Abstract: This disclosure relates to methods, computer products, computer-implemented methods, and systems for predicting the probability or risk of prostate cancer recurrence and tumor aggressiveness in a patient. The method is based, in part, on the patient's risk profile that includes the presence/degree of specific copy number variations and predictive clinical factors. The methods and systems can be used to aid in treatment selection.

Abstract: The invention relates to a method for predicting graft alterations in a transplanted patient, comprising a step of determining the expression levels of bactericidal/permeability-increasing protein (BPI), chemokine (C motif) ligand 1 (XCL1) and thioredoxin domain containing 3 (TXNDC3) genes in a biological sample obtained from said transplanted patient.

Abstract: The present invention relates to methods, kits and means for diagnosing Parkinson's disease in a blood sample from a subject. Further, the present invention relates to a set of polynucleotides for detecting sets of miRNAs for diagnosing Parkinson's disease in a blood sample from a subject.

Abstract: The present invention is based on the discovery of genetic polymorphisms that are associated with psoriasis and related pathologies. In particular, the present invention relates to nucleic acid molecules containing the polymorphisms, including groups of nucleic acid molecules that may be used as a signature marker set, such as a haplotype, a diplotype, 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: A method for identifying a renal allograft recipient at risk for chronic allograft damage or interstutial fibrosis and tubular atrophy (IF/TA) by comparing the transcription level of a preselected gene signature set with the transcription level of a comparison standard, and diagnosing the recipient as being at risk for chronic allograft damage if the transcription level of the preselected gene signature set is significantly higher than the transcription level of the comparison standard.

Abstract: Provided herein is a method for identifying a genetic variant that is associated with development of a condition of interest (e.g., Alzheimer's disease), and genetic variants so identified. Methods of treatment with an active agent (e.g., with a particular active agent and/or at an earlier age) is also provided, upon detecting a genetic variant described herein. In some embodiments, the genetic variant is a deletion/insertion polymorphism (DIP) of the TOMM40 gene. Kits for determining if a subject is at increased risk of developing late onset Alzheimer's disease is also provided. Kits for determining if a subject is responsive to treatment for a condition of interest with an active agent are further provided.

Abstract: The invention provides methods to monitor cell free nucleic acids.

Abstract: A multi-gene-based assay for analysis of the following: (a) oncogene expression; (b) DNA methylation of tumor suppressor genes; (c) non-coding RNA expression (microRNA profiling); and (d) long non-coding RNA expression in cancer samples is disclosed. The assay method and device for conducting the assay are applicable to diagnosis, prognosis, and treatment of various cancers such as lung, breast, colorectal, prostate, liver, bladder; kidney, cervix, pancreatic, gastric, brain, oral, endometrium, and ovary. The assay methods find use in avoidance or postponement of surgical removal of cancer tissue.

Abstract: A method of detecting a predisposition to, or the incidence of, cancer in a sample comprises detecting an epigenetic change in at least one gene selected from an NDRG4/NDRG2 subfamily gene, GATA4, OSMR, GATA5, SFRP1, ADAM23, JPH3, SFRP2, APC, MGMT, TFPI2, BNIP3, FOXE1, SYNE1, SOX17, PHACTR3 and JAM3, wherein detection of the epigenetic change is indicative of a predisposition to, or the incidence of, cancer. Also described are pharmacogenetic methods for determining suitable treatment regimens for cancer and methods for treating cancer patients, based around selection of the patients according to the methods of the invention. The present invention is also concerned with improved methods of collecting, processing and analyzing samples, in particular body fluid samples. These methods may be useful in diagnosing, staging or otherwise characterizing various diseases.

Abstract: A multi-gene-based assay for analysis of the following: (a) oncogene expression; (b) DNA methylation of tumor suppressor genes; (c) non-coding RNA expression (microRNA profiling); and (d) long non-coding RNA expression in cancer samples is disclosed. The assay method and device for conducting the assay are applicable to diagnosis, prognosis, and treatment of various cancers such as lung, breast, colorectal, prostate, liver, bladder; kidney, cervix, pancreatic, gastric, brain, oral, endometrium, and ovary. The assay methods allow avoidance of surgery to remove cancerous tissue.

Abstract: Provided herein is a method of detecting cancer through generalized loss of stability of epigenetic domains as well as compositions useful therein. The present invention is based on the discovery that generalized loss of stability of epigenetic domains was determined to be a characteristic across various cancer types. Genome-scale bisulfite sequencing of cancers revealed a surprising loss of methylation stability in the cancer methylome, involving both CpG islands and shores, as well as large (up to several megabases) blocks of hypomethylation affecting more than half of the genome, with concomitant stochastic variability in gene expression.

Abstract: Collections of polynucleotides useful for estimating breeding value or detecting likelihood of an increased susceptibility to contracting paratuberculosis are disclosed. The polynucleotides are used to detect genomic sequences quantitatively associated with an increased susceptibility to contracting paratuberculosis. Methods for using the collections to estimate breeding value or predict likelihood of an increased susceptibility to contracting paratuberculosis are also provided. Kits comprising the collection of polynucleotides are also provided.

Abstract: The invention relates to a method which is capable of determining, at an initial stage of differentiation, the differentiated state of undifferentiated stem cells. The invention provides a method for determining a differentiated state of a cell comprising detecting expression of FOXB2 gene of a stem cell, and determining the differentiated state based on the result, and a differentiation marker selected from mRNA or protein derived from the FOXB2 gene. The invention is applicable to quality management of the stem cells or to methods for preparation and isolation of the differentiated cells. Further, because the differentiated cells can be determined at an initial stage of culture, the invention is useful for an early stage screening of cells and for quality management of the stem cells, and reduction in culturing period and cost reduction in expenditure regarding a culture medium, or the like, can be expected.

Abstract: The invention provides compositions and methods for selecting milk-producing livestock with a preferred phenotype. In one embodiment, the method includes detecting methylation status of one or more genes and gene regulatory regions in a sample to identify the preferred phenotype.

Abstract: The present invention provides a method for assessing the presence and risk of developing type 2 diabetes, cancer of all sites, or cardiovascular disease in a subject by detecting sequence variation in one or more genes such as carboxypeptidase E (CPE) and insulin degradation enzyme (IDE). A kit, array, and device useful for such a method are also provided. In addition, the present invention provides a method for treating type 2 diabetes, cancer of all sites, or cardiovascular disease in patients who have been tested and shown to have the pertinent genetic variations.

Abstract: The present disclosure provides methods of detecting a fusion gene of HNF4G and RSPO2 in a nucleic acid-containing sample, and a primer set, a probe set and a kit for detecting the fusion gene are also provided. Animal models for a human disease positive for the fusion gene are also provided herein. In addition, the present disclosure relates to the methods for assessing and identifying an agent effective on the fusion gene of HNF4G and RSPO2 or a human disease positive for a fusion gene of HNF4G and RSPO2 and thereby treating said disease are also provided.

Abstract: The present invention provides a kit or device for the detection of biliary tract cancer, and a method for detecting biliary tract cancer. The present invention relates to a kit or device for the detection of biliary tract cancer, comprising a nucleic acid capable of specifically binding to miRNA in a sample of a subject, and a method for detecting biliary tract cancer, comprising measuring the miRNA in vitro.

Abstract: Described are mismatch repair (MMR-)deficient tumors. Markers are presented herein having a high sensitivity to detect whether a tumor is mismatch repair deficient or not. The markers are particularly mutations in microsatellite regions. Accordingly, methods and materials are provided for diagnosing microsatellite instability of a tumor. Such a method comprises determining the presence of these markers. Further, kits are provided to detect the presence of these markers (or subsets thereof) in a sample.

Abstract: The present invention relates to a method and a kit for the identification of animals having greater potential for desirable characteristics of meat quality, rib eye area (REA), weaning weight and 18-month weight by means of the analysis of specific markers. The invention also refers to a method and a kit for the early identification of fat deposition in bovines.

Abstract: An object of the present invention is to provide a kit or a device for the detection of prostate cancer and a method for detecting prostate cancer. The present invention provides a kit or a device for the detection of prostate cancer, comprising a nucleic acid capable of specifically binding to a miRNA in a sample of a subject, and a method for detecting prostate cancer, comprising measuring the miRNA in vitro.