Abstract: A method of analyzing a tumor sample comprising: (a) acquiring a library comprising a plurality of tumor members from a tumor sample; (b) contacting the library with a bait set to provide selected members; (c) acquiring a read for a subgenomic interval from a tumor member from said library; (d) aligning said read; and (e) assigning a nucleotide value (e.g., calling a mutation) from said read for the preselected nucleotide position, thereby analyzing said tumor sample.

Abstract: The present invention relates to methods for haplotype determination and, in particular, haplotype determination at the whole genome level as well as targeted haplotype determination.

Abstract: Provided are devices and methods for capturing template sample nucleic acids in a spatially specific manner that is coordinated with the original location of the templates in a tissue sample. By preserving spatial information regarding a given sample, the disclosed technology allows for improved diagnostics as well as improved therapeutic decision making for patient care and therapy.

Abstract: Disclosed herein are detection methods that use magnetic nanoparticles (MNPs) to allow molecules to be identified. Embodiments of this disclosure include methods of using magnetic sensors (e.g., magnetoresistive sensors) to detect temperature-dependent magnetic fields (or changes in magnetic fields) emitted by MNPs, and, specifically to distinguish between the presence and absence of magnetic fields emitted, or not emitted, by MNPs at different temperatures selected to take advantage of knowledge of how the MNPs' magnetic properties change with temperature. Embodiments disclosed herein may be used for nucleic acid sequencing, such as deoxyribonucleic acid (DNA) sequencing.

Abstract: A splice variant of bcr-abl mRNA that produces BCR-ABL protein with a truncated C-terminus and its role in resistance to treatment with kinase inhibitors is disclosed. Vectors for expressing the truncated gene product are provided as well as recombinant cells that express the truncated gene product from a cDNA construct. Also provided are methods compositions and kits for detecting the BCR-ABL splice variant. Additionally, methods for screening BCR-ABL kinase domain inhibitors which rely on the recombinant cells and methods of predicting likelihood for resistance of a CML patient with a BCR/ABL translocation respond to treatment with one or more BCR-ABL kinase inhibitors are also disclosed.

Abstract: The present invention relates to novel primers and sloppy molecular beacon and molecular beacon probes for amplifying segments from different genes in Mycobacterium tuberculosis for identifying the presence of M.tb DNA and/or resistance to anti-tuberculosis drugs.

Abstract: Disclosed herein is Differential Subclone Eradication and Resistance Analysis (DSER), a method developed to identify molecular targets for improved therapy by direct comparison of genomic features of eradicated and resistant subclones in pre- and post-treatment samples from a patient with BRCA2-deficient metastatic prostate cancer. FANCI and EYA4 were identified as candidate DNA repair-related targets for converting subclones from resistant to eradicable, and RNAi-mediated depletion of FANCI confirmed it as a potential target. The EYA4 alteration was associated with adjacent L1 transposon insertion during cancer evolution upon treatment. L1 activation was inhibited by the antiretroviral drug azidothymidine. In conclusion DSER provides an informative intermediate step toward effective precision cancer medicine, especially in cases with dramatic but temporary metastatic tumor regression.

Abstract: Disclosed herein are methods and compositions for associating a genetic variant with intraretinal fluid. Also disclosed herein are methods and compositions for associating a genetic variant with visual acuity, anatomic outcomes or treatment frequency.

Abstract: The present invention discloses markers, primers, probes and a kit for early screening and diagnosis of endometrial cancer. The markers are partial methylated regions in the four genes of CDO1, CELF4, HAND2 and HS3ST2. Detection primers and probes are designed for these methylated regions and to have clasp structures. The kit includes the aforementioned primers and probes. The present invention screens and combines multiple methylated regions to determine the most suitable methylated position for combined diagnosis, which can significantly improve the sensitivity and specificity of the detection for early endometrial cancer. The kit is especially suitable for early screening and diagnosis of endometrial cancer with cervical exfoliated cells as a sample. Even if the DNA template concentration is low, endometrial cancer can be detected. The kit has the advantages of non-invasive sampling, fast detection speed, higher sensitivity and specificity, etc.

Abstract: A method of investigating the monotypia of a population of T-cells comprising detecting expression of the T cell receptor beta chain constant region TRBC1 and TRBC2, and/or the T cell receptor gamma chain constant region TRGC1 and TRGC, in a population of T-cells.

Abstract: A group of molecular biomarkers having the genes SLC35D3, POSTN, KLK6 and MUC2 can be used in objective and quantitative methods for the classification, prediction of prognosis and for guiding treatment decisions of a subject with colorectal cancer. More specifically, a method for determining the metastatic potential and/or tumor aggressiveness of a colorectal cancer in a subject can include determining the gene expression levels of genes SLC35D3, POSTN, KLK6 and/or MUC2 in a regional lymph node, a primary intestinal tumor, blood, or feces sample obtained from the subject.

Abstract: A kit for in vitro measurement of a at least one IL7R gene transcript in a blood sample, including specific reagents for measuring the transcript, and a control sample calibrated to contain the IL7R gene transcript corresponding to the mean quantity measured in a pool of reference blood samples from human patients in a state of septic shock when reference blood samples are taken, or who were in a state of septic shock within 72 h after taking the reference blood samples, and who were known to have survived, and/or a calibrated to contain the quantity of an IL7R gene transcript corresponding to the mean quantity measured in reference blood samples from patients in a state of septic shock when the reference blood samples are taken, or who were in a state of septic shock within 72 h after taking the reference blood samples, and not to have survived.

Abstract: The invention provides methods, nucleic acids and kits for determining the prognosis of a subject having cancer. The invention discloses genomic sequences the methylation patterns of which have utility for the improved detection of said disorder, thereby enabling the improved diagnosis and treatment of patients.

Abstract: The present invention discloses a unique panel of gene transcripts down-regulated in patients with coronary artery disease (CAD). Methods and compositions for detecting CAD in patient blood samples are provided.

Abstract: Provided herein is technology for lung neoplasia screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of lung cancer.

Abstract: The present invention provides compositions and methods based on genetic polymorphisms that are associated with vascular diseases such as stroke. In particular, the present invention relates to genetic polymorphisms that have utility for such uses as predicting disease risk or predicting an individual's response to a treatment such as statins, including groups of polymorphisms that may be used as a signature marker set for such uses, as well as nucleic acid molecules containing the polymorphisms, variant proteins encoded by such nucleic acid molecules, reagents for detecting the polymorphic nucleic acid molecules and proteins, and methods of using the nucleic acid and proteins as well as methods of using reagents for their detection.

Abstract: The present disclosure relates to methods for determining recombination diversity at a genomic locus of interest. The method includes fragmenting nucleic acids isolated from immune cells, ligating adaptors to the fragmented or amplified nucleic acids, and selectively amplifying nucleic acids containing a recombined junction at the genomic locus of interest. Selective amplification is achieved by using a first primer that hybridizes to an adaptor sequence and a second primer that hybridizes at a constant region downstream of the recombined junction. The selectively amplified nucleic acids may be sequences and analyzed to determine recombination diversity at the genomic locus.

Abstract: This application provides a kit or a device for detection of lung cancer, comprising a nucleic acid(s) for detecting a miRNA(s) in a sample from a subject, and a method for detecting lung cancer, comprising measuring the miRNA(s) in vitro.

Abstract: Provided are a set of primer pair and probe, having the oligonucleotide sequences as shown in SEQ ID NO: 1, SEQ ID NO: 2 and SEQ ID NO: 3, and a set of primer pair and probe of reference sequence, having the oligonucleotide sequences as shown in SEQ ID NO: 4, SEQ ID NO: 5 and SEQ ID NO: 6. Further provided is the use of the set of primer pair and probe for detecting the common deleted region “chr9:21970277-21985225,hg19”, of CDKN2A in the preparation of a kit for quantitatively detecting the deletion of a human CDKN2A gene copy in a DNA sample to be tested. The new method and the specific primer pair and probe can simply, conveniently and specifically detect the deletion of the CDKN2A gene copy in the sample, and have higher sensitivity than conventional detection methods for copy deletion.

Abstract: A method of detecting the presence of Neisseria gonorrhoeae in a sample. The method involves detecting a first target sequence taken from the NGO1642 gene and/or a second target sequence taken from the NGO1012 gene. The method may involve a step of amplifying the target sequence, and may involve hybridising the target sequence to a nucleic acid probe and identifying hybridisation. The method may involve simultaneous detection of other target sequences, e.g. from other pathogens.