Abstract: The present invention provides a DNA encoding a TADG-14 protein selected from the group consisting of: (a) isolated DNA which encodes a TADG-14 protein; (b) isolated DNA which hybridizes to isolated DNA of (a) above and which encodes a TADG-14 protein; and (c) isolated DNA differing from the isolated DNAs of (a) and (b) above in codon sequence due to the degeneracy of the genetic code, and which encodes a TADG-14 protein. Also provided is a vector capable of expressing the DNA of the present invention adapted for expression in a recombinant cell and regulatory elements necessary for expression of the DNA in the cell.

Abstract: A system for analyzing tissue samples, that generally comprises, a storage device for at least temporarily storing one or more images of one or more cells, wherein the images comprise a plurality of channels; and a processor that is adapted to determine the extent to which a biomarker may have translocated from at least one subcellular region to another subcellular region; and then to generate a score corresponding to the extent of translocation.

Abstract: Methods for detecting thyroid cancer or thyroid cancer status in a subject are described comprising measuring novel markers or polynucleotides encoding the markers in a sample from the subject. The invention also provides localization or imaging methods for thyroid cancer, and kits for carrying out the methods of the invention. The invention also contemplates therapeutic applications for thyroid cancer employing the novel markers, polynucleotides encoding the markers, and/or binding agents for the markers.

Abstract: It is an object of the present invention to identify a glypican-3-derived peptide which can bind to HLA-A2 and activate human killer T cells, so as to provide a means for carrying out an immunotherapy which is able to target approximately 40% of Japanese patients suffering from several types of cancers, which express GPC3 at a high level. The present invention provides a peptide of any of the following (A) or (B): (A) a peptide, which has the amino acid sequence as shown in any one of SEQ ID NOS: 1 to 3; or (B) a peptide, which has an amino acid sequence comprising a substitution or addition of one or two amino acids with respect to the amino acid sequence as shown in any one of SEQ ID NOS: 1 to 3, and which has ability to induce killer T cells.

Abstract: The invention relates to thrombospondin fragments found in plasma, their use or use of portions thereof in diagnostic methods, as method calibrators, method indicators, and as immunogens, and as analytes for methods with substantial clinical utility; and their detection in plasma or other bodily fluids for purpose of diagnostic methods, especially for cancer.

Abstract: A method of analyzing a biological specimen to detect cancer in a subject, involving determining an ultraconserved RNA in the specimen and comparing the expression level to a control. The ultraconseved RNA may be uc.338 and may be used to detect hepatocellular cancer. Transcript RNA encoding ultraconserved RNA may also be used to detect cancer. Anti-cancer compositions and tumor-suppressing agents for treating cancer are also provided.

Abstract: The present invention provides the method of predicting an non-small cell lung cancer (NSCLC) prognosis.

Abstract: Aspects of the invention provide methods, nucleic acids and kits for detecting, or for detecting and distinguishing between or among liver cell proliferative disorders or for detecting, or for detecting and distinguishing between or among colorectal cell proliferative disorders. Particular aspects disclose and provide genomic sequences the methylation patterns of which have substantial utility for the improved detection of and differentiation between said class of disorders, thereby enabling the improved diagnosis and treatment of patients.

Abstract: The present invention provides a method for accurately discriminating between prostate carcinoma and benign prostatic hyperplasia based on a glycan structure of prostate specific antigen (PSA). The method of the present invention includes the steps of: purifying PSA from a sample derived from a subject; preparing a PSA derivative from the PSA; labeling the PSA derivative; and analyzing the labeled PSA derivative by the mass spectrometry method, in which the subject is identified as having prostate carcinoma when the ratio of the signal intensity of fucose-unbound glycan to the signal intensity of fucose-bound glycan in the labeled PSA derivative is greater than 1.0, and identified as having benign prostatic hyperplasia when the ratio is 1.0 or less.

Abstract: The present invention provides a method for detecting a glycan structure of a prostate specific antigen (PSA) rapidly and with high sensitivity and determining prostate carcinoma based on the difference in the structure, in particular, a method for determining between prostate carcinoma and benign prostatic hyperplasia accurately. A method for determining prostate carcinoma, wherein the method includes a step of analyzing a PSA glycan structure in a sample derived from a test subject, and prostate carcinoma is determined in the case that amount of a glycan having LacdiNAc (N-acetylgalactosamine-N-acetylglucosamine) (LacdiNAc(+)) is more than 30% of amount of a glycan not having LacdiNAc but having LacNAc (galacotose-N-acetylglucosamine) (LacdiNAc(?)).

Abstract: The present invention provides methods and materials related to the detection of colorectal neoplasm-specific markers in or associated with a subject's stool sample. In particular, the present invention provides methods and materials for identifying mammals having a colorectal neoplasm by detecting the presence of exfoliated epithelial markers (e.g., human DNA, tumor associated gene alterations, tumor associated proteins) and blood markers (e.g., homoglobin, serum proteins) in a stool sample obtained from the mammal.

Abstract: A system for classification of a test object using a training set comprising a plurality of objects, each of which is assigned as a member of a class. Collectively, the objects in the training set are members of at least two classes. A computer system is configured as a probabilistic classifier. The classifier estimates the probability of the test object being a member of each of the classes in the training set. The probabilistic classifier estimates the probability with reference to the class assignments of the objects in the training set which are neighbors to the test object within a defined region within the training set. The probabilistic classifier takes into account the situation in which there is an imbalance in the number of objects in the different classes in the training set. Additionally, the probabilistic classifier does not require any knowledge of the probability distribution function of the classes in the training set.

Abstract: The present disclosure relates to a method for assessing if a patient is affected with a lung cancer. The method includes analyzing the presence and amount of cyclohexanone contained in the urine excreted from the patient and determining if the presence and amount of cyclohexanone is indicative of lung cancer.

Abstract: This invention provides methods of retentate chromatography for resolving analytes in a sample. The methods involve adsorbing the analytes to a substrate under a plurality of different selectivity conditions, and detecting the analytes retained on the substrate by desorption spectrometry. The methods are useful in biology and medicine, including clinical diagnostics and drug discovery.

Abstract: Provided herein are methods for the diagnosis, or management of liver diseases, e.g., hepatocellular carcinoma, using profiles of the miRNAs determined from cellular or acellular body fluids.

Abstract: The object of the present invention is to find out another tumor marker which is useful for early diagnosis of melanoma, and provide a diagnostic kit and diagnostic method for malignant melanoma using such marker. The present invention provides a diagnostic kit for malignant melanoma, which comprises an antibody against SPARC and an antibody against GPC3.

Abstract: The present invention provides prognostic methods for conditions such as cancer, for example, breast cancer, comprising classifying an individual by a plurality of phenotypic, genotypic or clinical characteristics of the condition into a plurality of patient subsets, and analyzing the pattern of expression of prognosis-informative genes identified for that subset in a sample from the individual. The present invention also provides methods for constructing such patient subsets and of identifying prognosis-informative genesets for such subsets. The invention further provides methods of assigning a therapeutic regimen to an individual, microarrays useful for performing prognosis, kits comprising these microarrays, and computer systems and programs for implementing the methods of the invention.

Abstract: The present invention relates to methods of treating a breast cancer in a subject, methods of identifying a subject with a breast cancer as a candidate for a therapy having efficacy for treating a breast cancer molecular subtype, and methods of selecting a therapy for a subject with a breast cancer. The methods comprise determining the molecular subtype of the breast cancer in the subject. In some embodiments, the methods further comprise administering to the subject a therapy that is effective for treating the molecular subtype of the breast cancer.

Abstract: The invention provides molecular markers that are associated with the progression of chronic myeloid leukemia (CML), and methods and computer systems for monitoring the progression of CML in a patient based on measurements of these molecular markers. The present invention also provides CML target genes, and methods and compositions for treating CML patients by modulating the expression or activity of these CML target genes and/or their encoded proteins. The invention also provides genes that are associated with resistance to imatinib mesylate (Gleevec™) treatment in CML patients, and methods and compositions for determining the responsiveness of a CML patient to imatinib mesylate treatment based on measurements of these genes and/or their encoded proteins. The invention also provides methods and compositions for enhancing the effect of Gleevec™ by modulating the expression or activity of these genes and/or their encoded proteins.

Abstract: The present invention relates to a method aiding in the assessment of cancer. It discloses the use of the proapoptotic caspase adaptor protein (=PACAP) as a universal marker of different types of cancer. PACAP aids in the assessment of pulmonary or lung cancer (LC), particularly of non-small cell lung carcinoma (NSCLC), but also of other specific types of cancer. Such specific types of cancer are e.g. colon, bladder, cervix, ovary, endometrial, head and neck, breast, melanoma, pancreas, kidney, prostate, esophagus, stomach or bile duct cancer. Furthermore, the present invention especially relates to a method for assessing cancer from a liquid sample, derived from an individual by measuring PACAP in said sample. Measurement of PACAP can, e.g., be used in the early detection of cancer or in the surveillance of patients who undergo surgery.

Abstract: Method of enriching specific cells from cellular samples are disclosed, comprising contacting in solution a cellular sample with affinity-tagged ligands (ATLs) each comprising a first ligand linked to an affinity tag, wherein the ligand selectively binds a cellular marker of the rare cells and the affinity tag can be selectively captured by a capture moiety, wherein the affinity tags do not comprise a magnetic particle; and flowing the sample through a microfluidic device comprising the capture moiety to selectively retain ATL-bound cells. Methods for enriching circulating tumor cells, and devices for enriching specific cells from cellular samples are also disclosed.

Abstract: The present invention relates to a method for determining whether or not a mammal is affected with a lung cancer. The method for determining whether or not a mammal is affected with a lung cancer of the present invention includes the steps of: (a) measuring a concentration of 2-hydroxy-3-methylbutyric acid contained in the urine excreted from the mammal; and (b) determining that the mammal is affected with a lung cancer if the concentration measured in the step (a) is 13.2 ?M or more.

Abstract: The present disclosure relates to a method for assessing if a patient is affected with a lung cancer. The method includes analyzing the presence and amount of ?-citronellol contained in the urine excreted from the patient and determining if the presence and amount of ?-citronellol is indicative of lung cancer.

Abstract: Described are methods and kits to detect early stage hepatocellular carcinoma or a change in the gradation of hepatocellular carcinoma in mammals. The diagnostic marker is based on the profiling and identification of diagnostic carbohydrates present in a body fluid, such as blood serum.

Abstract: The invention relates to cancer-testis antigens and the nucleic acid molecules that encode them. The invention further relates to the use of the nucleic acid molecules, polypeptides and fragments thereof in methods and compositions for the diagnosis and treatment of diseases, such as cancer. More specifically, the invention relates to the discovery of novel cancer-testis (CT) antigens.

Abstract: Antibodies that bind to a GPR49 protein and have cell proliferation inhibitory activity against cells expressing the GPR49 protein are disclosed. Cell proliferation inhibitory activities are cytotoxic activities such as antibody-dependent cell-mediated cytotoxicity and complement-dependent cytotoxicity. Pharmaceutical compositions, cell-proliferation inhibitors, and anticancer agents containing an antibody of the present invention as an active ingredient are also disclosed. Examples of cancer include gastric cancer, colon cancer, hepatocellular carcinoma, lung cancer, prostate cancer, ovarian cancer, Ewing's sarcoma, and glioma. Furthermore, methods for diagnosing cancer by detecting expression of a GPR49 protein or a gene encoding a GPR49 protein, and diagnostic agents and kits to be used in these methods are also disclosed.

Abstract: Compositions and methods for the therapy and diagnosis of cancer, particularly ovarian cancer, are disclosed. Illustrative compositions comprise one or more ovarian tumor polypeptides, immunogenic portions thereof, polynucleotides that encode such polypeptides, antigen presenting cell that expresses such polypeptides, and T cells that are specific for cells expressing such polypeptides. The disclosed compositions are useful, for example, in the diagnosis, prevention and/or treatment of diseases, particularly ovarian cancer.

Abstract: Patients with ErbB2-overexpressing cancers can be given an ErbB2 targeting agent as a therapeutic regimen but not all patients are responsive. The present invention concerns the diagnostic, prognostic and therapeutic methods and compositions for evaluating potential efficacy of an ErbB2 targeting agent in an ErbB2-overexpressing cancers by evaluating PTEN expression, which is predictive of responsiveness or resistance to ErbB2 targeting agents such as trastuzumab. Low PTEN expression is predictive of a patient who will respond poorly to trastuzumab.

Abstract: Disclosed are immunoassay methods for the diagnosis/prognosis of diseases and disease susceptibility traits associated with gene mutations that cause protein truncation or allelic loss. The levels of one or more targeted wild-type proteins expressed by a subject gene or genes are immunologically quantitated in biological samples. Results indicating that a targeted wild-type protein is not present in an assayed sample, or that approximately 50% of the normal amount of such a wild-type protein is present in an assayed sample are considered to be positive for a mutation in one or both alleles of a subject gene, and correlated with the disease or the disease susceptibility trait associated with that mutation or mutations. Normal cells, particularly normal peripheral blood lymphocytes, are preferred biological samples.

Abstract: The invention relates to KLK protease inhibitors. In particular, the invention is directed to KLK4 protease inhibitors and their uses in the treatment of a cancer, such as prostate cancer.

Abstract: An improved method for preparing a cell culture is disclosed. The method includes culturing a multicellular tissue explant in the presence of growth medium that is substantially free of enzymes capable of digesting the explant and, subsequently, removing the explant at a predetermined time.

Abstract: An example method for detecting an analyte in a sample of a bodily fluid comprises the steps of exposing the bodily fluid sample to electromagnetic energy to cause a thermoelastic expansion in the analyte, and detecting a photoacoustic signal in the sample that results from the thermoelastic expansion.

Abstract: Exosomes can be used for detecting biomarkers for diagnostic, therapy-related or prognostic methods to identify phenotypes, such as a condition or disease, for example, the stage or progression of a disease. Cell-of-origin exosomes can be used in profiling of physiological states or determining phenotypes. Biomarkers or markers from cell-of-origin specific exosomes can be used to determine treatment regimens for diseases, conditions, disease stages, and stages of a condition, and can also be used to determine treatment efficacy. Markers from cell-of-origin specific exosomes can also be used to identify conditions of diseases of unknown origin.

Abstract: The present invention relates to cancer markers. In particular, the present invention provides metabolites and panels of metabolites that are differentially present in cancer (e.g., prostate or breast cancer).

Abstract: Compositions and methods for the therapy and diagnosis of cancer, particularly breast cancer, are disclosed. Illustrative compositions comprise one or more breast tumor polypeptides, immunogenic portions thereof, polynucleotides that encode such polypeptides, antigen presenting cell that expresses such polypeptides, and T cells that are specific for cells expressing such polypeptides. The disclosed compositions are useful, for example, in the diagnosis, prevention and/or treatment of diseases, particularly breast cancer.

Abstract: A method of using a bioactive lysophospholipid (LL) as a biomarker for detecting the presence and recurrence of ovarian cancer. Subspecies of LL, such as lysophosphatidic acid (LPA), lysophosphatidylinositol (LPI), lysophosphatidylcholine (LPC), and lysosphingolipid sphinsosine-1-phosphate (S1P), are used alone or in conjunction to increase the specificity and sensitivity of the assay.

Abstract: A biosensor device (1) providing an analysis platform for detecting cell growth, comprising of an aluminium nitride (AlN) base (2), a shear horizontal-surface acoustic wave (SH-SAW) resonator including an input transducer (4) and an output transducer (5) symmetrically positioned on the aluminum nitride (AlN) base (2), a counter electrode (6) positioned parallel to working electrodes (7) on the aluminum nitride (AlN) base (2), for transmitting frequency voltage towards the living cell (3), a plurality of working electrodes (7) positioned beneath the living cell (3) on the aluminium nitride (AlN) base (2) for receiving frequency voltage from the living cell (3), an impedance analyzer (8) for receiving impedance readings from the counter electrode (6) and working electrodes (7), and a back-etched silicon substrate (9) coupled to the aluminium nitride (AlN) base (2), for reducing current loss, wherein the living cell (3) is positioned in between of the input transducer and output transducer on the aluminium nitri

Abstract: A method of providing a risk evaluation and diagnosis of human oral cancer, by examining at the presence in human saliva sample of a combination of particulate nucleic acids from bacteria, virus, as well as human, and/or the presence of particulate biochemical volatile organic compounds, which are indicative of an increased risk of oral cancer.

Abstract: The invention provides methods and kits to detect early stage hepatocellular carcinoma or a change in the gradation of hepatocellular carcinoma in mammals. The diagnostic marker is based on the profiling and identification of diagnostic carbohydrates present in a body fluid such as blood serum.

Abstract: The present invention relates to screening methods for diagnosis, prognosis, or susceptibility to cancer in a subject by means of detecting the presence of serum autoantibodies to specific annexin protein antigens in sera from subjects. The present invention also provides screening methods for diagnosis and prognosis of cancer in a subject by means of detecting increased expression levels of annexin proteins in biological samples of the subject. The method of the invention can also be used to identify subjects at risk for developing cancer. The method of the invention involves the use of subject derived biological samples to determine the occurrence and level of expression of annexin proteins or expression of annexin derived peptides or antigens, and/or the occurrence and level of circulating autoantibodies to specific annexin protein antigens. The present invention further provides for kits for carrying out the above described screening methods.

Abstract: The invention relates to a simple screening test for neoplasia, a precancerous condition, or cancer of the breast. A method is described whereby a breast cancer marker is detected in breast fluid. In a particular embodiment, the method involves treating samples of breast fluids with an aldehyde detecting reagent without any prewashing. The appearance in breast fluids of a marker that is detected by an aldehyde detecting reagent, such as a Schiff's reagent, correlates very well with the disease status of the breast cancer subjects from which the fluids were obtained. Screening test kits are also provided.

Abstract: The determination (test, diagnosis) of pancreatic cancer can be performed with high accuracy by detecting a fucosylated sugar chain (N-glycan) present in a specific site of the human haptoglobin and using an amount of the fucosylated sugar chain as a tumor marker for pancreatic cancer.

Abstract: The invention relates to novel nucleic acids encoding a mammalian PCADM-1 gene, and proteins encoded thereby, whose expression is increased in certain diseases, disorders, or conditions, including, but not limited to, prostate cancer. The invention further relates to methods of detecting and treating prostate cancer, comprising modulating or detecting PCADM-1 expression and/or production and activity of PCADM-1 polypeptide. Further, the invention relates to novel assays for the identification of DNA-binding proteins and the double-stranded oligonucleotide sequences that specifically bind with them. Finally, the invention relates to DNAZYMs or DNA enzymes which specifically bind PCADM-1 mRNA to inhibit PCADM-1 gene expression and thereby destroy tumor cells and tumor tissue.

Abstract: The present invention provides an approach for the simultaneous determination of the activation states of a plurality of proteins in single cells. This approach permits the rapid detection of heterogeneity in a complex cell population based on activation states, and the identification of cellular subsets that exhibit correlated changes in activation within the cell population. Moreover, this approach allows the correlation of cellular activities or properties. In addition, the use of potentiators of cellular activation allows for characterization of such pathways and cell populations.

Abstract: The present invention provides DNA encoding a TADG-15 protein as well as a TADG-15 protein. Also provided is a vector capable of expressing the DNA of the present invention adapted for expression in a recombinant cell and regulatory elements necessary for expression of the DNA in the cell. The present invention further provides for methods of inhibiting TADG-15 expression and/or protease activity, methods of detecting TADG-15 mRNA and/or protein and methods of screening for TADG-15 inhibitors. Additionally, the present invention provides for cell-specific targeting via TADG-15 and methods of vaccinating an individual against TADG-15. The methods described are useful in the diagnosis, treatment and prevention of cancer, particularly breast and ovarian cancer.

Abstract: The present invention relates to an antibody against FGF-8, particularly a humanized antibody against FGF-8 and the antibody fragment thereof, a DNA sequence encoding the above antibody or the antibody fragment, a vector comprising the DNA sequence and a host cell transformed by the vector, a production process of the above antibody or the antibody fragment using the host cell, and a therapeutic agent and a diagnostic agent for cancer using the antibody or the antibody fragment.

Abstract: Devices, methods, and systems for processing sample materials are disclosed. The present invention may provide a bridge between standard microtiter plate systems, methods, protocols, etc. (that include wells arranged in rectangular arrays) and rotating sample processing devices and systems that allow users to obtain the rapid processing advantages of the more advanced sample processing devices. The sample processing devices preferably include a rectangular body to improve compatibility of the sample processing devices of the present invention with equipment designed for use with more conventional microtiter plates (which are typically rectangular in shape). The sample processing devices also include at least one set of process chambers arranged in one or more circular arcs and may include input and/or output chambers arranged in a rectilinear grid array.

Abstract: Methods and compositions are provided for detecting biomolecular interactions. The use of labels is not required and the methods can be performed in a high-throughput manner. The invention also provides optical devices useful as narrow band filters.

Abstract: A method of assessing recurrence status in a breast cancer patient comprises a step of assaying a biological sample from the patient for a level of a biomarker selected from S100? or HOX-C1I, wherein positive detection of one or both of the biomarkers is indicative of a positive recurrence status. Suitably, the method is a method of prognosis of poor disease free survival in a breast cancer patient, wherein positive detection of one or both of the biomarkers is indicative of poor disease survival. The method may also be a method of diagnosis of recurrence, wherein positive detection of circulating S100? is a diagnostic variable of recurrence. The method of diagnosis is carried out on a patient who is undergoing first line therapy and/or a patient who has had surgery to remove a primary breast tumour.

Abstract: We analyzed bone marrow from 67 patients from a phase 2 study of farnesyltransferase inhibition with tipifarnib (R115777, ZARNESTRA®), in older adults with previously untreated, poor-risk acute myeloid leukemia (AML) for N-Ras mutations, global gene expression, and/or quantitative PCR (qPCR) of specific genes. Microarray profiling identified a two-gene expression ratio (RASGRP1:APTX) which provided the greatest accuracy for predicting response to tipifarnib. We demonstrated that this classifier could predict response to tipifarnib in an independent set of 54 samples from relapsed or refractory AML, with a NPV and PPV of 92% and 28%, respectively (odds ratio of 4.4). Therefore, in both newly diagnosed and relapsed or refractory AML, this classifier improves the overall response rate by approximately 50% while maintaining a high NPV, and significantly improves patient overall survival.