Abstract: This document provides methods and materials related to genetic variations associated with endometriosis. For example, this document provides methods for using such genetic variations to assess risk of, or susceptibility of developing or diagnosing endometriosis.

Abstract: Truncation variants of BCR-ABL mRNA that produces BCR-ABL proteins with a truncated C-terminus and its role in resistance to treatment with kinase inhibitors is described. Vectors for expressing the truncated gene products are described as well as recombinant cells that express the truncated gene products from cDNA constructs. Also provided are methods compositions and kits for detecting the BCR-ABL truncation variants. Also provided are methods for determining the prognosis of a patient diagnosed as having myeloproliferative disease, and methods for predicting the likelihood for resistance to a treatment with tyrosine kinase inhibitor in a patient diagnosed as having myeloproliferative disease. Additionally, methods for screening BCR-ABL tyrosine kinase domain inhibitors which rely on the recombinant cells are also disclosed.

Abstract: Methods for the rapid detection of the presence or absence of Mycobacterium tuberculosis (MTB) resistant to rifampicin (MTB-RIF) and/or MTB resistant to isoniazid (MTB-INH) in a biological or non-biological sample are described. The methods can include performing an amplifying step, a hybridizing step, and a detecting step. Furthermore, primers, probes targeting the genes for rpoB, inhA, and katG, along with kits are provided that are designed for the detection of MTB-RIF and/or MTB-INH.

Abstract: The invention provides nucleic acid segments of the human genome, particularly nucleic acid segments from a gene, including polymorphic sites. Allele-specific primers and probes hybridizing to regions flanking or containing these sites are also provided. The nucleic acids, primers and probes are used in applications such as phenotype correlations, forensics, paternity testing, medicine and genetic analysis.

Abstract: A fluorescent DNA probes specific to the conserved terminal 3′-noncoding region (nucleotides 10653-10678) of dengue virus and a pair of flanking primers are designed to formulate a dengue specific fluorogenic polymerase chain reaction (PCR). Optimal assay conditions with zero background are disclosed which permit the detection of low levels of dengue virus from clinical specimens. Dengue virus isolates from different geographic regions can be universally detected and identified by the fluorogenic RT-PCR assay. Moreover, the assay is specific for dengue 2 virus and does not recognize other related flaviviruses, including dengue serotypes Louis encephalitis, yellow fever, and Kunjin viruses. The ) 3, and 4, Japanese encephalitis, St. assay also efficiently detected immunocomplexed dengue viruses. The fluorogenic RT-PCR assay readily detected viremia in sera collected from individuals ill with dengue fever.

Abstract: A process for obtaining a DNA fragment for a plant characterized by obtaining a polymorphic DNA fragment by genomic comparison using a plant material, and then using an RNA-derived labeled probe to select a DNA fragment therefrom; a gene coding for the DNA fragment; a promoter; expression vector and transformed plant obtained using the gene; as well as a breeding method for plants using the DNA fragment as a marker are provided.

Abstract: The identity of the polymorphic nucleotide in a target sequence having at least two known variants can be easily and efficiently detected by hybridizing at least one primer upstream of the biallelic marker and performing extension reactions using the target DNA with the hybridized primer, where a first reaction is conducted in the absence of a deoxyribonucleoside triphosphate or ribonucleoside triphosphate complementary to the first known variant, and a second reaction is conducted in absence of a deoxyribonucleoside triphosphate or ribonucleoside triphosphate complementary to the second known variant. Determining the lengths of the primers and any extension products from both reactions will indicate which variant or variants are present in a DNA sample.

Abstract: The invention is directed to a method of diagnosing a cell proliferative disorder of breast tissue by determining the methylation status of nucleic acids obtained from a subject. Aberrant methylation of several genes including TWIST, HOXA5, NES-1, retinoic acid receptor beta (RAR&bgr;), estrogen receptor (ER), cyclin D2, WT-1, 14.3.3 sigma, and combinations of such genes serve as markers of breast malignancy.

Abstract: The present invention discloses the existence of two novel proteins UspA1 and UspA2, and their respective genes uspA1 and uspA2. Each protein encompasses a region that is conserved between the two proteins and comprises an epitope that is recognized by the MAb 17C7. One or more than one of these species may aggregate to form the very high molecular weight form (i.e. greater than 200 kDa) of the UspA antigen. Compositions and both diagnostic and therapeutic methods for the treatment and study of M. catarrhalis are disclosed.

Abstract: The invention provides nucleic acid segments of the human genome, particularly nucleic acid segments from a gene, including polymorphic sites. Allele-specific primers and probes hybridizing to regions flanking or containing these sites are also provided. The nucleic acids, primers and probes are used in applications such as phenotype correlations, forensics, paternity testing, medicine and genetic analysis. A role for the thrombospondin gene(s) in vascular disease is also disclosed. Use of single nucleotide polymorphisms in the thrombospondin gene(s) for diagnosis, prediction of clinical course and treatment response, development of therapeutics and development of cell-culture-based and animal models for research and treatment are disclosed.

Abstract: A method for comparing the variable reactivity of multiple, differentially mutated copies of 16S subsequences found in a number of ribosomal RNA operons of a single bacterial cell is described. The application of this method for distinguishing between closely related organisms, such as the genera Escherichia and Shigella, and between species of Shigella including S. boydii, S. dysenteriae, S. flexneri, and S. sonnei using nucleic acid probes is also presented.

Abstract: Method for detecting the presence of at least one single allele of a deletion mutant, specially as PCR assay for detecting the presence of at least one GST1*0 allele wherein a PCR is performed with two primers, of which one stems from the sequence upstream of the deletion area, and the other stems from the sequence downstream of the deletion area and wherein the production of the corresponding DNA fragment in the PCR is checked. Useful for testing of patients to check whether they are susceptible to toxins or resistant or overly sensitive to certain therapeutic agents or belonging to risk groups.

Abstract: A method for the identification of the presence of E. coli, and Enterococcus faecalis and/or Enterococcus faecium in liquid or liquified samples. The method employs novel oligonucleotide primers based on sequences of the E. coli LamB gene and the Enterococcus faecalis/faecium transposase gene Tn1546. The method involves enrichment of the liquid or liquified sample, preferably using a selective medium, obtaining DNA from bacteria in the sample, and PCR amplification of the DNA using the novel oligonucleotide primers. Kits with the primers are also contemplated.

Abstract: The present invention relates to a nucleic acid molecule or molecules and to a process for the detection of bacteria of the Salmonella genus. The invention relates also to a test kit or test kits for carrying out the mentioned detection processes.

Abstract: The present invention relates to methods for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The 5′ nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based by charge.

Abstract: This invention relates to a diagnostic method for detecting cell-proliferating diseases characterized by analysis of the methylation level of cytosine residues in the region involved in the expression of cytokine receptor gene.

Abstract: Nucleic acids encoding NRIF3 are described. Polypeptides having amino acid sequences of NRIF3 proteins are also provided. A method is also provided for isolating and cloning NRIF3 cDNA. NRIF3 is useful in development/implementation of high throughput screens to identify novel thyroid hormone receptor (TR) and retinoid X receptor (RXR) agonists and antagonists. Methods are also provided for identifying compounds that directly interfere with the interaction of NRIF3 and TR or RXR. Finally, therapies based on modulation of NRIF3 activity are disclosed.

Abstract: The disclosure describes building blocks for preparing oligonucleotides carrying non-standard nucleobases that can pair with complementary non-standard nucleobases so as to fit the Watson-Crick geometry, in that the resulting base pair joins a monocyclic six membered ring pairing with a fused bicyclic heterocyclic ring system composed of a five member ring fused with a six membered ring, with the orientation of the heterocycles with respect to each other and with respect to the backbone chain analogous to that found in DNA and RNA, but with a pattern of hydrogen bonds holding the base pair together different from that found in the AT and GC base pairs (a “non-standard base pair”).

Abstract: The present invention relates generally to the field of human genetics. Specifically, the present invention relates to the discovery that some alleles of the A-T gene cause susceptibility to cancer, in particular breast cancer. More specifically, the present invention relates to germline mutations in the A-T gene and their use in the diagnosis of predisposition to breast cancer. The invention further relates to somatic mutations in the A-T gene in human breast cancer and their use in the diagnosis and prognosis of human breast cancer.

Abstract: The invention provides novel APM1 genomic sequences, polypeptides, antibodies, and polynucleotides including biallelic markers derived from the APM1 locus. Primers hybridizing to regions flanking these biallelic markers are also provided. This invention also provides polynucleotides and methods suitable for genotyping a nucleic acid containing sample for one or more biallelic markers of the invention. Additionally, the invention provides methods to detect a statistical correlation between a biallelic marker allele and a phenotype and/or between a biallelic marker haplotype and a phenotype. Further, the invention provides diagnostic methods for early detection of obesity-related disorders.