Abstract: The present invention is based on the discovery of methods and combinations of probes to chromosomal regions that are gained or lost or imbalanced in melanoma that provide highly specific and sensitive assays for the detection of melanoma cells.

Abstract: Disclosed is a diagnostic panel of methylated genomic loci encoding microRNA (mgmiR) markers that demonstrated 90% sensitivity and 100% specificity in the detection of head and neck squamous cell carcinoma (HNSCC). These results represent the first use of quantitative MS-PCR for the detection of mgmiRs. In addition, this panel demonstrates the ability to detect hypermethylation in the adjacent mucosa of cancer patients, suggesting its utility in early detection. This panel is also capable of detecting cancer by using saliva, blood and FNA tissue samples.

Abstract: The invention described in the application relates to a panel of gene expression markers for patient with a tumor. The invention thus provides methods and compositions, e.g., kits, for evaluating gene expression levels of the markers and methods of using such gene expression levels to evaluate the likelihood of disease progression or response to chemotherapy or radiation therapy. Such information can be used in determining prognosis and treatment options for cancer patients.

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 describes a method for predicting the response of a subject suffering from lung cancer to treatment with FGFR inhibitors. The relationship between the expression of the biomarkers and the treatment response allows the subjects to be classified as responsive or unresponsive to the treatment, which facilitates the therapeutic decision-making of the attending clinician. The present invention also describes the biomarkers N-cadherin, FGFR1 and FGFR4, how to analyse them and how to interpret the results obtained, in order to administer FGFR inhibitors only to the subjects that are responsive to the treatment, thereby optimising the same, which allows the unresponsive subjects to be treated with alternative therapies to the FGFR inhibitors.

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: In some embodiments, a method for aiding prediction of the likelihood of progression from Barrett's esophagus to high grade dysplasia or esophageal adenocarcinoma in a subject, is disclosed. The method can include (a) providing an oesophagal sample from said subject (b) determining if said sample stains abnormally with Aspergillus oryzae lectin; (c) determining if there is a DNA content abnormality in said sample; and (d) determining if there is low grade dysplasia in said sample; wherein if (b) is abnormal and (c) is abnormal and low grade dysplasia is present, then an increased likelihood of progression is determined. The disclosed subject matter also relates to an apparatus, and to different uses of certain materials.

Abstract: A method of detecting the presence of a prostate cancer field defect in a human subject comprising the step of (a) obtaining genomic DNA from the human subject and (b) quantitating methylation in at least one target region selected from the group consisting of CAV1, EVX1, MCF2L, FGF1, NCR2 and WNT2 and EXT1 and SPAG4 target, wherein significant methylation changes indicate the presence of prostate cancer or a prostate cancer field defect, wherein the change is relative to tissue from a second human subject who does not have prostate cancer.

Abstract: Technology provided herein relates in part to methods, processes and apparatuses for non-invasive assessment of genetic variations. In particular the invention relates to methods and kits for detecting aneuploidy of a fetal chromosome by determining the amounts of differentially methylated regions in each of chromosomes 13, 18 and 21 in circulating cell-free nucleic acid from a human pregnant female.

Abstract: Compositions and methods for detecting Trichomonas vaginalis are provided.

Abstract: The invention concerns a method of in vitro or ex vivo evaluation of the risk of complications in a patient who has sustained an insult or an infection generating a systemic inflammatory response syndrome, the method being characterized in that it comprises the step of detecting, in a biological sample obtained from said patient, at least one transcript of the IL7R gene, as well as measuring, in vitro or ex vivo, the quantity of at least one transcript of the IL7R gene, in a biological sample from a patient who has sustained an insult or an infection generating a systemic inflammatory response syndrome, in order to evaluate the risk of complications, and in particular of mortality, in said patient. The invention also concerns kits for measuring, in vitro or ex vivo, the quantity of at least one transcript of the IL7R gene in a biological sample.

Abstract: Various methods and compositions are provided for identifying and/or selecting a soybean plant or soybean germplasm with one or more preferred or desired reproductive growth phenotypes. In certain embodiments, the method comprises detecting at least one allele of one or more marker locus within or linked to a QTL associated with days to initiation of flowering. In other embodiments, the method additionally comprises detecting at least one allele of one or more marker locus within or linked to a QTL associated with days to maturity. In further embodiments, the method comprises crossing a selected soybean plant with a recurrent soybean parent plant. Further provided herein are marker loci, marker alleles, primers, probes, and kits suitable for identifying and/or selecting soybean plants or soybean germplasms with one or more reproductive growth phenotypes.

Abstract: A microRNA (miRNA) expression signature for predicting triple-negative breast cancer (TNBC) recurrence is provided. The miRNA expression signature consists essentially of hsa-miR-139-5p, hsa-miR-10b-5p, hsa-miR-486-5p, hsa-miR-455-3p, hsa-miR-107, hsa-miR-146b-5p, hsa-miR-324-5p, and hsa-miR-20a-5p.

Abstract: Disclosed herein are methods for identifying a genetic susceptibility to colon cancer in as subject, the method comprising determining the mRNA expression level of one or more of FSCN1, ZIC2, ZIC5, CRYBA2, MUC6, TRNP1 and SEMG1 in a colon tissue sample in the subject, where a ratio of the sample expression level of one or more genes in the panel to a reference expression level of one or more genes in the panel indicates cancer or and increased susceptibility of cancer. Disclosed herein are diagnostic devices comprising one or more biomarkers, wherein the biomarkers are FSCN1, ZIC2, ZIC5, CRYBA2, MUC6, TRNP1 and SEMG1; and a gene expression panel consisting of primers or probes for detecting FSCN1, ZIC2, ZIC5, CRYBA2, MUC6, TRNP1 and SEMG1 in a sample, and methods for assessing risk of developing colon cancer in a subject.

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 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: 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.

Abstract: An immune response subtype of cancer is associated with DNA damage which allows subjects to be stratified for particular therapies including immune therapies which may be combined with DNA damage therapeutics. A method for predicting responsiveness to an antagonist of an inhibitory immune checkpoint and/or an agonist of a stimulatory immune checkpoint comprises determining the expression level of at least one gene selected from Table 2B, 2A or 1 in a sample from the subject. The determined expression level is used to predict responsiveness to an antagonist of an inhibitory immune checkpoint and/or an agonist of a stimulatory immune checkpoint.

Abstract: The invention provides methods of using expression levels of one or more immune cell gene signatures and/or combinations of immune cell gene signatures as selection criteria for selecting a patient having cancer for treatment with an immunotherapy. The invention further provides methods for selecting a patient having cancer who may benefit from a particular immunotherapy, such as an activating immunotherapy or a suppressing immunotherapy and administering to the patient the activating immunotherapy or suppressing immunotherapy to treat the cancer.

Abstract: Methods and kits are described for testing for the presence or absence of any fungus in a sample. Examples of fungi that can be detected include, but are not limited to, those belonging to the genera Candida, Aspergillus and Pneumocystis. The methods include obtaining a sample suspected of containing fungal nucleic acid, including at least one universal region of fungal nucleic acid, and testing for the presence or absence in the sample of the at least one universal region of fungal nucleic acid. Samples may be biological or non-biological.