I

L

G

Y

D

R

C

D

A

G

W

L

A

8

307

G

W

L

A

D

G

S

V

R

Y

P

I

S

R

P

8

318

I

S

R

P

R

R

R

C

S

P

T

E

A

A

V

8

321

P

R

R

R

C

S

P

T

E

A

A

V

R

F

V

8

327

P

T

E

A

A

V

R

F

V

G

F

P

D

K

K

8

88

Y

L

K

E

V

D

V

F

V

S

M

G

Y

H

K

7

146

E

D

D

T

V

V

V

A

L

D

L

Q

G

V

V

7

285

Q

I

A

K

V

G

Q

I

F

A

A

W

K

I

L

7

330

A

A

V

R

F

V

G

F

P

D

K

K

H

K

L

7

50

F

S

H

R

G

G

N

V

T

L

P

C

K

F

Y

6

51

S

H

R

G

G

N

V

T

L

P

C

K

F

Y

R

6

77

I

R

I

K

W

T

K

L

T

S

D

Y

L

K

E

6

135

G

R

Y

K

C

E

V

I

E

G

L

E

D

D

T

6

144

G

L

E

D

D

T

V

V

V

A

L

D

L

Q

G

6

173

N

F

H

E

A

Q

Q

A

C

L

D

Q

D

A

V

6

187

V

I

A

S

F

D

Q

L

Y

D

A

W

R

G

G

6

209

W

L

S

D

G

S

V

Q

Y

P

I

T

K

P

R

6

213

G

S

V

Q

Y

P

I

T

K

P

R

E

P

C

G

6

225

P

C

G

G

Q

N

T

V

P

G

V

R

N

Y

G

6

263

Y

L

I

H

P

T

K

L

T

Y

D

E

A

V

Q

6

271

T

Y

D

E

A

V

Q

A

C

L

N

D

G

A

Q

6

309

L

A

D

G

S

V

R

Y

P

I

S

R

P

R

R

6

312

G

S

V

R

Y

P

I

S

R

P

R

R

R

C

S

6

137

Y

K

C

E

V

I

E

G

L

E

D

D

T

V

V

5

44

A

E

Q

A

K

V

F

S

H

R

G

G

N

V

T

4

45

E

Q

A

K

V

F

S

H

R

G

G

N

V

T

L

4

69

A

F

G

S

G

I

H

K

I

R

I

K

W

T

K

4

72

S

G

I

H

K

I

R

I

K

W

T

K

L

T

S

4

100

Y

H

K

K

T

Y

G

G

Y

Q

G

R

V

F

L

4

25

D

H

D

R

A

I

H

I

Q

A

E

N

G

P

H

3

133

D

Y

G

R

Y

K

C

E

V

I

E

G

L

E

D

3

162

P

Y

F

P

R

L

G

R

Y

N

L

N

F

H

E

3

190

S

F

D

Q

L

Y

D

A

W

R

G

G

L

D

W

3

227

G

G

Q

N

T

V

P

G

V

R

N

Y

G

F

W

3

252

C

F

T

S

N

F

N

G

R

F

Y

Y

L

I

H

3

57

V

T

L

P

C

K

F

Y

R

D

P

T

A

F

G

2

79

I

K

W

T

K

L

T

S

D

Y

L

K

E

V

D

2

132

E

D

Y

G

R

Y

K

C

E

V

I

E

G

L

E

2

165

P

R

L

G

R

Y

N

L

N

F

H

E

A

Q

Q

2

198

W

R

G

G

L

D

W

C

N

A

G

W

L

S

D

2

218

P

I

T

K

P

R

E

P

C

G

G

Q

N

T

V

2

233

P

G

V

R

N

Y

G

F

W

D

K

D

K

S

R

2

243

K

D

K

S

R

Y

D

V

F

C

F

T

S

N

F

2

249

D

V

F

C

F

T

S

N

F

N

G

R

F

Y

Y

2

294

A

A

W

K

I

L

G

Y

D

R

C

D

A

G

W

2

297

K

I

L

G

Y

D

R

C

D

A

G

W

L

A

D

2

335

V

G

F

P

D

K

K

H

K

L

Y

G

V

Y

C

2

14

W

A

D

H

L

S

D

N

Y

T

L

D

H

D

R

1

17

H

L

S

D

N

Y

T

L

D

H

D

R

A

I

H

1

28

R

A

I

H

I

Q

A

E

N

G

P

H

L

L

V

1

32

I

Q

A

E

N

G

P

H

L

L

V

E

A

E

Q

1

70

F

G

S

G

I

H

K

I

R

I

K

W

T

K

L

1

80

K

W

T

K

L

T

S

D

Y

L

K

E

V

D

V

1

94

V

F

V

S

M

G

Y

H

K

K

T

Y

G

G

Y

1

124

L

V

I

T

D

L

T

L

E

D

Y

G

R

Y

K

1

129

L

T

L

E

D

Y

G

R

Y

K

C

E

V

I

E

1

155

D

L

Q

G

V

V

F

P

Y

F

P

R

L

G

R

1

159

V

V

F

P

Y

F

P

R

L

G

R

Y

N

L

N

1

194

L

Y

D

A

W

R

G

G

L

D

W

C

N

A

G

1

197

A

W

R

G

G

L

D

W

C

N

A

G

W

L

S

1

202

L

D

W

C

N

A

G

W

L

S

D

G

S

V

Q

1

228

G

Q

N

T

V

P

G

V

R

N

Y

G

F

W

D

1

234

G

V

R

N

Y

G

F

W

D

K

D

K

S

R

Y

1

236

R

N

Y

G

F

W

D

K

D

K

S

R

Y

D

V

1

241

W

D

K

D

K

S

R

Y

D

V

F

C

F

T

S

1

272

Y

D

E

A

V

Q

A

C

L

N

D

G

A

Q

I

1

300

G

Y

D

R

C

D

A

G

W

L

A

D

G

S

V

1

314

V

R

Y

P

I

S

R

P

R

R

R

C

S

P

T

1

337

F

P

D

K

K

H

K

L

Y

G

V

Y

C

F

R

1

151P3D4 v.2

HLA Peptide Scoring Results DRB1*0101

15 - mers SYFPEITHI

301

S

S

T

Y

D

S

L

S

P

Y

G

P

R

N

P

34

Portion of

32

D

K

K

V

D

L

L

V

P

T

K

V

T

G

I

33

SEQ ID NO:

236

F

K

T

I

A

P

L

A

A

T

R

A

T

R

I

33

5; each start

43

V

T

G

I

I

T

Q

G

A

K

D

F

G

H

V

32

position is

40

P

T

K

V

T

G

I

I

T

Q

G

A

K

D

F

31

specified, the

54

F

G

H

V

Q

F

V

G

S

Y

K

L

A

Y

S

31

length of

128

R

R

P

Y

H

F

Q

V

P

S

R

I

F

W

R

31

peptide is 15

233

G

F

I

F

K

T

I

A

P

L

A

A

T

R

A

31

amino acids,

158

S

E

A

Y

K

K

V

C

L

S

G

A

P

H

E

29

the end

217

I

D

K

Y

T

E

S

P

G

G

G

S

P

R

G

29

position for

18

V

E

S

I

R

D

H

S

G

Q

K

M

K

Q

D

27

each peptide is

82

Q

R

K

D

K

V

L

L

G

R

K

A

V

V

V

27

the start

357

N

N

S

W

Y

V

E

N

G

R

P

A

D

L

A

27

position plus

51

A

K

D

F

G

H

V

Q

F

V

G

S

Y

K

L

26

fourteen

92

K

A

V

V

V

S

C

E

G

I

N

I

S

G

S

26

232

L

G

F

I

F

K

T

I

A

P

L

A

A

T

R

26

247

A

T

R

I

G

H

P

G

G

R

T

P

R

A

G

26

174

G

W

K

Y

Q

A

V

T

A

T

L

E

E

K

R

25

202

L

M

R

L

Q

K

Q

A

E

K

N

M

K

K

K

25

239

I

A

P

L

A

A

T

R

A

T

R

I

G

H

P

25

264

A

H

R

P

P

A

L

S

A

R

A

P

V

P

A

25

284

W

L

P

L

R

T

P

W

T

R

P

S

S

C

P

25

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P

H

2

164

V

C

L

S

G

A

P

H

E

V

G

W

K

Y

Q

2

203

M

R

L

Q

K

Q

A

E

K

N

M

K

K

K

I

2

205

L

Q

K

Q

A

E

K

N

M

K

K

K

I

D

K

2

208

Q

A

E

K

N

M

K

K

K

I

D

K

Y

T

E

2

227

G

S

P

R

G

L

G

F

I

F

K

T

I

A

P

2

248

T

R

I

G

H

P

G

G

R

T

P

R

A

G

S

2

262

S

S

A

H

R

P

P

A

L

S

A

R

A

P

V

2

280

S

P

A

A

W

L

P

L

R

T

P

W

T

R

P

2

328

G

L

K

K

P

A

R

H

C

Q

G

Q

K

H

N

2

335

H

C

Q

G

Q

K

H

N

V

L

A

R

G

K

P

2

355

S

E

N

N

S

W

Y

V

E

N

G

R

P

A

D

2

392

G

K

Q

K

D

K

E

R

K

A

E

N

G

P

H

2

1

M

L

E

H

T

T

K

T

F

P

L

R

A

L

H

1

20

S

I

R

D

H

S

G

Q

K

M

K

Q

D

K

K

1

30

K

Q

D

K

K

V

D

L

L

V

P

T

K

V

T

1

66

A

Y

S

N

D

G

E

H

W

T

V

Y

Q

D

E

1

75

T

V

Y

Q

D

E

K

Q

R

K

D

K

V

L

L

1

103

I

S

G

S

F

C

R

N

K

L

K

Y

L

A

F

1

113

K

Y

L

A

F

L

H

K

R

M

N

T

N

P

S

1

121

R

M

N

T

N

P

S

R

R

P

Y

H

F

Q

V

1

131

Y

H

F

Q

V

P

S

R

I

F

W

R

Q

E

K

1

154

Q

G

H

A

S

E

A

Y

K

K

V

C

L

S

G

1

165

C

L

S

G

A

P

H

E

V

G

W

K

Y

Q

A

1

176

K

Y

Q

A

V

T

A

T

L

E

E

K

R

K

E

1

180

V

T

A

T

L

E

E

K

R

K

E

K

A

E

I

1

185

E

E

K

R

K

E

K

A

E

I

H

Y

R

K

N

1

187

K

R

K

E

K

A

E

I

H

Y

R

K

N

K

Q

1

190

E

K

A

E

I

H

Y

R

K

N

K

Q

L

M

R

1

204

R

L

Q

K

Q

A

E

K

N

M

K

K

K

I

D

1

299

T

S

S

S

T

Y

D

S

L

S

P

Y

G

P

R

1

302

S

T

Y

D

S

L

S

P

Y

G

P

R

N

P

L

1

327

G

G

L

K

K

P

A

R

H

C

Q

G

Q

K

H

1

336

C

Q

G

Q

K

H

N

V

L

A

R

G

K

P

Q

1

350

Q

R

K

P

K

S

E

N

N

S

W

Y

V

E

N

1

353

P

K

S

E

N

N

S

W

Y

V

E

N

G

R

P

1

354

K

S

E

N

N

S

W

Y

V

E

N

G

R

P

A

1

386

L

E

E

G

L

G

G

K

Q

K

D

K

E

R

K

1

389

G

L

G

G

K

Q

K

D

K

E

R

K

A

E

N

1

399

R

K

A

E

N

G

P

H

L

L

V

E

A

E

Q

1

TABLE XLIX

151P3D4 v.1:

HLA Peptide Scoring Results DRB1*0301

15 - mers SYFPEITHI

SEQ. ID

Pos

1

2

3

4

5

6

7

8

9

0

1

2

3

4

5

score

NO.

149

T

V

V

V

A

L

D

L

Q

G

V

V

F

P

Y

28

Portion of

333

R

F

V

G

F

P

D

K

K

H

K

L

Y

G

V

27

SEQ ID NO:

261

F

Y

Y

L

I

H

P

T

K

L

T

Y

D

E

A

26

3; each start

161

F

P

Y

F

P

R

L

G

R

Y

N

L

N

F

H

24

position is

171

N

L

N

F

H

E

A

Q

Q

A

C

L

D

Q

D

24

specified, the

191

F

D

Q

L

Y

D

A

W

R

G

G

L

D

W

C

24

length of

229

Q

N

T

V

P

G

V

R

N

Y

G

F

W

D

K

24

peptide is 15

250

V

F

C

F

T

S

N

F

N

G

R

F

Y

Y

L

24

amino acids,

122

A

S

L

V

I

T

D

L

T

L

E

D

Y

G

R

23

the end

206

N

A

G

W

L

S

D

G

S

V

Q

Y

P

I

T

23

position for

267

P

T

K

L

T

Y

D

E

A

V

Q

A

C

L

N

23

each peptide

81

W

T

K

L

T

S

D

Y

L

K

E

V

D

V

F

22

is the start

237

N

Y

G

F

W

D

K

D

K

S

R

Y

D

V

F

22

position plus

305

D

A

G

W

L

A

D

G

S

V

R

Y

P

I

S

22

fourteen

38

P

H

L

L

V

E

A

E

Q

A

K

V

F

S

H

21

113

F

L

K

G

G

S

D

S

D

A

S

L

V

I

T

21

142

I

E

G

L

E

D

D

T

V

V

V

A

L

D

L

21

179

Q

A

C

L

D

Q

D

A

V

I

A

S

F

D

Q

21

184

Q

D

A

V

I

A

S

F

D

Q

L

Y

D

A

W

21

296

W

K

I

L

G

Y

D

R

C

D

A

G

W

L

A

21

21

N

Y

T

L

D

H

D

R

A

I

H

I

Q

A

E

20

37

G

P

H

L

L

V

E

A

E

Q

A

K

V

F

S

20

60

P

C

K

F

Y

R

D

P

T

A

F

G

S

G

I

20

126

I

T

D

L

T

L

E

D

Y

G

R

Y

K

C

E

20

123

S

L

V

I

T

D

L

T

L

E

D

Y

G

R

Y

19

138

K

C

E

V

I

E

G

L

E

D

D

T

V

V

V

19

156

L

Q

G

V

V

F

P

Y

F

P

R

L

G

R

Y

19

7

L

V

L

I

S

I

C

W

A

D

H

L

S

D

N

18

29

A

I

H

I

Q

A

E

N

G

P

H

L

L

V

E

18

39

H

L

L

V

E

A

E

Q

A

K

V

F

S

H

R

18

54

G

G

N

V

T

L

P

C

K

F

Y

R

D

P

T

18

89

L

K

E

V

D

V

F

V

S

M

G

Y

H

K

K

18

128

D

L

T

L

E

D

Y

G

R

Y

K

C

E

V

I

18

153

A

L

D

L

Q

G

V

V

F

P

Y

F

P

R

L

18

163

Y

F

P

R

L

G

R

Y

N

L

N

F

H

E

A

18

185

D

A

V

I

A

S

F

D

Q

L

Y

D

A

W

R

18

199

R

G

G

L

D

W

C

N

A

G

W

L

S

D

G

18

290

G

Q

I

F

A

A

W

K

I

L

G

Y

D

R

C

18

295

A

W

K

I

L

G

Y

D

R

C

D

A

G

W

L

18

334

F

V

G

F

P

D

K

K

H

K

L

Y

G

V

Y

18

27

D

R

A

I

H

I

Q

A

E

N

G

P

H

L

L

17

95

F

V

S

M

G

Y

H

K

K

T

Y

G

G

Y

Q

17

216

Q

Y

P

I

T

K

P

R

E

P

C

G

G

Q

N

17

273

D

E

A

V

Q

A

C

L

N

D

G

A

Q

I

A

17

277

Q

A

C

L

N

D

G

A

Q

I

A

K

V

G

Q

17

283

G

A

Q

I

A

K

V

G

Q

I

F

A

A

W

K

17

289

V

G

Q

I

F

A

A

W

K

I

L

G

Y

D

R

17

48

K

V

F

S

H

R

G

G

N

V

T

L

P

C

K

16

103

K

T

Y

G

G

Y

Q

G

R

V

F

L

K

G

G

16

158

G

V

V

F

P

Y

F

P

R

L

G

R

Y

N

L

16

248

Y

D

V

F

C

F

T

S

N

F

N

G

R

F

Y

16

269

K

L

T

Y

D

E

A

V

Q

A

C

L

N

D

G

16

315

R

Y

P

I

S

R

P

R

R

R

C

S

P

T

E

16

332

V

R

F

V

G

F

P

D

K

K

H

K

L

Y

G

16

13

C

W

A

D

H

L

S

D

N

Y

T

L

D

H

D

15

252

C

F

T

S

N

F

N

G

R

F

Y

Y

L

I

H

15

2

K

S

L

L

L

L

V

L

I

S

I

C

W

A

D

14

14

W

A

D

H

L

S

D

N

Y

T

L

D

H

D

R

14

94

V

F

V

S

M

G

Y

H

K

K

T

Y

G

G

Y

14

141

V

I

E

G

L

E

D

D

T

V

V

V

A

L

D

14

276

V

Q

A

C

L

N

D

G

A

Q

I

A

K

V

G

14

1

M

K

S

L

L

L

L

V

L

I

S

I

C

W

A

13

4

L

L

L

L

V

L

I

S

I

C

W

A

D

H

L

13

5

L

L

L

V

L

I

S

I

C

W

A

D

H

L

S

13

6

L

L

V

L

I

S

I

C

W

A

D

H

L

S

D

13

19

S

D

N

Y

T

L

D

H

D

R

A

I

H

I

Q

13

127

T

D

L

T

L

E

D

Y

G

R

Y

K

C

E

V

13

147

D

D

T

V

V

V

A

L

D

L

Q

G

V

V

F

13

151

V

V

A

L

D

L

Q

G

V

V

F

P

Y

F

P

13

197

A

W

R

G

G

L

D

W

C

N

A

G

W

L

S

13

3

S

L

L

L

L

V

L

I

S

I

C

W

A

D

H

12

46

Q

A

K

V

F

S

H

R

G

G

N

V

T

L

P

12

74

I

H

K

I

R

I

K

W

T

K

L

T

S

D

Y

12

76

K

I

R

I

K

W

T

K

L

T

S

D

Y

L

K

12

86

S

D

Y

L

K

E

V

D

V

F

V

S

M

G

Y

12

92

V

D

V

F

V

S

M

G

Y

H

K

K

T

Y

G

12

93

D

V

F

V

S

M

G

Y

H

K

K

T

Y

G

G

12

109

Q

G

R

V

F

L

K

G

G

S

D

S

D

A

S

12

111

R

V

F

L

K

G

G

S

D

S

D

A

S

L

V

12

115

K

G

G

S

D

S

D

A

S

L

V

I

T

D

L

12

121

D

A

S

L

V

I

T

D

L

T

L

E

D

Y

G

12

148

D

T

V

V

V

A

L

D

L

Q

G

V

V

F

P

12

157

Q

G

V

V

F

P

Y

F

P

R

L

G

R

Y

N

12

169

R

Y

N

L

N

F

H

E

A

Q

Q

A

C

L

D

12

177

A

Q

Q

A

C

L

D

Q

D

A

V

I

A

S

F

12

190

S

F

D

Q

L

Y

D

A

W

R

G

G

L

D

W

12

207

A

G

W

L

S

D

G

S

V

Q

Y

P

I

T

K

12

232

V

P

G

V

R

N

Y

G

F

W

D

K

D

K

S

12

262

Y

Y

L

I

H

P

T

K

L

T

Y

D

E

A

V

12

299

L

G

Y

D

R

C

D

A

G

W

L

A

D

G

S

12

329

E

A

A

V

R

F

V

G

F

P

D

K

K

H

K

12

9

L

I

S

I

C

W

A

D

H

L

S

D

N

Y

T

11

15

A

D

H

L

S

D

N

Y

T

L

D

H

D

R

A

11

30

I

H

I

Q

A

E

N

G

P

H

L

L

V

E

A

11

73

G

I

H

K

I

R

I

K

W

T

K

L

T

S

D

11

87

D

Y

L

K

E

V

D

V

F

V

S

M

G

Y

H

11

110

G

R

V

F

L

K

G

G

S

D

S

D

A

S

L

11

120

S

D

A

S

L

V

I

T

D

L

T

L

E

D

Y

11

139

C

E

V

I

E

G

L

E

D

D

T

V

V

V

A

11

150

V

V

V

A

L

D

L

Q

G

V

V

F

P

Y

F

11

164

F

P

R

L

G

R

Y

N

L

N

F

H

E

A

Q

11

227

G

G

Q

N

T

V

P

G

V

R

N

Y

G

F

W

11

236

R

N

Y

G

F

W

D

K

D

K

S

R

Y

D

V

11

238

Y

G

F

W

D

K

D

K

S

R

Y

D

V

F

C

11

243

K

D

K

S

R

Y

D

V

F

C

F

T

S

N

F

11

247

R

Y

D

V

F

C

F

T

S

N

F

N

G

R

F

11

286

I

A

K

V

G

Q

I

F

A

A

W

K

I

L

G

11

306

A

G

W

L

A

D

G

S

V

R

Y

P

I

S

R

11

311

D

G

S

V

R

Y

P

I

S

R

P

R

R

R

C

11

331

A

V

R

F

V

G

F

P

D

K

K

H

K

L

Y

11

339

D

K

K

H

K

L

Y

G

V

Y

C

F

R

A

Y

11

10

I

S

I

C

W

A

D

H

L

S

D

N

Y

T

L

10

11

S

I

C

W

A

D

H

L

S

D

N

Y

T

L

D

10

47

A

K

V

F

S

H

R

G

G

N

V

T

L

P

C

10

52

H

R

G

G

N

V

T

L

P

C

K

F

Y

R

D

10

53

R

G

G

N

V

T

L

P

C

K

F

Y

R

D

P

10

56

N

V

T

L

P

C

K

F

Y

R

D

P

T

A

F

10

71

G

S

G

I

H

K

I

R

I

K

W

T

K

L

T

10

84

L

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D

W

C

N

A

G

1

196

D

A

W

R

G

G

L

D

W

C

N

A

G

W

L

1

200

G

G

L

D

W

C

N

A

G

W

L

S

D

G

S

1

203

D

W

C

N

A

G

W

L

S

D

G

S

V

Q

Y

1

204

W

C

N

A

G

W

L

S

D

G

S

V

Q

Y

P

1

205

C

N

A

G

W

L

S

D

G

S

V

Q

Y

P

I

1

209

W

L

S

D

G

S

V

Q

Y

P

I

T

K

P

R

1

214

S

V

Q

Y

P

I

T

K

P

R

E

P

C

G

G

1

218

P

I

T

K

P

R

E

P

C

G

G

Q

N

T

V

1

223

R

E

P

C

G

G

Q

N

T

V

P

G

V

R

N

1

231

T

V

P

G

V

R

N

Y

G

F

W

D

K

D

K

1

233

P

G

V

R

N

Y

G

F

W

D

K

D

K

S

R

1

249

D

V

F

C

F

T

S

N

F

N

G

R

F

Y

Y

1

255

S

N

F

N

G

R

F

Y

Y

L

I

H

P

T

K

1

256

N

F

N

G

R

F

Y

Y

L

I

H

P

T

K

L

1

257

F

N

G

R

F

Y

Y

L

I

H

P

T

K

L

T

1

263

Y

L

I

H

P

T

K

L

T

Y

D

E

A

V

Q

1

264

L

I

H

P

T

K

L

T

Y

D

E

A

V

Q

A

1

270

L

T

Y

D

E

A

V

Q

A

C

L

N

D

G

A

1

274

E

A

V

Q

A

C

L

N

D

G

A

Q

I

A

K

1

281

N

D

G

A

Q

I

A

K

V

G

Q

I

F

A

A

1

287

A

K

V

G

Q

I

F

A

A

W

K

I

L

G

Y

1

292

I

F

A

A

W

K

I

L

G

Y

D

R

C

D

A

1

297

K

I

L

G

Y

D

R

C

D

A

G

W

L

A

D

1

301

Y

D

R

C

D

A

G

W

L

A

D

G

S

V

R

1

302

D

R

C

D

A

G

W

L

A

D

G

S

V

R

Y

1

304

C

D

A

G

W

L

A

D

G

S

V

R

Y

P

I

1

308

W

L

A

D

G

S

V

R

Y

P

I

S

R

P

R

1

318

I

S

R

P

R

R

R

C

S

P

T

E

A

A

V

1

328

T

E

A

A

V

R

F

V

G

F

P

D

K

K

H

1

330

A

A

V

R

F

V

G

F

P

D

K

K

H

K

L

1

338

P

D

K

K

H

K

L

Y

G

V

Y

C

F

R

A

1

151P3D4 v.2:

HLA Peptide Scoring Results DRB1*0301

15 - mers SYFPEITHI

Pos

1

2

3

4

5

6

7

8

9

0

1

2

3

4

5

score

SEQ. ID NO.

26

G

Q

K

M

K

Q

D

K

K

V

D

L

L

V

P

37

Portion of

73

H

W

T

V

Y

Q

D

E

K

Q

R

K

D

K

V

28

SEQ ID NO:

56

H

V

Q

F

V

G

S

Y

K

L

A

Y

S

N

D

25

5; each start

191

K

A

E

I

H

Y

R

K

N

K

Q

L

M

R

L

25

position is

43

V

T

G

I

I

T

Q

G

A

K

D

F

G

H

V

20

specified, the

54

F

G

H

V

Q

F

V

G

S

Y

K

L

A

Y

S

20

length of

84

K

D

K

V

L

L

G

R

K

A

V

V

V

S

C

20

peptide is 15

200

K

Q

L

M

R

L

Q

K

Q

A

E

K

N

M

K

20

amino acids,

299

T

S

S

S

T

Y

D

S

L

S

P

Y

G

P

R

20

the end

34

K

V

D

L

L

V

P

T

K

V

T

G

I

I

I

19

position for

177

Y

Q

A

V

T

A

T

L

E

E

K

R

K

E

K

19

each peptide is

340

K

H

N

V

L

A

R

G

K

P

Q

R

K

P

K

19

the start

359

S

W

Y

V

E

N

G

R

P

A

D

L

A

G

S

19

position plus

380

W

K

A

I

E

S

L

E

E

G

L

G

G

K

Q

19

fourteen

14

L

H

I

V

V

E

S

I

R

D

H

S

G

Q

K

18

181

T

A

T

L

E

E

K

R

K

E

K

A

E

I

H

18

199

N

K

Q

L

M

R

L

Q

K

Q

A

E

K

N

M

18

231

G

L

G

F

I

F

K

T

I

A

P

L

A

A

T

18

390

L

G

G

K

Q

K

D

K

E

R

K

A

E

N

G

18

44

T

G

I

I

T

Q

G

A

K

D

F

G

H

V

Q

17

64

K

L

A

Y

S

N

D

G

E

H

W

T

V

Y

Q

17

91

R

K

A

V

V

V

S

C

E

G

I

N

I

S

G

17

101

I

N

I

S

G

S

F

C

R

N

K

L

K

Y

L

17

104

S

G

S

F

C

R

N

K

L

K

Y

L

A

F

L

17

115

L

A

F

L

H

K

R

M

N

T

N

P

S

R

R

17

136

P

S

R

I

F

W

R

Q

E

K

A

D

G

G

S

17

170

P

H

E

V

G

W

K

Y

Q

A

V

T

A

T

L

17

202

L

M

R

L

Q

K

Q

A

E

K

N

M

K

K

K

17

326

G

G

G

L

K

K

P

A

R

H

C

Q

G

Q

K

17

376

C

G

A

L

W

K

A

I

E

S

L

E

E

G

L

17

379

L

W

K

A

I

E

S

L

E

E

G

L

G

G

K

17

387

E

E

G

L

G

G

K

Q

K

D

K

E

R

K

A

17

11

L

R

A

L

H

I

V

V

E

S

I

R

D

H

S

16

78

Q

D

E

K

Q

R

K

D

K

V

L

L

G

R

K

16

103

I

S

G

S

F

C

R

N

K

L

K

Y

L

A

F

16

112

L

K

Y

L

A

F

L

H

K

R

M

N

T

N

P

16

120

K

R

M

N

T

N

P

S

R

R

P

Y

H

F

Q

16

137

S

R

I

F

W

R

Q

E

K

A

D

G

G

S

C

16

155

G

H

A

S

E

A

Y

K

K

V

C

L

S

G

A

16

185

E

E

K

R

K

E

K

A

E

I

H

Y

R

K

N

16

214

K

K

K

I

D

K

Y

T

E

S

P

G

G

G

S

16

229

P

R

G

L

G

F

I

F

K

T

I

A

P

L

A

16

305

D

S

L

S

P

Y

G

P

R

N

P

L

P

N

P

16

350

Q

R

K

P

K

S

E

N

N

S

W

Y

V

E

N

16

130

P

Y

H

F

Q

V

P

S

R

I

F

W

R

Q

E

15

18

V

E

S

I

R

D

H

S

G

Q

K

M

K

Q

D

14

79

D

E

K

Q

R

K

D

K

V

L

L

G

R

K

A

14

85

D

K

V

L

L

G

R

K

A

V

V

V

S

C

E

14

92

K

A

V

V

V

S

C

E

G

I

N

I

S

G

S

14

30

K

Q

D

K

K

V

D

L

L

V

P

T

K

V

T

13

35

V

D

L

L

V

P

T

K

V

T

G

I

I

T

Q

13

57

V

Q

F

V

G

S

Y

K

L

A

Y

S

N

D

G

13

273

R

A

P

V

P

A

A

S

P

A

A

W

L

P

L

13

304

Y

D

S

L

S

P

Y

G

P

R

N

P

L

P

N

13

383

I

E

S

L

E

E

G

L

G

G

K

Q

K

D

K

13

8

T

F

P

L

R

A

L

H

I

V

V

E

S

I

R

12

13

A

L

H

I

V

V

E

S

I

R

D

H

S

G

Q

12

32

D

K

K

V

D

L

L

V

P

T

K

V

T

G

I

12

40

P

T

K

V

T

G

I

I

T

Q

G

A

K

D

F

12

93

A

V

V

V

S

C

E

G

I

N

I

S

G

S

F

12

109

R

N

K

L

K

Y

L

A

F

L

H

K

R

M

N

12

141

W

R

Q

E

K

A

D

G

G

S

C

C

P

Q

G

12

161

Y

K

K

V

C

L

S

G

A

P

H

E

V

G

W

12

212

N

M

K

K

K

I

D

K

Y

T

E

S

P

G

G

12

341

H

N

V

L

A

R

G

K

P

Q

R

K

P

K

S

12

3

E

H

T

T

K

T

F

P

L

R

A

L

H

I

V

11

15

H

I

V

V

E

S

I

R

D

H

S

G

Q

K

M

11

17

V

V

E

S

I

R

D

H

S

G

Q

K

M

K

Q

11

48

T

Q

G

A

K

D

F

G

H

V

Q

F

V

G

S

11

86

K

V

L

L

G

R

K

A

V

V

V

S

C

E

G

11

98

C

E

G

I

N

I

S

G

S

F

C

R

N

K

L

11

100

G

I

N

I

S

G

S

F

C

R

N

K

L

K

Y

11

106

S

F

C

R

N

K

L

K

Y

L

A

F

L

H

K

11

107

F

C

R

N

K

L

K

Y

L

A

F

L

H

K

R

11

114

Y

L

A

F

L

H

K

R

M

N

T

N

P

S

R

11

119

H

K

R

M

N

T

N

P

S

R

R

P

Y

H

F

11

132

H

F

Q

V

P

S

R

I

F

W

R

Q

E

K

A

11

163

K

V

C

L

S

G

A

P

H

E

V

G

W

K

Y

11

210

E

K

N

M

K

K

K

I

D

K

Y

T

E

S

P

11

232

L

G

F

I

F

K

T

I

A

P

L

A

A

T

R

11

233

G

F

I

F

K

T

I

A

P

L

A

A

T

R

A

11

236

F

K

T

I

A

P

L

A

A

T

R

A

T

R

I

11

247

A

T

R

I

G

H

P

G

G

R

T

P

R

A

G

11

267

P

P

A

L

S

A

R

A

P

V

P

A

A

S

P

11

282

A

A

W

L

P

L

R

T

P

W

T

R

P

S

S

11

284

W

L

P

L

R

T

P

W

T

R

P

S

S

C

P

11

348

K

P

Q

R

K

P

K

S

E

N

N

S

W

Y

V

11

363

E

N

G

R

P

A

D

L

A

G

S

G

Y

C

G

11

367

P

A

D

L

A

G

S

G

Y

C

G

A

L

W

K

11

397

K

E

R

K

A

E

N

G

P

H

L

L

V

E

A

11

4

H

T

T

K

T

F

P

L

R

A

L

H

I

V

V

10

27

Q

K

M

K

Q

D

K

K

V

D

L

L

V

P

T

10

36

D

L

L

V

P

T

K

V

T

G

I

I

T

Q

G

10

47

I

T

Q

G

A

K

D

F

G

H

V

Q

F

V

G

10

62

S

Y

K

L

A

Y

S

N

D

G

E

H

W

T

V

10

77

Y

Q

D

E

K

Q

R

K

D

K

V

L

L

G

R

10

83

R

K

D

K

V

L

L

G

R

K

A

V

V

V

S

10

179

A

V

T

A

T

L

E

E

K

R

K

E

K

A

E

10

180

V

T

A

T

L

E

E

K

R

K

E

K

A

E

I

10

198

K

N

K

Q

L

M

R

L

Q

K

Q

A

E

K

N

10

209

A

E

K

N

M

K

K

K

I

D

K

Y

T

E

S

10

223

S

P

G

G

G

S

P

R

G

L

G

F

I

F

K

10

239

I

A

P

L

A

A

T

R

A

T

R

I

G

H

P

10

274

A

P

V

P

A

A

S

P

A

A

W

L

P

L

R

10

276

V

P

A

A

S

P

A

A

W

L

P

L

R

T

P

10

293

R

P

S

S

C

P

T

S

S

S

T

Y

D

S

L

10

312

P

R

N

P

L

P

N

P

R

H

S

P

S

G

G

10

313

R

N

P

L

P

N

P

R

H

S

P

S

G

G

G

10

318

N

P

R

H

S

P

S

G

G

G

G

L

K

K

P

10

333

A

R

H

C

Q

G

Q

K

H

N

V

L

A

R

G

10

358

N

S

W

Y

V

E

N

G

R

P

A

D

L

A

G

10

368

A

D

L

A

G

S

G

Y

C

G

A

L

W

K

A

10

375

Y

C

G

A

L

W

K

A

I

E

S

L

E

E

G

10

385

S

L

E

E

G

L

G

G

K

Q

K

D

K

E

R

10

6

T

K

T

F

P

L

R

A

L

H

I

V

V

E

S

9

51

A

K

D

F

G

H

V

Q

F

V

G

S

Y

K

L

9

61

G

S

Y

K

L

A

Y

S

N

D

G

E

H

W

T

9

105

G

S

F

C

R

N

K

L

K

Y

L

A

F

L

H

9

113

K

Y

L

A

F

L

H

K

R

M

N

T

N

P

S

9

122

M

N

T

N

P

S

R

R

P

Y

H

F

Q

V

P

9

129

R

P

Y

H

F

Q

V

P

S

R

I

F

W

R

Q

9

150

S

C

C

P

Q

G

H

A

S

E

A

Y

K

K

V

9

166

L

S

G

A

P

H

E

V

G

W

K

Y

Q

A

V

9

173

V

G

W

K

Y

Q

A

V

T

A

T

L

E

E

K

9

183

T

L

E

E

K

R

K

E

K

A

E

I

H

Y

R

9

190

E

K

A

E

I

H

Y

R

K

N

K

Q

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E

S

P

G

G

G

S

P

R

G

L

G

2

224

P

G

G

G

S

P

R

G

L

G

F

I

F

K

T

2

226

G

G

S

P

R

G

L

G

F

I

F

K

T

I

A

2

227

G

S

P

R

G

L

G

F

I

F

K

T

I

A

P

2

228

S

P

R

G

L

G

F

I

F

K

T

I

A

P

L

2

230

R

G

L

G

F

I

F

K

T

I

A

P

L

A

A

2

237

K

T

I

A

P

L

A

A

T

R

A

T

R

I

G

2

244

A

T

R

A

T

R

I

G

H

P

G

G

R

T

P

2

246

R

A

T

R

I

G

H

P

G

G

R

T

P

R

A

2

253

P

G

G

R

T

P

R

A

G

S

S

A

H

R

P

2

254

G

G

R

T

P

R

A

G

S

S

A

H

R

P

P

2

261

G

S

S

A

H

R

P

P

A

L

S

A

R

A

P

2

264

A

H

R

P

P

A

L

S

A

R

A

P

V

P

A

2

268

P

A

L

S

A

R

A

P

V

P

A

A

S

P

A

2

275

P

V

P

A

A

S

P

A

A

W

L

P

L

R

T

2

278

A

A

S

P

A

A

W

L

P

L

R

T

P

W

T

2

288

R

T

P

W

T

R

P

S

S

C

P

T

S

S

S

2

291

W

T

R

P

S

S

C

P

T

S

S

S

T

Y

D

2

297

C

P

T

S

S

S

T

Y

D

S

L

S

P

Y

G

2

301

S

S

T

Y

D

S

L

S

P

Y

G

P

R

N

P

2

302

S

T

Y

D

S

L

S

P

Y

G

P

R

N

P

L

2

307

L

S

P

Y

G

P

R

N

P

L

P

N

P

R

H

2

308

S

P

Y

G

P

R

N

P

L

P

N

P

R

H

S

2

316

L

P

N

P

R

H

S

P

S

G

G

G

G

L

K

2

317

P

N

P

R

H

S

P

S

G

G

G

G

L

K

K

2

321

H

S

P

S

G

G

G

G

L

K

K

P

A

R

H

2

327

G

G

L

K

K

P

A

R

H

C

Q

G

Q

K

H

2

335

H

C

Q

G

Q

K

H

N

V

L

A

R

G

K

P

2

336

C

Q

G

Q

K

H

N

V

L

A

R

G

K

P

Q

2

339

Q

K

H

N

V

L

A

R

G

K

P

Q

R

K

P

2

354

K

S

E

N

N

S

W

Y

V

E

N

G

R

P

A

2

360

W

Y

V

E

N

G

R

P

A

D

L

A

G

S

G

2

361

Y

V

E

N

G

R

P

A

D

L

A

G

S

G

Y

2

365

G

R

P

A

D

L

A

G

S

G

Y

C

G

A

L

2

369

D

L

A

G

S

G

Y

C

G

A

L

W

K

A

I

2

370

L

A

G

S

G

Y

C

G

A

L

W

K

A

I

E

2

372

G

S

G

Y

C

G

A

L

W

K

A

I

E

S

L

2

374

G

Y

C

G

A

L

W

K

A

I

E

S

L

E

E

2

21

I

R

D

H

S

G

Q

K

M

K

Q

D

K

K

V

1

37

L

L

V

P

T

K

V

T

G

I

I

T

Q

G

A

1

39

V

P

T

K

V

T

G

I

I

T

Q

G

A

K

D

1

45

G

I

I

T

Q

G

A

K

D

F

G

H

V

Q

F

1

49

Q

G

A

K

D

F

G

H

V

Q

F

V

G

S

Y

1

53

D

F

G

H

V

Q

F

V

G

S

Y

K

L

A

Y

1

58

Q

F

V

G

S

Y

K

L

A

Y

S

N

D

G

E

1

59

F

V

G

S

Y

K

L

A

Y

S

N

D

G

E

H

1

63

Y

K

L

A

Y

S

N

D

G

E

H

W

T

V

Y

1

65

L

A

Y

S

N

D

G

E

H

W

T

V

Y

Q

D

1

69

N

D

G

E

H

W

T

V

Y

Q

D

E

K

Q

R

1

81

K

Q

R

K

D

K

V

L

L

G

R

K

A

V

V

1

88

L

L

G

R

K

A

V

V

V

S

C

E

G

I

N

1

123

N

T

N

P

S

R

R

P

Y

H

F

Q

V

P

S

1

124

T

N

P

S

R

R

P

Y

H

F

Q

V

P

S

R

1

139

I

F

W

R

Q

E

K

A

D

G

G

S

C

C

P

1

142

R

Q

E

K

A

D

G

G

S

C

C

P

Q

G

H

1

143

Q

E

K

A

D

G

G

S

C

C

P

Q

G

H

A

1

147

D

G

G

S

C

C

P

Q

G

H

A

S

E

A

Y

1

157

A

S

E

A

Y

K

K

V

C

L

S

G

A

P

H

1

158

S

E

A

Y

K

K

V

C

L

S

G

A

P

H

E

1

171

H

E

V

G

W

K

Y

Q

A

V

T

A

T

L

E

1

174

G

W

K

Y

Q

A

V

T

A

T

L

E

E

K

R

1

175

W

K

Y

Q

A

V

T

A

T

L

E

E

K

R

K

1

176

K

Y

Q

A

V

T

A

T

L

E

E

K

R

K

E

1

186

E

K

R

K

E

K

A

E

I

H

Y

R

K

N

K

1

187

K

R

K

E

K

A

E

I

H

Y

R

K

N

K

Q

1

213

M

K

K

K

I

D

K

Y

T

E

S

P

G

G

G

1

216

K

I

D

K

Y

T

E

S

P

G

G

G

S

P

R

1

220

Y

T

E

S

P

G

G

G

S

P

R

G

L

G

F

1

242

L

A

A

T

R

A

T

R

I

G

H

P

G

G

R

1

245

T

R

A

T

R

I

G

H

P

G

G

R

T

P

R

1

250

I

G

H

P

G

G

R

T

P

R

A

G

S

S

A

1

252

H

P

G

G

R

T

P

R

A

G

S

S

A

H

R

1

256

R

T

P

R

A

G

S

S

A

H

R

P

P

A

L

1

257

T

P

R

A

G

S

S

A

H

R

P

P

A

L

S

1

277

P

A

A

S

P

A

A

W

L

P

L

R

T

P

W

1

279

A

S

P

A

A

W

L

P

L

R

T

P

W

T

R

1

287

L

R

T

P

W

T

R

P

S

S

C

P

T

S

S

1

290

P

W

T

R

P

S

S

C

P

T

S

S

S

T

Y

1

294

P

S

S

C

P

T

S

S

S

T

Y

D

S

L

S

1

298

P

T

S

S

S

T

Y

D

S

L

S

P

Y

G

P

1

300

S

S

S

T

Y

D

S

L

S

P

Y

G

P

R

N

1

311

G

P

R

N

P

L

P

N

P

R

H

S

P

S

G

1

314

N

P

L

P

N

P

R

H

S

P

S

G

G

G

G

1

315

P

L

P

N

P

R

H

S

P

S

G

G

G

G

L

1

328

G

L

K

K

P

A

R

H

C

Q

G

Q

K

H

N

1

337

Q

G

Q

K

H

N

V

L

A

R

G

K

P

Q

R

1

345

A

R

G

K

P

Q

R

K

P

K

S

E

N

N

S

1

351

R

K

P

K

S

E

N

N

S

W

Y

V

E

N

G

1

352

K

P

K

S

E

N

N

S

W

Y

V

E

N

G

R

1

353

P

K

S

E

N

N

S

W

Y

V

E

N

G

R

P

1

371

A

G

S

G

Y

C

G

A

L

W

K

A

I

E

S

1

378

A

L

W

K

A

I

E

S

L

E

E

G

L

G

G

1

384

E

S

L

E

E

G

L

G

G

K

Q

K

D

K

E

1

388

E

G

L

G

G

K

Q

K

D

K

E

R

K

A

E

1

399

R

K

A

E

N

G

P

H

L

L

V

E

A

E

Q

1

TABLE L

151P3D4 v.1:

HLA Peptide Scoring Results DRB1*0401

15 - mers SYFPEITHI

SEQ. ID

Pos

1

2

3

4

5

6

7

8

9

0

1

2

3

4

5

score

NO.

78

R

I

K

W

T

K

L

T

S

D

Y

L

K

E

V

28

Portion of

161

F

P

Y

F

P

R

L

G

R

Y

N

L

N

F

H

28

SEQ ID NO:

171

N

L

N

F

H

E

A

Q

Q

A

C

L

D

Q

D

28

3; each start

258

N

G

R

F

Y

Y

L

I

H

P

T

K

L

T

Y

28

position is

269

K

L

T

Y

D

E

A

V

Q

A

C

L

N

D

G

28

specified, the

38

P

H

L

L

V

E

A

E

Q

A

K

V

F

S

H

26

length of

149

T

V

V

V

A

L

D

L

Q

G

V

V

F

P

Y

26

peptide is 15

191

F

D

Q

L

Y

D

A

W

R

G

G

L

D

W

C

26

amino acids,

247

R

Y

D

V

F

C

F

T

S

N

F

N

G

R

F

26

the end

283

G

A

Q

I

A

K

V

G

Q

I

F

A

A

W

K

26

position for

19

S

D

N

Y

T

L

D

H

D

R

A

I

H

I

Q

22

each peptide

60

P

C

K

F

Y

R

D

P

T

A

F

G

S

G

I

22

is the start

85

T

S

D

Y

L

K

E

V

D

V

F

V

S

M

G

22

position plus

134

Y

G

R

Y

K

C

E

V

I

E

G

L

E

D

D

22

fourteen

158

G

V

V

F

P

Y

F

P

R

L

G

R

Y

N

L

22

167

L

G

R

Y

N

L

N

F

H

E

A

Q

Q

A

C

22

206

N

A

G

W

L

S

D

G

S

V

Q

Y

P

I

T

22

238

Y

G

F

W

D

K

D

K

S

R

Y

D

V

F

C

22

245

K

S

R

Y

D

V

F

C

F

T

S

N

F

N

G

22

259

G

R

F

Y

Y

L

I

H

P

T

K

L

T

Y

D

22

260

R

F

Y

Y

L

I

H

P

T

K

L

T

Y

D

E

22

305

D

A

G

W

L

A

D

G

S

V

R

Y

P

I

S

22

1

M

K

S

L

L

L

L

V

L

I

S

I

C

W

A

20

3

S

L

L

L

L

V

L

I

S

I

C

W

A

D

H

20

4

L

L

L

L

V

L

I

S

I

C

W

A

D

H

L

20

9

L

I

S

I

C

W

A

D

H

L

S

D

N

Y

T

20

21

N

Y

T

L

D

H

D

R

A

I

H

I

Q

A

E

20

29

A

I

H

I

Q

A

E

N

G

P

H

L

L

V

E

20

37

G

P

H

L

L

V

E

A

E

Q

A

K

V

F

S

20

71

G

S

G

I

H

K

I

R

I

K

W

T

K

L

T

20

81

W

T

K

L

T

S

D

Y

L

K

E

V

D

V

F

20

86

S

D

Y

L

K

E

V

D

V

F

V

S

M

G

Y

20

89

L

K

E

V

D

V

F

V

S

M

G

Y

H

K

K

20

93

D

V

F

V

S

M

G

Y

H

K

K

T

Y

G

G

20

122

A

S

L

V

I

T

D

L

T

L

E

D

Y

G

R

20

139

C

E

V

I

E

G

L

E

D

D

T

V

V

V

A

20

142

I

E

G

L

E

D

D

T

V

V

V

A

L

D

L

20

148

D

T

V

V

V

A

L

D

L

Q

G

V

V

F

P

20

179

Q

A

C

L

D

Q

D

A

V

I

A

S

F

D

Q

20

185

D

A

V

I

A

S

F

D

Q

L

Y

D

A

W

R

20

229

Q

N

T

V

P

G

V

R

N

Y

G

F

W

D

K

20

267

P

T

K

L

T

Y

D

E

A

V

Q

A

C

L

N

20

273

D

E

A

V

Q

A

C

L

N

D

G

A

Q

I

A

20

277

Q

A

C

L

N

D

G

A

Q

I

A

K

V

G

Q

20

286

I

A

K

V

G

Q

I

F

A

A

W

K

I

L

G

20

295

A

W

K

I

L

G

Y

D

R

C

D

A

G

W

L

20

315

R

Y

P

I

S

R

P

R

R

R

C

S

P

T

E

20

329

E

A

A

V

R

F

V

G

F

P

D

K

K

H

K

20

18

L

S

D

N

Y

T

L

D

H

D

R

A

I

H

I

18

23

T

L

D

H

D

R

A

I

H

I

Q

A

E

N

G

18

57

V

T

L

P

C

K

F

Y

R

D

P

T

A

F

G

18

115

K

G

G

S

D

S

D

A

S

L

V

I

T

D

L

18

119

D

S

D

A

S

L

V

I

T

D

L

T

L

E

D

18

141

V

I

E

G

L

E

D

D

T

V

V

V

A

L

D

18

176

E

A

Q

Q

A

C

L

D

Q

D

A

V

I

A

S

18

182

L

D

Q

D

A

V

I

A

S

F

D

Q

L

Y

D

18

11

S

I

C

W

A

D

H

L

S

D

N

Y

T

L

D

16

61

C

K

F

Y

R

D

P

T

A

F

G

S

G

I

H

16

67

P

T

A

F

G

S

G

I

H

K

I

R

I

K

W

16

92

V

D

V

F

V

S

M

G

Y

H

K

K

T

Y

G

16

110

G

R

V

F

L

K

G

G

S

D

S

D

A

S

L

16

131

L

E

D

Y

G

R

Y

K

C

E

V

I

E

G

L

16

188

I

A

S

F

D

Q

L

Y

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Q

6

173

N

F

H

E

A

Q

Q

A

C

L

D

Q

D

A

V

6

174

F

H

E

A

Q

Q

A

C

L

D

Q

D

A

V

I

6

175

H

E

A

Q

Q

A

C

L

D

Q

D

A

V

I

A

6

178

Q

Q

A

C

L

D

Q

D

A

V

I

A

S

F

D

6

180

A

C

L

D

Q

D

A

V

I

A

S

F

D

Q

L

6

181

C

L

D

Q

D

A

V

I

A

S

F

D

Q

L

Y

6

190

S

F

D

Q

L

Y

D

A

W

R

G

G

L

D

W

6

197

A

W

R

G

G

L

D

W

C

N

A

G

W

L

S

6

198

W

R

G

G

L

D

W

C

N

A

G

W

L

S

D

6

200

G

G

L

D

W

C

N

A

G

W

L

S

D

G

S

6

205

C

N

A

G

W

L

S

D

G

S

V

Q

Y

P

I

6

210

L

S

D

G

S

V

Q

Y

P

I

T

K

P

R

E

6

213

G

S

V

Q

Y

P

I

T

K

P

R

E

P

C

G

6

219

I

T

K

P

R

E

P

C

G

G

Q

N

T

V

P

6

220

T

K

P

R

E

P

C

G

G

Q

N

T

V

P

G

6

222

P

R

E

P

C

G

G

Q

N

T

V

P

G

V

R

6

223

R

E

P

C

G

G

Q

N

T

V

P

G

V

R

N

6

224

E

P

C

G

G

Q

N

T

V

P

G

V

R

N

Y

6

228

G

Q

N

T

V

P

G

V

R

N

Y

G

F

W

D

6

236

R

N

Y

G

F

W

D

K

D

K

S

R

Y

D

V

6

246

S

R

Y

D

V

F

C

F

T

S

N

F

N

G

R

6

251

F

C

F

T

S

N

F

N

G

R

F

Y

Y

L

I

6

252

C

F

T

S

N

F

N

G

R

F

Y

Y

L

I

H

6

253

F

T

S

N

F

N

G

R

F

Y

Y

L

I

H

P

6

255

S

N

F

N

G

R

F

Y

Y

L

I

H

P

T

K

6

257

F

N

G

R

F

Y

Y

L

I

H

P

T

K

L

T

6

265

I

H

P

T

K

L

T

Y

D

E

A

V

Q

A

C

6

266

H

P

T

K

L

T

Y

D

E

A

V

Q

A

C

L

6

268

T

K

L

T

Y

D

E

A

V

Q

A

C

L

N

D

6

272

Y

D

E

A

V

Q

A

C

L

N

D

G

A

Q

I

6

275

A

V

Q

A

C

L

N

D

G

A

Q

I

A

K

V

6

284

A

Q

I

A

K

V

G

Q

I

F

A

A

W

K

I

6

292

I

F

A

A

W

K

I

L

G

Y

D

R

C

D

A

6

300

G

Y

D

R

C

D

A

G

W

L

A

D

G

S

V

6

302

D

R

C

D

A

G

W

L

A

D

G

S

V

R

Y

6

304

C

D

A

G

W

L

A

D

G

S

V

R

Y

P

I

6

319

S

R

P

R

R

R

C

S

P

T

E

A

A

V

R

6

321

P

R

R

R

C

S

P

T

E

A

A

V

R

F

V

6

323

R

R

C

S

P

T

E

A

A

V

R

F

V

G

F

6

326

S

P

T

E

A

A

V

R

F

V

G

F

P

D

K

6

328

T

E

A

A

V

R

F

V

G

F

P

D

K

K

H

6

330

A

A

V

R

F

V

G

F

P

D

K

K

H

K

L

6

336

G

F

P

D

K

K

H

K

L

Y

G

V

Y

C

F

6

338

P

D

K

K

H

K

L

Y

G

V

Y

C

F

R

A

6

97

S

M

G

Y

H

K

K

T

Y

G

G

Y

Q

G

R

5

105

Y

G

G

Y

Q

G

R

V

F

L

K

G

G

S

D

5

237

N

Y

G

F

W

D

K

D

K

S

R

Y

D

V

F

5

56

N

V

T

L

P

C

K

F

Y

R

D

P

T

A

F

3

22

Y

T

L

D

H

D

R

A

I

H

I

Q

A

E

N

1

70

F

G

S

G

I

H

K

I

R

I

K

W

T

K

L

1

72

S

G

I

H

K

I

R

I

K

W

T

K

L

T

S

1

77

I

R

I

K

W

T

K

L

T

S

D

Y

L

K

E

1

96

V

S

M

G

Y

H

K

K

T

Y

G

G

Y

Q

G

1

130

T

L

E

D

Y

G

R

Y

K

C

E

V

I

E

G

1

163

Y

F

P

R

L

G

R

Y

N

L

N

F

H

E

A

1

215

V

Q

Y

P

I

T

K

P

R

E

P

C

G

G

Q

1

263

Y

L

I

H

P

T

K

L

T

Y

D

E

A

V

Q

1

314

V

R

Y

P

I

S

R

P

R

R

R

C

S

P

T

1

316

Y

P

I

S

R

P

R

R

R

C

S

P

T

E

A

1

317

P

I

S

R

P

R

R

R

C

S

P

T

E

A

A

1

318

I

S

R

P

R

R

R

C

S

P

T

E

A

A

V

1

42

V

E

A

E

Q

A

K

V

F

S

H

R

G

G

N

−5

59

L

P

C

K

F

Y

R

D

P

T

A

F

G

S

G

−5

84

L

T

S

D

Y

L

K

E

V

D

V

F

V

S

M

−5

132

E

D

Y

G

R

Y

K

C

E

V

I

E

G

L

E

−5

193

Q

L

Y

D

A

W

R

G

G

L

D

W

C

N

A

−5

217

Y

P

I

T

K

P

R

E

P

C

G

G

Q

N

T

−5

230

N

T

V

P

G

V

R

N

Y

G

F

W

D

K

D

−5

241

W

D

K

D

K

S

R

Y

D

V

F

C

F

T

S

−5

282

D

G

A

Q

I

A

K

V

G

Q

I

F

A

A

W

−5

291

Q

I

F

A

A

W

K

I

L

G

Y

D

R

C

D

−5

297

K

I

L

G

Y

D

R

C

D

A

G

W

L

A

D

−5

309

L

A

D

G

S

V

R

Y

P

I

S

R

P

R

R

−5

327

P

T

E

A

A

V

R

F

V

G

F

P

D

K

K

−5

335

V

G

F

P

D

K

K

H

K

L

Y

G

V

Y

C

−5

337

F

P

D

K

K

H

K

L

Y

G

V

Y

C

F

R

−5

151P3D4 v.2:

HLA Peptide Scoring Results DRB1*0401

15 - mers SYFPEITHI

Pos

1

2

3

4

5

6

7

8

9

0

1

2

3

4

5

score

SEQ. ID NO.

111

K

L

K

Y

L

A

F

L

H

K

R

M

N

T

N

28

Portion of

281

P

A

A

W

L

P

L

R

T

P

W

T

R

P

S

28

SEQ ID NO:

40

P

T

K

V

T

G

I

I

T

Q

G

A

K

D

F

26

5; each start

54

F

G

H

V

Q

F

V

G

S

Y

K

L

A

Y

S

26

position is

51

A

K

D

F

G

H

V

Q

F

V

G

S

Y

K

L

22

specified, the

60

V

G

S

Y

K

L

A

Y

S

N

D

G

E

H

W

22

length of

64

K

L

A

Y

S

N

D

G

E

H

W

T

V

Y

Q

22

peptide is 15

74

W

T

V

Y

Q

D

E

K

Q

R

K

D

K

V

L

22

amino acids,

158

S

E

A

Y

K

K

V

C

L

S

G

A

P

H

E

22

the end

233

G

F

I

F

K

T

I

A

P

L

A

A

T

R

A

22

position for

288

R

T

P

W

T

R

P

S

S

C

P

T

S

S

S

22

each peptide is

357

N

N

S

W

Y

V

E

N

G

R

P

A

D

L

A

22

the start

372

G

S

G

Y

C

G

A

L

W

K

A

I

E

S

L

22

position plus

377

G

A

L

W

K

A

I

E

S

L

E

E

G

L

G

22

fourteen

14

L

H

I

V

V

E

S

I

R

D

H

S

G

Q

K

20

26

G

Q

K

M

K

Q

D

K

K

V

D

L

L

V

P

20

32

D

K

K

V

D

L

L

V

P

T

K

V

T

G

I

20

73

H

W

T

V

Y

Q

D

E

K

Q

R

K

D

K

V

20

93

A

V

V

V

S

C

E

G

I

N

I

S

G

S

F

20

109

R

N

K

L

K

Y

L

A

F

L

H

K

R

M

N

20

112

L

K

Y

L

A

F

L

H

K

R

M

N

T

N

P

20

163

K

V

C

L

S

G

A

P

H

E

V

G

W

K

Y

20

200

K

Q

L

M

R

L

Q

K

Q

A

E

K

N

M

K

20

229

P

R

G

L

G

F

I

F

K

T

I

A

P

L

A

20

236

F

K

T

I

A

P

L

A

A

T

R

A

T

R

I

20

284

W

L

P

L

R

T

P

W

T

R

P

S

S

C

P

20

313

R

N

P

L

P

N

P

R

H

S

P

S

G

G

G

20

326

G

G

G

L

K

K

P

A

R

H

C

Q

G

Q

K

20

7

K

T

F

P

L

R

A

L

H

I

V

V

E

S

I

18

17

V

V

E

S

I

R

D

H

S

G

Q

K

M

K

Q

18

33

K

K

V

D

L

L

V

P

T

K

V

T

G

I

I

18

41

T

K

V

T

G

I

I

T

Q

G

A

K

D

F

G

18

70

D

G

E

H

W

T

V

Y

Q

D

E

K

Q

R

K

18

83

R

K

D

K

V

L

L

G

R

K

A

V

V

V

S

18

101

I

N

I

S

G

S

F

C

R

N

K

L

K

Y

L

18

134

Q

V

P

S

R

I

F

W

R

Q

E

K

A

D

G

18

173

V

G

W

K

Y

Q

A

V

T

A

T

L

E

E

K

18

180

V

T

A

T

L

E

E

K

R

K

E

K

A

E

I

18

187

K

R

K

E

K

A

E

I

H

Y

R

K

N

K

Q

18

196

Y

R

K

N

K

Q

L

M

R

L

Q

K

Q

A

E

18

204

R

L

Q

K

Q

A

E

K

N

M

K

K

K

I

D

18

237

K

T

I

A

P

L

A

A

T

R

A

T

R

I

G

18

258

P

R

A

G

S

S

A

H

R

P

P

A

L

S

A

18

263

S

A

H

R

P

P

A

L

S

A

R

A

P

V

P

18

272

A

R

A

P

V

P

A

A

S

P

A

A

W

L

P

18

71

G

E

H

W

T

V

Y

Q

D

E

K

Q

R

K

D

16

104

S

G

S

F

C

R

N

K

L

K

Y

L

A

F

L

16

128

R

R

P

Y

H

F

Q

V

P

S

R

I

F

W

R

16

130

P

Y

H

F

Q

V

P

S

R

I

F

W

R

Q

E

16

138

R

I

F

W

R

Q

E

K

A

D

G

G

S

C

C

16

172

E

V

G

W

K

Y

Q

A

V

T

A

T

L

E

E

16

174

G

W

K

Y

Q

A

V

T

A

T

L

E

E

K

R

16

193

E

I

H

Y

R

K

N

K

Q

L

M

R

L

Q

K

16

217

I

D

K

Y

T

E

S

P

G

G

G

S

P

R

G

16

301

S

S

T

Y

D

S

L

S

P

Y

G

P

R

N

P

16

358

N

S

W

Y

V

E

N

G

R

P

A

D

L

A

G

16

36

D

L

L

V

P

T

K

V

T

G

I

I

T

Q

G

15

170

P

H

E

V

G

W

K

Y

Q

A

V

T

A

T

L

15

191

K

A

E

I

H

Y

R

K

N

K

Q

L

M

R

L

15

8

T

F

P

L

R

A

L

H

I

V

V

E

S

I

R

14

11

L

R

A

L

H

I

V

V

E

S

I

R

D

H

S

14

13

A

L

H

I

V

V

E

S

I

R

D

H

S

G

Q

14

15

H

I

V

V

E

S

I

R

D

H

S

G

Q

K

M

14

18

V

E

S

I

R

D

H

S

G

Q

K

M

K

Q

D

14

35

V

D

L

L

V

P

T

K

V

T

G

I

I

T

Q

14

57

V

Q

F

V

G

S

Y

K

L

A

Y

S

N

D

G

14

84

K

D

K

V

L

L

G

R

K

A

V

V

V

S

C

14

91

R

K

A

V

V

V

S

C

E

G

I

N

I

S

G

14

92

K

A

V

V

V

S

C

E

G

I

N

I

S

G

S

14

98

C

E

G

I

N

I

S

G

S

F

C

R

N

K

L

14

100

G

I

N

I

S

G

S

F

C

R

N

K

L

K

Y

14

119

H

K

R

M

N

T

N

P

S

R

R

P

Y

H

F

14

199

N

K

Q

L

M

R

L

Q

K

Q

A

E

K

N

M

14

202

L

M

R

L

Q

K

Q

A

E

K

N

M

K

K

K

14

232

L

G

F

I

F

K

T

I

A

P

L

A

A

T

R

14

239

I

A

P

L

A

A

T

R

A

T

R

I

G

H

P

14

273

R

A

P

V

P

A

A

S

P

A

A

W

L

P

L

14

341

H

N

V

L

A

R

G

K

P

Q

R

K

P

K

S

14

359

S

W

Y

V

E

N

G

R

P

A

D

L

A

G

S

14

367

P

A

D

L

A

G

S

G

Y

C

G

A

L

W

K

14

376

C

G

A

L

W

K

A

I

E

S

L

E

E

G

L

14

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K

I

D

K

Y

T

E

S

P

G

6

215

K

K

I

D

K

Y

T

E

S

P

G

G

G

S

P

6

216

K

I

D

K

Y

T

E

S

P

G

G

G

S

P

R

6

220

Y

T

E

S

P

G

G

G

S

P

R

G

L

G

F

6

221

T

E

S

P

G

G

G

S

P

R

G

L

G

F

I

6

222

E

S

P

G

G

G

S

P

R

G

L

G

F

I

F

6

227

G

S

P

R

G

L

G

F

I

F

K

T

I

A

P

6

246

R

A

T

R

I

G

H

P

G

G

R

T

P

R

A

6

248

T

R

I

G

H

P

G

G

R

T

P

R

A

G

S

6

252

H

P

G

G

R

T

P

R

A

G

S

S

A

H

R

6

255

G

R

T

P

R

A

G

S

S

A

H

R

P

P

A

6

257

T

P

R

A

G

S

S

A

H

R

P

P

A

L

S

6

259

R

A

G

S

S

A

H

R

P

P

A

L

S

A

R

6

261

G

S

S

A

H

R

P

P

A

L

S

A

R

A

P

6

264

A

H

R

P

P

A

L

S

A

R

A

P

V

P

A

6

266

R

P

P

A

L

S

A

R

A

P

V

P

A

A

S

6

269

A

L

S

A

R

A

P

V

P

A

A

S

P

A

A

6

270

L

S

A

R

A

P

V

P

A

A

S

P

A

A

W

6

271

S

A

R

A

P

V

P

A

A

S

P

A

A

W

L

6

274

A

P

V

P

A

A

S

P

A

A

W

L

P

L

R

6

277

P

A

A

S

P

A

A

W

L

P

L

R

T

P

W

6

278

A

A

S

P

A

A

W

L

P

L

R

T

P

W

T

6

279

A

S

P

A

A

W

L

P

L

R

T

P

W

T

R

6

280

S

P

A

A

W

L

P

L

R

T

P

W

T

R

P

6

289

T

P

W

T

R

P

S

S

C

P

T

S

S

S

T

6

290

P

W

T

R

P

S

S

C

P

T

S

S

S

T

Y

6

293

R

P

S

S

C

P

T

S

S

S

T

Y

D

S

L

6

294

P

S

S

C

P

T

S

S

S

T

Y

D

S

L

S

6

296

S

C

P

T

S

S

S

T

Y

D

S

L

S

P

Y

6

297

C

P

T

S

S

S

T

Y

D

S

L

S

P

Y

G

6

298

P

T

S

S

S

T

Y

D

S

L

S

P

Y

G

P

6

299

T

S

S

S

T

Y

D

S

L

S

P

Y

G

P

R

6

300

S

S

S

T

Y

D

S

L

S

P

Y

G

P

R

N

6

303

T

Y

D

S

L

S

P

Y

G

P

R

N

P

L

P

6

306

S

L

S

P

Y

G

P

R

N

P

L

P

N

P

R

6

311

G

P

R

N

P

L

P

N

P

R

H

S

P

S

G

6

312

P

R

N

P

L

P

N

P

R

H

S

P

S

G

G

6

316

L

P

N

P

R

H

S

P

S

G

G

G

G

L

K

6

318

N

P

R

H

S

P

S

G

G

G

G

L

K

K

P

6

319

P

R

H

S

P

S

G

G

G

G

L

K

K

P

A

6

320

R

H

S

P

S

G

G

G

G

L

K

K

P

A

R

6

322

S

P

S

G

G

G

G

L

K

K

P

A

R

H

C

6

323

P

S

G

G

G

G

L

K

K

P

A

R

H

C

Q

6

332

P

A

R

H

C

Q

G

Q

K

H

N

V

L

A

R

6

344

L

A

R

G

K

P

Q

R

K

P

K

S

E

N

N

6

349

P

Q

R

K

P

K

S

E

N

N

S

W

Y

V

E

6

353

P

K

S

E

N

N

S

W

Y

V

E

N

G

R

P

6

363

E

N

G

R

P

A

D

L

A

G

S

G

Y

C

G

6

364

N

G

R

P

A

D

L

A

G

S

G

Y

C

G

A

6

368

A

D

L

A

G

S

G

Y

C

G

A

L

W

K

A

6

370

L

A

G

S

G

Y

C

G

A

L

W

K

A

I

E

6

371

A

G

S

G

Y

C

G

A

L

W

K

A

I

E

S

6

373

S

G

Y

C

G

A

L

W

K

A

I

E

S

L

E

6

374

G

Y

C

G

A

L

W

K

A

I

E

S

L

E

E

6

378

A

L

W

K

A

I

E

S

L

E

E

G

L

G

G

6

379

L

W

K

A

I

E

S

L

E

E

G

L

G

G

K

6

381

K

A

I

E

S

L

E

E

G

L

G

G

K

Q

K

6

397

K

E

R

K

A

E

N

G

P

H

L

L

V

E

A

6

400

K

A

E

N

G

P

H

L

L

V

E

A

E

Q

A

6

136

P

S

R

I

F

W

R

Q

E

K

A

D

G

G

S

3

282

A

A

W

L

P

L

R

T

P

W

T

R

P

S

S

3

340

K

H

N

V

L

A

R

G

K

P

Q

R

K

P

K

3

387

E

E

G

L

G

G

K

Q

K

D

K

E

R

K

A

3

22

R

D

H

S

G

Q

K

M

K

Q

D

K

K

V

D

1

24

H

S

G

Q

K

M

K

Q

D

K

K

V

D

L

L

1

27

Q

K

M

K

Q

D

K

K

V

D

L

L

V

P

T

1

28

K

M

K

Q

D

K

K

V

D

L

L

V

P

T

K

1

46

I

I

T

Q

G

A

K

D

F

G

H

V

Q

F

V

1

58

Q

F

V

G

S

Y

K

L

A

Y

S

N

D

G

E

1

77

Y

Q

D

E

K

Q

R

K

D

K

V

L

L

G

R

1

78

Q

D

E

K

Q

R

K

D

K

V

L

L

G

R

K

1

105

G

S

F

C

R

N

K

L

K

Y

L

A

F

L

H

1

107

F

C

R

N

K

L

K

Y

L

A

F

L

H

K

R

1

123

N

T

N

P

S

R

R

P

Y

H

F

Q

V

P

S

1

139

I

F

W

R

Q

E

K

A

D

G

G

S

C

C

P

1

156

H

A

S

E

A

Y

K

K

V

C

L

S

G

A

P

1

183

T

L

E

E

K

R

K

E

K

A

E

I

H

Y

R

1

192

A

E

I

H

Y

R

K

N

K

Q

L

M

R

L

Q

1

194

I

H

Y

R

K

N

K

Q

L

M

R

L

Q

K

Q

1

201

Q

L

M

R

L

Q

K

Q

A

E

K

N

M

K

K

1

205

L

Q

K

Q

A

E

K

N

M

K

K

K

I

D

K

1

208

Q

A

E

K

N

M

K

K

K

I

D

K

Y

T

E

1

213

M

K

K

K

I

D

K

Y

T

E

S

P

G

G

G

1

224

P

G

G

G

S

P

R

G

L

G

F

I

F

K

T

1

240

A

P

L

A

A

T

R

A

T

R

I

G

H

P

G

1

253

P

G

G

R

T

P

R

A

G

S

S

A

H

R

P

1

260

A

G

S

S

A

H

R

P

P

A

L

S

A

R

A

1

287

L

R

T

P

W

T

R

P

S

S

C

P

T

S

S

1

314

N

P

L

P

N

P

R

H

S

P

S

G

G

G

G

1

328

G

L

K

K

P

A

R

H

C

Q

G

Q

K

H

N

1

342

N

V

L

A

R

G

K

P

Q

R

K

P

K

S

E

1

346

R

G

K

P

Q

R

K

P

K

S

E

N

N

S

W

1

348

K

P

Q

R

K

P

K

S

E

N

N

S

W

Y

V

1

360

W

Y

V

E

N

G

R

P

A

D

L

A

G

S

G

1

375

Y

C

G

A

L

W

K

A

I

E

S

L

E

E

G

1

389

G

L

G

G

K

Q

K

D

K

E

R

K

A

E

N

1

391

G

G

K

Q

K

D

K

E

R

K

A

E

N

G

P

1

1

M

L

E

H

T

T

K

T

F

P

L

R

A

L

H

−5

80

E

K

Q

R

K

D

K

V

L

L

G

R

K

A

V

−5

103

I

S

G

S

F

C

R

N

K

L

K

Y

L

A

F

−5

122

M

N

T

N

P

S

R

R

P

Y

H

F

Q

V

P

−5

157

A

S

E

A

Y

K

K

V

C

L

S

G

A

P

H

−5

182

A

T

L

E

E

K

R

K

E

K

A

E

I

H

Y

−5

185

E

E

K

R

K

E

K

A

E

I

H

Y

R

K

N

−5

209

A

E

K

N

M

K

K

K

I

D

K

Y

T

E

S

−5

243

A

A

T

R

A

T

R

I

G

H

P

G

G

R

T

−5

250

I

G

H

P

G

G

R

T

P

R

A

G

S

S

A

−5

324

S

G

G

G

G

L

K

K

P

A

R

H

C

Q

G

−5

325

G

G

G

G

L

K

K

P

A

R

H

C

Q

G

Q

−5

345

A

R

G

K

P

Q

R

K

P

K

S

E

N

N

S

−5

393

K

Q

K

D

K

E

R

K

A

E

N

G

P

H

L

−5

394

Q

K

D

K

E

R

K

A

E

N

G

P

H

L

L

−5

TABLE LI

SEQ. ID

Pos

1

2

3

4

5

6

7

8

9

0

1

2

3

4

5

score

NO.

151P3D4 v.1: HLA Peptide Scoring Results

DRB1*1101 15 - mers SYFPEITHI

235

V

R

N

Y

G

F

W

D

K

D

K

S

R

Y

D

25

Portion of

161

F

P

Y

F

P

R

L

G

R

Y

N

L

N

F

H

24

SEQ ID NO:

258

N

G

R

F

Y

Y

L

I

H

P

T

K

L

T

Y

24

3; each start

18

L

S

D

N

Y

T

L

D

H

D

R

A

I

H

I

22

position is

289

V

G

Q

I

F

A

A

W

K

I

L

G

Y

D

R

22

specified, the

315

R

Y

P

I

S

R

P

R

R

R

C

S

P

T

E

21

length of

95

F

V

S

M

G

Y

H

K

K

T

Y

G

G

Y

Q

20

peptide is 15

237

N

Y

G

F

W

D

K

D

K

S

R

Y

D

V

F

20

amino acids,

295

A

W

K

I

L

G

Y

D

R

C

D

A

G

W

L

20

the end

67

P

T

A

F

G

S

G

I

H

K

I

R

I

K

W

19

position for

86

S

D

Y

L

K

E

V

D

V

F

V

S

M

G

Y

19

each peptide

105

Y

G

G

Y

Q

G

R

V

F

L

K

G

G

S

D

19

is the start

334

F

V

G

F

P

D

K

K

H

K

L

Y

G

V

Y

19

position plus

4

L

L

L

L

V

L

I

S

I

C

W

A

D

H

L

18

fourteen

78

R

I

K

W

T

K

L

T

S

D

Y

L

K

E

V

18

158

G

V

V

F

P

Y

F

P

R

L

G

R

Y

N

L

18

167

L

G

R

Y

N

L

N

F

H

E

A

Q

Q

A

C

18

283

G

A

Q

I

A

K

V

G

Q

I

F

A

A

W

K

18

293

F

A

A

W

K

I

L

G

Y

D

R

C

D

A

G

18

92

V

D

V

F

V

S

M

G

Y

H

K

K

T

Y

G

17

214

S

V

Q

Y

P

I

T

K

P

R

E

P

C

G

G

17

259

G

R

F

Y

Y

L

I

H

P

T

K

L

T

Y

D

17

325

C

S

P

T

E

A

A

V

R

F

V

G

F

P

D

17

44

A

E

Q

A

K

V

F

S

H

R

G

G

N

V

T

16

54

G

G

N

V

T

L

P

C

K

F

Y

R

D

P

T

16

60

P

C

K

F

Y

R

D

P

T

A

F

G

S

G

I

16

61

C

K

F

Y

R

D

P

T

A

F

G

S

G

I

H

16

68

T

A

F

G

S

G

I

H

K

I

R

I

K

W

T

16

188

I

A

S

F

D

Q

L

Y

D

A

W

R

G

G

L

16

213

G

S

V

Q

Y

P

I

T

K

P

R

E

P

C

G

16

228

G

Q

N

T

V

P

G

V

R

N

Y

G

F

W

D

16

248

Y

D

V

F

C

F

T

S

N

F

N

G

R

F

Y

16

312

G

S

V

R

Y

P

I

S

R

P

R

R

R

C

S

16

93

D

V

F

V

S

M

G

Y

H

K

K

T

Y

G

G

15

107

G

Y

Q

G

R

V

F

L

K

G

G

S

D

S

D

15

128

D

L

T

L

E

D

Y

G

R

Y

K

C

E

V

I

15

157

Q

G

V

V

F

P

Y

F

P

R

L

G

R

Y

N

15

1

M

K

S

L

L

L

L

V

L

I

S

I

C

W

A

14

9

L

I

S

I

C

W

A

D

H

L

S

D

N

Y

T

14

23

T

L

D

H

D

R

A

I

H

I

Q

A

E

N

G

14

40

L

L

V

E

A

E

Q

A

K

V

F

S

H

R

G

14

43

E

A

E

Q

A

K

V

F

S

H

R

G

G

N

V

14

75

H

K

I

R

I

K

W

T

K

L

T

S

D

Y

L

14

123

S

L

V

I

T

D

L

T

L

E

D

Y

G

R

Y

14

153

A

L

D

L

Q

G

V

V

F

P

Y

F

P

R

L

14

191

F

D

Q

L

Y

D

A

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Q

Y

6

204

W

C

N

A

G

W

L

S

D

G

S

V

Q

Y

P

6

212

D

G

S

V

Q

Y

P

I

T

K

P

R

E

P

C

6

217

Y

P

I

T

K

P

R

E

P

C

G

G

Q

N

T

6

223

R

E

P

C

G

G

Q

N

T

V

P

G

V

R

N

6

232

V

P

G

V

R

N

Y

G

F

W

D

K

D

K

S

6

256

N

F

N

G

R

F

Y

Y

L

I

H

P

T

K

L

6

262

Y

Y

L

I

H

P

T

K

L

T

Y

D

E

A

V

6

272

Y

D

E

A

V

Q

A

C

L

N

D

G

A

Q

I

6

274

E

A

V

Q

A

C

L

N

D

G

A

Q

I

A

K

6

277

Q

A

C

L

N

D

G

A

Q

I

A

K

V

G

Q

6

292

I

F

A

A

W

K

I

L

G

Y

D

R

C

D

A

6

301

Y

D

R

C

D

A

G

W

L

A

D

G

S

V

R

6

302

D

R

C

D

A

G

W

L

A

D

G

S

V

R

Y

6

303

R

C

D

A

G

W

L

A

D

G

S

V

R

Y

P

6

319

S

R

P

R

R

R

C

S

P

T

E

A

A

V

R

6

320

R

P

R

R

R

C

S

P

T

E

A

A

V

R

F

6

326

S

P

T

E

A

A

V

R

F

V

G

F

P

D

K

6

338

P

D

K

K

H

K

L

Y

G

V

Y

C

F

R

A

6

227

G

G

Q

N

T

V

P

G

V

R

N

Y

G

F

W

4

64

Y

R

D

P

T

A

F

G

S

G

I

H

K

I

R

3

87

D

Y

L

K

E

V

D

V

F

V

S

M

G

Y

H

3

225

P

C

G

G

Q

N

T

V

P

G

V

R

N

Y

G

3

282

D

G

A

Q

I

A

K

V

G

Q

I

F

A

A

W

3

324

R

C

S

P

T

E

A

A

V

R

F

V

G

F

P

3

330

A

A

V

R

F

V

G

F

P

D

K

K

H

K

L

3

42

V

E

A

E

Q

A

K

V

F

S

H

R

G

G

N

2

50

F

S

H

R

G

G

N

V

T

L

P

C

K

F

Y

2

52

H

R

G

G

N

V

T

L

P

C

K

F

Y

R

D

2

55

G

N

V

T

L

P

C

K

F

Y

R

D

P

T

A

2

66

D

P

T

A

F

G

S

G

I

H

K

I

R

I

K

2

69

A

F

G

S

G

I

H

K

I

R

I

K

W

T

K

2

100

Y

H

K

K

T

Y

G

G

Y

Q

G

R

V

F

L

2

101

H

K

K

T

Y

G

G

Y

Q

G

R

V

F

L

K

2

143

E

G

L

E

D

D

T

V

V

V

A

L

D

L

Q

2

152

V

A

L

D

L

Q

G

V

V

F

P

Y

F

P

R

2

159

V

V

F

P

Y

F

P

R

L

G

R

Y

N

L

N

2

180

A

C

L

D

Q

D

A

V

I

A

S

F

D

Q

L

2

208

G

W

L

S

D

G

S

V

Q

Y

P

I

T

K

P

2

243

K

D

K

S

R

Y

D

V

F

C

F

T

S

N

F

2

323

R

R

C

S

P

T

E

A

A

V

R

F

V

G

F

2

328

T

E

A

A

V

R

F

V

G

F

P

D

K

K

H

2

340

K

K

H

K

L

Y

G

V

Y

C

F

R

A

Y

N

2

14

W

A

D

H

L

S

D

N

Y

T

L

D

H

D

R

1

22

Y

T

L

D

H

D

R

A

I

H

I

Q

A

E

N

1

30

I

H

I

Q

A

E

N

G

P

H

L

L

V

E

A

1

32

I

Q

A

E

N

G

P

H

L

L

V

E

A

E

Q

1

59

L

P

C

K

F

Y

R

D

P

T

A

F

G

S

G

1

79

I

K

W

T

K

L

T

S

D

Y

L

K

E

V

D

1

80

K

W

T

K

L

T

S

D

Y

L

K

E

V

D

V

1

84

L

T

S

D

Y

L

K

E

V

D

V

F

V

S

M

1

104

T

Y

G

G

Y

Q

G

R

V

F

L

K

G

G

S

1

114

L

K

G

G

S

D

S

D

A

S

L

V

I

T

D

1

115

K

G

G

S

D

S

D

A

S

L

V

I

T

D

L

1

116

G

G

S

D

S

D

A

S

L

V

I

T

D

L

T

1

127

T

D

L

T

L

E

D

Y

G

R

Y

K

C

E

V

1

132

E

D

Y

G

R

Y

K

C

E

V

I

E

G

L

E

1

140

E

V

I

E

G

L

E

D

D

T

V

V

V

A

L

1

141

V

I

E

G

L

E

D

D

T

V

V

V

A

L

D

1

155

D

L

Q

G

V

V

F

P

Y

F

P

R

L

G

R

1

162

P

Y

F

P

R

L

G

R

Y

N

L

N

F

H

E

1

170

Y

N

L

N

F

H

E

A

Q

Q

A

C

L

D

Q

1

172

L

N

F

H

E

A

Q

Q

A

C

L

D

Q

D

A

1

177

A

Q

Q

A

C

L

D

Q

D

A

V

I

A

S

F

1

187

V

I

A

S

F

D

Q

L

Y

D

A

W

R

G

G

1

205

C

N

A

G

W

L

S

D

G

S

V

Q

Y

P

I

1

210

L

S

D

G

S

V

Q

Y

P

I

T

K

P

R

E

1

230

N

T

V

P

G

V

R

N

Y

G

F

W

D

K

D

1

233

P

G

V

R

N

Y

G

F

W

D

K

D

K

S

R

1

236

R

N

Y

G

F

W

D

K

D

K

S

R

Y

D

V

1

240

F

W

D

K

D

K

S

R

Y

D

V

F

C

F

T

1

249

D

V

F

C

F

T

S

N

F

N

G

R

F

Y

Y

1

251

F

C

F

T

S

N

F

N

G

R

F

Y

Y

L

I

1

253

F

T

S

N

F

N

G

R

F

Y

Y

L

I

H

P

1

255

S

N

F

N

G

R

F

Y

Y

L

I

H

P

T

K

1

257

F

N

G

R

F

Y

Y

L

I

H

P

T

K

L

T

1

266

H

P

T

K

L

T

Y

D

E

A

V

Q

A

C

L

1

271

T

Y

D

E

A

V

Q

A

C

L

N

D

G

A

Q

1

278

A

C

L

N

D

G

A

Q

I

A

K

V

G

Q

I

1

287

A

K

V

G

Q

I

F

A

A

W

K

I

L

G

Y

1

288

K

V

G

Q

I

F

A

A

W

K

I

L

G

Y

D

1

294

A

A

W

K

I

L

G

Y

D

R

C

D

A

G

W

1

304

C

D

A

G

W

L

A

D

G

S

V

R

Y

P

I

1

309

L

A

D

G

S

V

R

Y

P

I

S

R

P

R

R

1

322

R

R

R

C

S

P

T

E

A

A

V

R

F

V

G

1

337

F

P

D

K

K

H

K

L

Y

G

V

Y

C

F

R

1

151P3D4 v.2: HLA Peptide Scoring Results

DRB1*1101 15 - mers SYFPEITHI

229

P

R

G

L

G

F

I

F

K

T

I

A

P

L

A

27

Portion of

137

S

R

I

F

W

R

Q

E

K

A

D

G

G

S

C

24

SEQ ID NO:

44

T

G

I

I

T

Q

G

A

K

D

F

G

H

V

Q

22

5; each start

51

A

K

D

F

G

H

V

Q

F

V

G

S

Y

K

L

22

position is

158

S

E

A

Y

K

K

V

C

L

S

G

A

P

H

E

22

specified, the

233

G

F

I

F

K

T

I

A

P

L

A

A

T

R

A

22

length of

244

A

T

R

A

T

R

I

G

H

P

G

G

R

T

P

22

peptide is 15

301

S

S

T

Y

D

S

L

S

P

Y

G

P

R

N

P

22

amino acids,

338

G

Q

K

H

N

V

L

A

R

G

K

P

Q

R

K

22

the end

34

K

V

D

L

L

V

P

T

K

V

T

G

I

I

T

21

position for

112

L

K

Y

L

A

F

L

H

K

R

M

N

T

N

P

21

each peptide is

163

K

V

C

L

S

G

A

P

H

E

V

G

W

K

Y

21

the start

181

T

A

T

L

E

E

K

R

K

E

K

A

E

I

H

21

position plus

14

L

H

I

V

V

E

S

I

R

D

H

S

G

Q

K

20

fourteen

40

P

T

K

V

T

G

I

I

T

Q

G

A

K

D

F

20

111

K

L

K

Y

L

A

F

L

H

K

R

M

N

T

N

20

199

N

K

Q

L

M

R

L

Q

K

Q

A

E

K

N

M

20

236

F

K

T

I

A

P

L

A

A

T

R

A

T

R

I

20

313

R

N

P

L

P

N

P

R

H

S

P

S

G

G

G

20

130

P

Y

H

F

Q

V

P

S

R

I

F

W

R

Q

E

19

380

W

K

A

I

E

S

L

E

E

G

L

G

G

K

Q

19

15

H

I

V

V

E

S

I

R

D

H

S

G

Q

K

M

18

56

H

V

Q

F

V

G

S

Y

K

L

A

Y

S

N

D

18

217

I

D

K

Y

T

E

S

P

G

G

G

S

P

R

G

18

357

N

N

S

W

Y

V

E

N

G

R

P

A

D

L

A

18

358

N

S

W

Y

V

E

N

G

R

P

A

D

L

A

G

18

174

G

W

K

Y

Q

A

V

T

A

T

L

E

E

K

R

17

60

V

G

S

Y

K

L

A

Y

S

N

D

G

E

H

W

16

73

H

W

T

V

Y

Q

D

E

K

Q

R

K

D

K

V

16

138

R

I

F

W

R

Q

E

K

A

D

G

G

S

C

C

16

281

P

A

A

W

L

P

L

R

T

P

W

T

R

P

S

16

285

L

P

L

R

T

P

W

T

R

P

S

S

C

P

T

16

377

G

A

L

W

K

A

I

E

S

L

E

E

G

L

G

16

11

L

R

A

L

H

I

V

V

E

S

I

R

D

H

S

15

32

D

K

K

V

D

L

L

V

P

T

K

V

T

G

I

15

82

Q

R

K

D

K

V

L

L

G

R

K

A

V

V

V

15

84

K

D

K

V

L

L

G

R

K

A

V

V

V

S

C

15

89

L

G

R

K

A

V

V

V

S

C

E

G

I

N

I

15

105

G

S

F

C

R

N

K

L

K

Y

L

A

F

L

H

15

119

H

K

R

M

N

T

N

P

S

R

R

P

Y

H

F

15

168

G

A

P

H

E

V

G

W

K

Y

Q

A

V

T

A

15

207

K

Q

A

E

K

N

M

K

K

K

I

D

K

Y

T

15

222

E

S

P

G

G

G

S

P

R

G

L

G

F

I

F

15

257

T

P

R

A

G

S

S

A

H

R

P

P

A

L

S

15

344

L

A

R

G

K

P

Q

R

K

P

K

S

E

N

N

15

373

S

G

Y

C

G

A

L

W

K

A

I

E

S

L

E

15

387

E

E

G

L

G

G

K

Q

K

D

K

E

R

K

A

15

26

G

Q

K

M

K

Q

D

K

K

V

D

L

L

V

P

14

71

G

E

H

W

T

V

Y

Q

D

E

K

Q

R

K

D

14

83

R

K

D

K

V

L

L

G

R

K

A

V

V

V

S

14

128

R

R

P

Y

H

F

Q

V

P

S

R

I

F

W

R

14

196

Y

R

K

N

K

Q

L

M

R

L

Q

K

Q

A

E

14

211

K

N

M

K

K

K

I

D

K

Y

T

E

S

P

G

14

232

L

G

F

I

F

K

T

I

A

P

L

A

A

T

R

14

251

G

H

P

G

G

R

T

P

R

A

G

S

S

A

H

14

258

P

R

A

G

S

S

A

H

R

P

P

A

L

S

A

14

312

P

R

N

P

L

P

N

P

R

H

S

P

S

G

G

14

322

S

P

S

G

G

G

G

L

K

K

P

A

R

H

C

14

323

P

S

G

G

G

G

L

K

K

P

A

R

H

C

Q

14

326

G

G

G

L

K

K

P

A

R

H

C

Q

G

Q

K

14

327

G

G

L

K

K

P

A

R

H

C

Q

G

Q

K

H

14

340

K

H

N

V

L

A

R

G

K

P

Q

R

K

P

K

14

356

E

N

N

S

W

Y

V

E

N

G

R

P

A

D

L

14

8

T

F

P

L

R

A

L

H

I

V

V

E

S

I

R

13

29

M

K

Q

D

K

K

V

D

L

L

V

P

T

K

V

13

54

F

G

H

V

Q

F

V

G

S

Y

K

L

A

Y

S

13

86

K

V

L

L

G

R

K

A

V

V

V

S

C

E

G

13

93

A

V

V

V

S

C

E

G

I

N

I

S

G

S

F

13

247

A

T

R

I

G

H

P

G

G

R

T

P

R

A

G

13

264

A

H

R

P

P

A

L

S

A

R

A

P

V

P

A

13

279

A

S

P

A

A

W

L

P

L

R

T

P

W

T

R

13

284

W

L

P

L

R

T

P

W

T

R

P

S

S

C

P

13

304

Y

D

S

L

S

P

Y

G

P

R

N

P

L

P

N

13

57

V

Q

F

V

G

S

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G

G

6

213

M

K

K

K

I

D

K

Y

T

E

S

P

G

G

G

6

215

K

K

I

D

K

Y

T

E

S

P

G

G

G

S

P

6

216

K

I

D

K

Y

T

E

S

P

G

G

G

S

P

R

6

218

D

K

Y

T

E

S

P

G

G

G

S

P

R

G

L

6

226

G

G

S

P

R

G

L

G

F

I

F

K

T

I

A

6

242

L

A

A

T

R

A

T

R

I

G

H

P

G

G

R

6

243

A

A

T

R

A

T

R

I

G

H

P

G

G

R

T

6

252

H

P

G

G

R

T

P

R

A

G

S

S

A

H

R

6

261

G

S

S

A

H

R

P

P

A

L

S

A

R

A

P

6

268

P

A

L

S

A

R

A

P

V

P

A

A

S

P

A

6

272

A

R

A

P

V

P

A

A

S

P

A

A

W

L

P

6

273

R

A

P

V

P

A

A

S

P

A

A

W

L

P

L

6

282

A

A

W

L

P

L

R

T

P

W

T

R

P

S

S

6

287

L

R

T

P

W

T

R

P

S

S

C

P

T

S

S

6

289

T

P

W

T

R

P

S

S

C

P

T

S

S

S

T

6

290

P

W

T

R

P

S

S

C

P

T

S

S

S

T

Y

6

291

W

T

R

P

S

S

C

P

T

S

S

S

T

Y

D

6

298

P

T

S

S

S

T

Y

D

S

L

S

P

Y

G

P

6

300

S

S

S

T

Y

D

S

L

S

P

Y

G

P

R

N

6

308

S

P

Y

G

P

R

N

P

L

P

N

P

R

H

S

6

314

N

P

L

P

N

P

R

H

S

P

S

G

G

G

G

6

315

P

L

P

N

P

R

H

S

P

S

G

G

G

G

L

6

316

L

P

N

P

R

H

S

P

S

G

G

G

G

L

K

6

317

P

N

P

R

H

S

P

S

G

G

G

G

L

K

K

6

348

K

P

Q

R

K

P

K

S

E

N

N

S

W

Y

V

6

354

K

S

E

N

N

S

W

Y

V

E

N

G

R

P

A

6

359

S

W

Y

V

E

N

G

R

P

A

D

L

A

G

S

6

361

Y

V

E

N

G

R

P

A

D

L

A

G

S

G

Y

6

362

V

E

N

G

R

P

A

D

L

A

G

S

G

Y

C

6

363

E

N

G

R

P

A

D

L

A

G

S

G

Y

C

G

6

364

N

G

R

P

A

D

L

A

G

S

G

Y

C

G

A

6

366

R

P

A

D

L

A

G

S

G

Y

C

G

A

L

W

6

374

G

Y

C

G

A

L

W

K

A

I

E

S

L

E

E

6

378

A

L

W

K

A

I

E

S

L

E

E

G

L

G

G

6

381

K

A

I

E

S

L

E

E

G

L

G

G

K

Q

K

6

384

E

S

L

E

E

G

L

G

G

K

Q

K

D

K

E

6

393

K

Q

K

D

K

E

R

K

A

E

N

G

P

H

L

6

394

Q

K

D

K

E

R

K

A

E

N

G

P

H

L

L

6

400

K

A

E

N

G

P

H

L

L

V

E

A

E

Q

A

6

1

M

L

E

H

T

T

K

T

F

P

L

R

A

L

H

3

28

K

M

K

Q

D

K

K

V

D

L

L

V

P

T

K

3

166

L

S

G

A

P

H

E

V

G

W

K

Y

Q

A

V

3

53

D

F

G

H

V

Q

F

V

G

S

Y

K

L

A

Y

2

69

N

D

G

E

H

W

T

V

Y

Q

D

E

K

Q

R

2

80

E

K

Q

R

K

D

K

V

L

L

G

R

K

A

V

2

87

V

L

L

G

R

K

A

V

V

V

S

C

E

G

I

2

99

E

G

I

N

I

S

G

S

F

C

R

N

K

L

K

2

118

L

H

K

R

M

N

T

N

P

S

R

R

P

Y

H

2

173

V

G

W

K

Y

Q

A

V

T

A

T

L

E

E

K

2

194

I

H

Y

R

K

N

K

Q

L

M

R

L

Q

K

Q

2

195

H

Y

R

K

N

K

Q

L

M

R

L

Q

K

Q

A

2

234

F

I

F

K

T

I

A

P

L

A

A

T

R

A

T

2

246

R

A

T

R

I

G

H

P

G

G

R

T

P

R

A

2

278

A

A

S

P

A

A

W

L

P

L

R

T

P

W

T

2

299

T

S

S

S

T

Y

D

S

L

S

P

Y

G

P

R

2

303

T

Y

D

S

L

S

P

Y

G

P

R

N

P

L

P

2

324

S

G

G

G

G

L

K

K

P

A

R

H

C

Q

G

2

355

S

E

N

N

S

W

Y

V

E

N

G

R

P

A

D

2

3

E

H

T

T

K

T

F

P

L

R

A

L

H

I

V

1

24

H

S

G

Q

K

M

K

Q

D

K

K

V

D

L

L

1

27

Q

K

M

K

Q

D

K

K

V

D

L

L

V

P

T

1

30

K

Q

D

K

K

V

D

L

L

V

P

T

K

V

T

1

38

L

V

P

T

K

V

T

G

I

I

T

Q

G

A

K

1

42

K

V

T

G

I

I

T

Q

G

A

K

D

F

G

H

1

47

I

T

Q

G

A

K

D

F

G

H

V

Q

F

V

G

1

52

K

D

F

G

H

V

Q

F

V

G

S

Y

K

L

A

1

66

A

Y

S

N

D

G

E

H

W

T

V

Y

Q

D

E

1

77

Y

Q

D

E

K

Q

R

K

D

K

V

L

L

G

R

1

102

N

I

S

G

S

F

C

R

N

K

L

K

Y

L

A

1

108

C

R

N

K

L

K

Y

L

A

F

L

H

K

R

M

1

110

N

K

L

K

Y

L

A

F

L

H

K

R

M

N

T

1

152

C

P

Q

G

H

A

S

E

A

Y

K

K

V

C

L

1

153

P

Q

G

H

A

S

E

A

Y

K

K

V

C

L

S

1

175

W

K

Y

Q

A

V

T

A

T

L

E

E

K

R

K

1

184

L

E

E

K

R

K

E

K

A

E

I

H

Y

R

K

1

201

Q

L

M

R

L

Q

K

Q

A

E

K

N

M

K

K

1

204

R

L

Q

K

Q

A

E

K

N

M

K

K

K

I

D

1

205

L

Q

K

Q

A

E

K

N

M

K

K

K

I

D

K

1

209

A

E

K

N

M

K

K

K

I

D

K

Y

T

E

S

1

221

T

E

S

P

G

G

G

S

P

R

G

L

G

F

I

1

225

G

G

G

S

P

R

G

L

G

F

I

F

K

T

I

1

227

G

S

P

R

G

L

G

F

I

F

K

T

I

A

P

1

237

K

T

I

A

P

L

A

A

T

R

A

T

R

I

G

1

277

P

A

A

S

P

A

A

W

L

P

L

R

T

P

W

1

319

P

R

H

S

P

S

G

G

G

G

L

K

K

P

A

1

320

R

H

S

P

S

G

G

G

G

L

K

K

P

A

R

1

325

G

G

G

G

L

K

K

P

A

R

H

C

Q

G

Q

1

330

K

K

P

A

R

H

C

Q

G

Q

K

H

N

V

L

1

352

K

P

K

S

E

N

N

S

W

Y

V

E

N

G

R

1

369

D

L

A

G

S

G

Y

C

G

A

L

W

K

A

I

1

397

K

E

R

K

A

E

N

G

P

H

L

L

V

E

A

1

399

R

K

A

E

N

G

P

H

L

L

V

E

A

E

Q

1

TABLE LII (A)
Exon compositions of 151P3D4 v.1
	Exon Number	Start	End
	Exon 1	1	289
	Exon 2	290	415
	Exon 3	416	787
	Exon 4	788	1090
	Exon 5	1091	1957

TABLE LII (B)
Exon compositions of 151P3D4 v.2
	Exon Number	Start	End
	Exon 1	1	102
	Exon 2	103	258
	Exon 3	259	425
	Exon 4	426	667
	Exon 5	668	863
	Exon 6	864	999
	Exon 7	1000	1201
	Exon 8	1202	1573
	Exon 9	1574	1876
	Exon 10	1877	2166

TABLE LIII
Nucleotide sequence of transcript variant
151P3D4 v.2 (SEQ ID NO: 61).
atgttggagc atactactaa gacattcccc ttaagagcac tgcacatagt tgtggaaagc 60
attagggacc acagtggcca aaaaatgaag caggataaga aggtggatct tcttgttcca 120
accaaagtga ctggcatcat tacacaagga gctaaagatt ttggtcatgt acagtttgtt 180
ggctcctaca aactggctta cagcaatgat ggagaacact ggactgtata ccaggatgaa 240
aagcaaagaa aagataaggt actgctgggc cggaaggcgg tggtcgtaag ctgcgaaggc 300
atcaacattt ctggcagttt ctgcagaaac aagttgaagt acctggcttt cctccacaag 360
cggatgaaca ccaacccttc tcgacgcccc taccacttcc aggtccccag ccgcatcttc 420
tggcgacaag aaaaagcaga tggtggttcc tgctgccctc aaggtcatgc gtctgaagcc 480
tacaagaaag tttgcctatc tggggcgcct cacgaggttg gctggaagta ccaggcagtg 540
acagccaccc tggaggaaaa gaggaaagag aaagccgaga tccactaccg gaagaataaa 600
cagctcatga ggctacagaa acaggccgag aagaacatga agaagaaaat tgacaaatac 660
acagagagtc caggaggagg cagtccccgt ggcttaggct ttatctttaa gacaatagcg 720
ccgctcgccg ccacccgcgc gactcggatc gggcatcccg gcggccgcac cccgcgcgct 780
ggctcatctg cacaccggcc acctgcattg tcggccagag cccccgtccc ggcggcttcc 840
ccagcagctt ggctgcccct caggacgccc tggacccgcc catcctcctg ccccactagc 900
tcatcgactt acgactccct cagtccctac ggcccacgga accctctccc caacccgcgc 960
cacagcccga gcggcggcgg cggccttaag aagcccgcaa gacactgtca aggtcaaaag 1020
cacaatgtgc tagccagggg gaaaccccag agaaagccaa aatctgaaaa taacagctgg 1080
tatgtagaaa acggcagacc tgctgacttg gcaggctcag gatattgtgg tgctctttgg 1140
aaggcaatag agtccttgga ggaaggactt ggaggaaaac aaaaggacaa ggaaaggaaa 1200
gcagaaaatg gcccccatct acttgtggaa gcagagcaag ccaaggtgtt ttcacacaga 1260
ggtggcaatg ttacactgcc atgtaaattt tatcgagacc ctacagcatt tggctcagga 1320
atccataaaa tccgaattaa gtggaccaag ctaacttcgg attacctcaa ggaagtggat 1380
gtttttgttt ccatgggata ccacaaaaaa acctatggag gctaccaggg tagagtgttt 1440
ctgaagggag gcagtgatag tgatgcttct ctggtcatca cagacctcac tctggaagat 1500
tatgggagat ataagtgtga ggtgattgaa ggattagaag atgatactgt tgtggtagca 1560
ctggacttac aaggtgtggt attcccttac tttccacgac tggggcgcta caatctcaat 1620
tttcacgagg cgcagcaggc gtgtctggac caggatgctg tgatcgcctc cttcgaccag 1680
ctgtacgacg cctggcgggg cgggctggac tggtgcaatg ccggctggct cagtgatggc 1740
tctgtgcaat atcccatcac aaagcccaga gagccctgtg gggggcagaa cacagtgccc 1800
ggagtcagga actacggatt ttgggataaa gataaaagca gatatgatgt tttctgtttt 1860
acatccaatt tcaatggccg tttttactat ctgatccacc ccaccaaact gacctatgat 1920
gaagcggtgc aagcttgtct caatgatggt gctcagattg caaaagtggg ccagatattt 1980
gctgcctgga aaattctcgg atatgaccgc tgtgatgcgg gctggttggc ggatggcagc 2040
gtccgctacc ccatctctag gccaagaagg cgctgcagtc ctactgaggc tgcagtgcgc 2100
ttcgtgggtt tcccagataa aaagcataag ctgtatggtg tctactgctt cagagcatac 2160
aactga                           2166

TABLE LIV
Nucleotide sequence alignment of 121P1F1 v.1 (SEQ ID NO: 62) and
151P3D4 v.2 (SEQ ID NO: 63).
151P3D4v.1	------------------------------------------------------------
151P3D4v.2	ATGTTGGAGCATACTACTAAGACATTCCCCTTAAGAGCACTGCACATAGTTGTGGAAAGC	60
151P3D4v.1	------------------------------------------------------------
151P3D4v.2	ATTAGGGACCACAGTGGCCAAAAAATGAAGCAGGATAAGAAGGTGGATCTTCTTGTTCCA	120
151P3D4v.1	------------------------------------------------------------
151P3D4v.2	ACCAAAGTGACTGGCATCATTACACAAGGAGCTAAAGATTTTGGTCATGTACAGTTTGTT	180
151P3D4v.1	------------------------------------------------------------
151P3D4v.2	GGCTCCTACAAACTGGCTTACAGCAATGATGGAGAACACTGGACTGTATACCAGGATGAA	240
151P3D4v.1	------------------------------------------------------------
151P3D4v.2	AAGCAAAGAAAAGATAAGGTACTGCTGGGCCGGAAGGCGGTGGTCGTAAGCTGCGAAGGC	300
151P3D4v.1	------------------------------------------------------------
151P3D4v.2	ATCAACATTTCTGGCAGTTTCTGCAGAAACAAGTTGAAGTACCTGGCTTTCCTCCACAAG	360
151P3D4v.1	------------------------------------------------------------
151P3D4v.2	CGGATGAACACCAACCCTTCTCGACGCCCCTACCACTTCCAGGTCCCCAGCCGCATCTTC	420
151P3D4v.1	------------------------------------------------------------
151P3D4v.2	TGGCGACAAGAAAAAGCAGATGGTGGTTCCTGCTGCCCTCAAGGTCATGCGTCTGAAGCC	480
151P3D4v.1	------------------------------------------------------------
151P3D4v.2	TACAAGAAAGTTTGCCTATCTGGGGCGCCTCACGAGGTTGGCTGGAAGTACCAGGCAGTG	540
151P3D4v.1	------------------------------------------------------------
151P3D4v.2	ACAGCCACCCTGGAGGAAAAGAGGAAAGAGAAAGCCGAGATCCACTACCGGAAGAATAAA	600
151P3D4v.1	------------------------------------------------------------
151P3D4v.2	CAGCTCATGAGGCTACAGAAACAGGCCGAGAAGAACATGAAGAAGAAAATTGACAAATAC	660
151P3D4v.1	------------------------------------------------------------
151P3D4v.2	ACAGAGAGTCCAGGAGGAGGCAGTCCCCGTGGCTTAGGCTTTATCTTTAAGACAATAGCG	720
151P3D4v.1	----------------------------------------------TTAGGCTGTA-ATT	13
151P3D4v.2	CCGCTCGCCGCCACCCGCGCGACTCGGATCGGGCATCCCGGCGGCCGCACCCCGCGCGCT	780
	*  * *     *
151P3D4v.1	AGGGGATTTGGGAGGAGA--ACTTTCCTGGTGACGCTTTGCTTTTCTTCTGCT--CTTGG	69
151P3D4v.2	GGCTCATCTGCACACCGGCCACCTGCATTGTCGGCCAGAGCCCCCGTCCCGGCGGCTTCC	840
	*   ** **      *   ** * * * **    *   **     * * *    ***
151P3D4v.1	TGAGAAAGT-GCCTCCTTCTTCCCAGGATCAGGACCT--CTGCCATCCAGCGCCACAA--	124
151P3D4v.2	CCAGCAGCTTGGCTGCCCCTCAGGACGCCCTGGACCCGCCCATCCTCCTGCCCCACTAGC	900
	** *  * * ** *  **    * *  * *****   *   * *** ** **** *
151P3D4v.1	--AGAGACATTCTGCACACACACTCACACACACACACACACACACACTCTCACACTCGC-	181
151P3D4v.2	TCATCGACTTACGACTCCCTCAGTCCCTACGGCCCACGGA-ACCCTCTCCCCAACCCGCG	959
	*  *** * *  * * * ** ** *     * ***  * ** * *** *  ** ***
151P3D4v.1	CCAGAGACAAACTTAAGGTGAGG-----AGAAAGAGCGCTA--CGTTCACTTGATCTCCA	234
151P3D4v.2	CCACAGCCCGAGCGGCGGCGGCGGCCTTAAGAAGCCCGCAAGACACTGTCAAGGTCAAAA	1019
	*** ** *  *     ** *  *     *  ***  *** *  *  *  *  * **   *
151P3D4v.1	GC------TTCCAACTTAAGCAGAACTTGAGAGCATCCGAACTCCTGGATTTCAGGACAA	288
151P3D4v.2	GCACAATGTGCTAGCCAGGGGGAAACCCCAGAGAAAGCCAAAATCTGAAAATAACAGCTG	1079
	**      * * * *    *   ***   **** *  * **   *** *  * *   *
151P3D4v.1	GTGAAGAAGATTCTTTGGGC-TATAAAGATGA-AGAGTCTACTTCTTCTGGTGCTGATTT	346
151P3D4v.2	GTATGTAGAAAACGGCAGACCTGCTGACTTGGCAGGCTCAGGATATTGTGGTGCTCTTTG	1139
	**    *  *  *    * * *    *  **  **  **    * ** *******  **
151P3D4v.1	CAATCTGCTGGGCTGATCATCTTTCAGACAACTATACTCTGGATCATGACAGAGCTATTC	406
151P3D4v.2	GAAGGCAATAGA------GTCCTTGGAGGAAGGACTTGGAGGAAAACAAAAGGACAAGGA	1193
	**     * *        ** **     **  *      ***  *  * **  * *
151P3D4v.1	ACATCCAAGCAGAAAATGGCCCCCATCTACTTGTGGAAGCAGAGCAAGCCAAGGTGTTTT	466
151P3D4v.2	A-AGGAAAGCAGAAAATGGCCCCCATCTACTTGTGGAAGCAGAGCAAGCCAAGGTGTTTT	1252
	* *   ******************************************************
151P3D4v.1	CACACAGAGGTGGCAATGTTACACTGCCATGTAAATTTTATCGAGACCCTACAGCATTTG	526
151P3D4v.2	CACACAGAGGTGGCAATGTTACACTGCCATGTAAATTTTATCGAGACCCTACAGCATTTG	1312
	************************************************************
151P3D4v.1	GCTCAGGAATCCATAAAATCCGAATTAAGTGGACCAAGCTAACTTCGGATTACCTCAAGG	586
151P3D4v.2	GCTCAGGAATCCATAAAATCCGAATTAAGTGGACCAAGCTAACTTCGGATTACCTCAAGG	1372
	************************************************************
151P3D4v.1	AAGTGGATGTTTTTGTTTCCATGGGATACCACAAAAAAACCTATGGAGGCTACCAGGGTA	646
151P3D4v.2	AAGTGGATGTTTTTGTTTCCATGGGATACCACAAAAAAACCTATGGAGGCTACCAGGGTA	1432
	************************************************************
151P3D4v.1	GAGTGTTTCTGAAGGGAGGCAGTGATAGTGATGCTTCTCTGGTCATCACAGACCTCACTC	706
151P3D4v.2	GAGTGTTTCTGAAGGGAGGCAGTGATAGTGATGCTTCTCTGGTCATCACAGACCTCACTC	1492
	************************************************************
151P3D4v.1	TGGAAGATTATGGGAGATATAAGTGTGAGGTGATTGAAGGATTAGAAGATGATACTGTTG	766
151P3D4v.2	TGGAAGATTATGGGAGATATAAGTGTGAGGTGATTGAAGGATTAGAAGATGATACTGTTG	1552
	************************************************************
151P3D4v.1	TGGTAGCACTGGACTTACAAGGTGTGGTATTCCCTTACTTTCCACGACTGGGGCGCTACA	826
151P3D4v.2	TGGTAGCACTGGACTTACAAGGTGTGGTATTCCCTTACTTTCCACGACTGGGGCGCTACA	1612
	************************************************************
151P3D4v.1	ATCTCAATTTTCACGAGGCGCAGCAGGCGTGTCTGGACCAGGATGCTGTGATCGCCTCCT	886
151P3D4v.2	ATCTCAATTTTCACGAGGCGCAGCAGGCGTGTCTGGACCAGGATGCTGTGATCGCCTCCT	1672
	************************************************************
151P3D4v.1	TCGACCAGCTGTACGACGCCTGGCGGGGCGGGCTGGACTGGTGCAATGCCGGCTGGCTCA	946
151P3D4v.2	TCGACCAGCTGTACGACGCCTGGCGGGGCGGGCTGGACTGGTGCAATGCCGGCTGGCTCA	1732
	************************************************************
151P3D4v.1	GTGATGGCTCTGTGCAATATCCCATCACAAAGCCCAGAGAGCCCTGTGGGGGCCAGAACA	1006
151P3D4v.2	GTGATGGCTCTGTGCAATATCCCATCACAAAGCCCAGAGAGCCCTGTGGGGGGCAGAACA	1792
	**************************************************** *******
151P3D4v.1	CAGTGCCCGGAGTCAGGAACTACGGATTTTGGGATAAAGATAAAAGCAGATATGATGTTT	1066
151P3D4v.2	CAGTGCCCGGAGTCAGGAACTACGGATTTTGGGATAAAGATAAAAGCAGATATGATGTTT	1852
	************************************************************
151P3D4v.1	TCTGTTTTACATCCAATTTCAATGGCCGTTTTTACTATCTGATCCACCCCACCAAACTGA	1126
151P3D4v.2	TCTGTTTTACATCCAATTTCAATGGCCGTTTTTACTATCTGATCCACCCCACCAAACTGA	1912
	************************************************************
151P3D4v.1	CCTATGATGAAGCGGTGCAAGCTTGTCTCAATGATGGTGCTCAGATTGCAAAAGTGGGCC	1186
151P3D4v.2	CCTATGATGAAGCGGTGCAAGCTTGTCTCAATGATGGTGCTCAGATTGCAAAAGTGGGCC	1972
	************************************************************
151P3D4v.1	AGATATTTGCTGCCTGGAAAATTCTCGGATATGACCGCTGTGATGCGGGCTGGTTGGCGG	1246
151P3D4v.2	AGATATTTGCTGCCTGGAAAATTCTCGGATATGACCGCTGTGATGCGGGCTGGTTGGCGG	2032
	************************************************************
151P3D4v.1	ATGGCAGCGTCCGCTACCCCATCTCTAGGCCAAGAAGGCGCTGCAGTCCTACTGAGGCTG	1306
151P3D4v.2	ATGGCAGCGTCCGCTACCCCATCTCTAGGCCAAGAAGGCGCTGCAGTCCTACTGAGGCTG	2092
	************************************************************
151P3D4v.1	CAGTGCGCTTCGTGGGTTTCCCAGATAAAAAGCATAAGCTGTATGGTGTCTACTGCTTCA	1366
151P3D4v.2	CAGTGCGCTTCGTGGGTTTCCCAGATAAAAAGCATAAGCTGTATGGTGTCTACTGCTTCA	2152
	************************************************************
151P3D4v.1	GAGCATACAACTGAATGTGCCCTTAGAGCGCATCAGTTTTAAAGTCATTAAGAACATGTG	1426
151P3D4v.2	GAGCATACAACTGA----------------------------------------------	2166
	**************
151P3D4v.1	AAAGGTGTTTTTTTTTTCCAATATGAACTCATGCAAGTTACCAAAACTGTGATAACCCTT	1486
151P3D4v.2	------------------------------------------------------------
151P3D4v.1	TTTTACTTACTGTAAAGAGTCATTTTCATAAGATCAATTCATTGATTTGTTTTTTGTAAA	1546
151P3D4v.2	------------------------------------------------------------
151P3D4v.1	GCTATCATTCAATATATATTATAAATTAATATAAATTTAAGGGAAGCTCTATGTAAGGAG	1606
151P3D4v.2	------------------------------------------------------------
151P3D4v.1	ACTTAGAGCCAAACTGTTTAAGCTGTATCATCCCAACAAAGTATCCTTTCATGAACGGGG	1666
151P3D4v.2	------------------------------------------------------------
151P3D4v.1	CATGCAATAGCTTAAGAATTGCTAGGATTAAATTAAGGAAAGTAAAGCTACTCAGAGCAA	1726
151P3D4v.2	------------------------------------------------------------
151P3D4v.1	CAGGTTCCACAAGCACAAACTTTACACATTTGTACAATTTTGAAATGCACTACAATAAAC	1786
151P3D4v.2	------------------------------------------------------------
151P3D4v.1	AAATTAGAGCAACACATTTGAAATACAGGCTTCTTTACATAAACTGAGAGGTTATACAAA	1846
151P3D4v.2	------------------------------------------------------------
151P3D4v.1	ACTCAGTTTCACAAGGGAACAATCTATACCTTTCTAAAAGTTAATATTTCAAGTCTCTAA	1906
151P3D4v.2	------------------------------------------------------------
151P3D4v.1	TAGGCAGAATATTTTACTCTTTAAAATCCTGCCTTTCTGACCAAAAAAAAA	1957
151P3D4v.2	---------------------------------------------------

TABLE LV
Amino acid sequence alignment of 151P3D4 v.1 (SEQ ID NO: 64) and
151P3D4 v.2 (SEQ ID NO: 65).
151P3D4v.1	------------------------------------------------------------
151P3D4v.2	MLEHTTKTFPLRALHIVVESIRDHSGQKMKQDKKVDLLVPTKVTGIITQGAKDFGHVQFV	60
151P3D4v.1	------------------------------------------------------------
151P3D4v.2	GSYKLAYSNDGEHWTVYQDEKQRKDKVLLGRKAVVVSCEGINISGSFCRNKLKYLAFLHK	120
151P3D4v.1	-------MKSLLLLVLISICWADHLSDN--------------------------------	21
151P3D4v.2	RMNTNPSRRPYHFQVPSRIFWRQEKADGGSCCPQGHASEAYKKVCLSGAPHEVGWKYQAV	180
	:.  : *   * * :. :*.
151P3D4v.1	---------------------------------------YT-------------------	23
151P3D4v.2	TATLEEKRKEKAEIHYRKNKQLMRLQKQAEKNMKKKIDKYTESPGGGSPRGLGFIFKTIA	240
	**
151P3D4v.1	-LDHDRAIHI--------------------------------------------------	32
151P3D4v.2	PLAATRATRIGHPGGRTPRAGSSAHRPPALSARAPVPAASPAAWLPLRTPWTRPSSCPTS	300
	*   ** :*
151P3D4v.1	------------------------------------------------------------
151P3D4v.2	SSTYDSLSPYGPRNPLPNPRHSPSGGGGLKKPARHCQGQKHNVLARGKPQRKPKSENNSW	360
151P3D4v.1	---------------------------------------QAENGPHLLVEAEQAKVFSHR	53
151P3D4v.2	YVENGRPADLAGSGYCGALWKAIESLEEGLGGKQKDKERKAENGPHLLVEAEQAKVFSHR	420
	:********************
151P3D4v.1	GGNVTLPCKFYRDPTAFGSGIHKIRIKWTKLTSDYLKEVDVFVSMGYHKKTYGGYQGRVF	113
151P3D4v.2	GGNVTLPCKFYRDPTAFGSGIHKIRIKWTKLTSDYLKEVDVFVSMGYHKKTYGGYQGRVF	480
	************************************************************
151P3D4v.1	LKGGSDSDASLVITDLTLEDYGRYKCEVIEGLEDDTVVVALDLQGVVFPYFPRLGRYNLN	173
151P3D4v.2	LKGGSDSDASLVITDLTLEDYGRYKCEVIEGLEDDTVVVALDLQGVVFPYFPRLGRYNLN	540
	************************************************************
151P3D4v.1	FHEAQQACLDQDAVIASFDQLYDAWRGGLDWCNAGWLSDGSVQYPITKPREPCGGQNTVP	233
151P3D4v.2	FHEAQQACLDQDAVIASFDQLYDAWRGGLDWCNAGWLSDGSVQYPITKPREPCGGQNTVP	600
	************************************************************
151P3D4v.1	GVRNYGFWDKDKSRYDVFCFTSNFNGRFYYLIHPTKLTYDEAVQACLNDGAQIAKVGQIF	293
151P3D4v.2	GVRNYGFWDKDKSRYDVFCFTSNFNGRFYYLIHPTKLTYDEAVQACLNDGAQIAKVGQIF	660
	************************************************************
151P3D4v.1	AAWKILGYDRCDAGWLADGSVRYPISRPRRRCSPTEAAVRFVGFPDKKHKLYGVYCFRAY	353
151P3D4v.2	AAWKILGYDRCDAGWLADGSVRYPISRPRRRCSPTEAAVRFVGFPDKKHKLYGVYCFRAY	720
	************************************************************
151P3D4v.1	N	354
151P3D4v.2	N	721
	*

Claims

1. An isolated antibody or fragment thereof that specifically binds to a protein having an amino acid sequence comprising SEQ ID NO: 3 or SEQ ID NO: 5.

2. The antibody or fragment thereof of claim 1, which is monoclonal.

3. The isolated antibody or fragment thereof of claim 1, wherein the amino acid sequence comprises SEQ ID NO: 3.

4. The isolated antibody or fragment thereof of claim 3, wherein the amino acid sequence consists of SEQ ID NO: 3.

5. The isolated antibody or fragment thereof of claim 1, wherein the amino acid sequence comprises SEQ ID NO: 5.

6. The isolated antibody or fragment thereof of claim 5, wherein the amino acid sequence consists of SEQ ID NO: 5.

7. The antibody or fragment thereof of claim 1, wherein the antibody or fragment is recombinant.

8. The antibody or fragment thereof of claim 1, which is an Fab, F(ab′)2, Fv or Sfv fragment.

9. The antibody or fragment thereof of claim 1, which is a human antibody or fragment.

10. The antibody or fragment thereof of claim 1, wherein the antibody or fragment comprises murine antigen binding region residues and human constant region residues.

11. The antibody or fragment thereof of claim 1, wherein the antibody or fragment is labeled with a detectable marker.

12. The antibody or fragment thereof of claim 1, wherein the antibody or fragment is labeled with a cytotoxic agent.

13. The antibody or fragment thereof of claim 12, wherein the cytotoxic agent is selected from the group consisting of detectable markers, radioactive isotopes, chemotherapeutic agents, and toxins.

14. The antibody or fragment thereof of claim 13, wherein the cytotoxic agent is a radioactive isotope selected from the group consisting of 211At, 131I, 125I, 90Y, 186Re, 188Re, 153Sm, 212Bi, 32P and radioactive isotopes of Lu.

15. The antibody or fragment thereof of claim 13, wherein the cytotoxic agent is a chemotherapeutic agent selected from the group consisting of taxol, actinomycin, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicine, gelonin, and calicheamicin.

16. The antibody or fragment thereof of claim 13, wherein the cytotoxic agent is a toxin selected from the group consisting of diphtheria toxin, enomycin, phenomycin, Pseudomonas exotoxin (PE)A, PE40, abrin, abrin A chain, mitogellin, modeccin A chain, and alpha-sarcin.

17. A pharmaceutical composition, comprising the antibody or fragment thereof of claim 1 and a pharmaceutically acceptable carrier.

18. A cell that produces the antibody or fragment thereof of claim 1.

19. A process for producing an antibody or fragment thereof that specifically binds to a protein having an amino acid sequence comprising SEQ ID NO: 3 or SEQ ID NO: 5, comprising:

(a) culturing the cell of claim 18 under conditions sufficient for the production of the antibody or fragment thereof; and

(b) recovering the antibody or fragment thereof.