Abstract: The use of genes or biomarkers to more accurately diagnose aggressive prostate cancer in men of African descent or European descent is provided. More specifically, the genes or biomarkers of the present invention can be used in diagnostic tests and methods to determine, qualify, and/or assess aggressive prostate cancer or status, for example, to diagnose or identify aggressive prostate cancer, in an individual, subject, or patient, such as men of African descent or men of European descent.

Abstract: The present invention relates to methods, devices, instruments, processes, and systems for the highly specific, targeted molecular analysis of regions of human genomes and transcriptomes from the blood, i.e. from cell free circulating DNA, exosomes, microRNA, IncRNA, circulating tumor cells, or total blood cells. The technology enables highly sensitive identification and enumeration of mutation, expression, copy number, translocation, alternative splicing, and methylation changes using spatial multiplexing and combined nuclease, ligation, polymerase, and sequencing reactions. Such technology may be used for non-invasive early detection of cancer, non-invasive cancer prognosis, and monitoring both treatment efficacy and disease recurrence of cancer.

Abstract: A device is provided for capturing a nucleic acid in a single cell, having: a two-dimensional array comprising a substrate, a plurality of single cell capturing holes provided on one surface of the substrate, and a nucleic acid capturing region comprising, on the inside of the substrate, a nucleic acid capturing body, which is configured to capture the nucleic acids extracted from the individual cells respectively captured by the single cell capturing hole; a flow channel which is provided adjacent to the nucleic acid capturing region of the substrate, and is configured to discharge a solution in the nucleic acid capturing region; and a cylindrical structure body which is arranged on the substrate at the time of introducing a cell suspension and encloses a plurality of the single cell capturing holes, wherein the cylindrical structure body is removed after the cells are captured by the single cell capturing holes.

Abstract: The present invention relates to a novel method for an accurate quantification in intestinal samples of Faecalibacterium prausnitzii phylogroup I members (PHGI) and/or Faecalibacterium prausnitzii phylogroup II members (PHGII). It further relates to a method for detecting intestinal diseases, including the screening, diagnosis, differential diagnosis, and/or monitoring of disease activity or progression in a human subject comprising determining the abundance of PHGI and/or PHGII in an intestinal sample from said subject. Moreover, it relates to a method for the prediction of the efficacy of a drug in the therapeutic treatment of an intestinal disease in a human subject comprising determining the abundance of PHGI and/or PHGII in an intestinal sample from said subject.

Abstract: The present invention refers to a method of predicting susceptibility of a subject suffering from cancer to a treatment with an anti-cancer drug, wherein the method comprises detecting the presence or absence of a genetic alteration in a long non-coding RNA (IncRNA) that resides in an antisense strand of an oncogene, wherein the genetic alteration disrupts expression of the oncogene, and wherein the subject is predicted to be more susceptible to the treatment if the genetic alteration is present. In particular, the genetic alteration is a silent G>A mutation at Q787Q of the oncogene epidermal growth factor receptor (EGFR). Also disclosed herein is a method of treating a subject suffering from cancer, who was shown to have a genetic alteration in IncRNA that resides in an antisense strand of an oncogene.

Abstract: Compositions, methods and kits are disclosed for synthesizing and amplifying pools of probes using precursor oligonucleotides. In some aspects the precursor is amplified and nicking enzymes are used to separate the full length probes from the amplification products. The methods enable the preparation of single stranded DNA probes of defined sequence and length that are suitable for use in target detection assays.

Abstract: Methods are provided for the epigenetic analysis of cell-free DNA using organic boranes to convert oxidized 5-methylcytosine residues in the cell-free DNA to dihydrouracil (DHU) residues. Cell-free DNA is contacted with an organic borane selected to successively bring about reduction, deamination, and decarboxylation of oxidized 5-methylcytosine residues such as 5-carboxylcytosine and 5-formylcytosine, resulting in DHU residues in place thereof. Following amplification, the treated cell-free DNA is sequenced, with the DHU residues read as thymine residues. Reaction mixtures, kits and additional methods are also provided, as are related methods for the epigenetic analysis of DNA, including cell-free DNA.

Abstract: The present invention relates to a method of predicting the effectiveness of chemotherapy in a breast cancer patient, and more particularly, to a method for predicting the effectiveness of chemotherapy by measuring the expression levels of genes for predicting prognosis of breast cancer and a standard gene in a biological sample obtained from the breast cancer patient, and a method for predicting the difference between a patient group having a high effectiveness of chemotherapy and a patient group having a low effectiveness of chemotherapy. Therefore, the method of the present invention can accurately predict the effectiveness of chemotherapy for the breast cancer patient and can be used for the purpose of presenting clues about the direction of breast cancer treatment in the future.

Abstract: Provided are methods of detecting cancer in a patient that involve analyzing DNA in extracellular vesicles. Detection may involve screening for an insert in a 3? UTR of NANOGP8 present in extracellular vesicles. A method involves (i) obtaining a biological sample containing extracellular vesicles from the patient; (ii) isolating the vesicles from the biological sample; (iii) detecting an amount of NANOG DNA in the vesicles; (iv) comparing the amount of NANOG DNA in the vesicles with vesicles in a non-cancer cell sample, wherein an increased level of NANOG DNA in the vesicles from the patient as compared to the non-cancer cell sample provides a positive indication of cancer in the patient.

Abstract: Described herein are methods of diagnosing inflammatory bowel disease, including but not limited to Crohn's Disease (CD), Ulcerative Colitis (UC), and/or Medically Refractive Ulcerative Colitis (MR-UC), using RNA-SET2, TL1A and/or IFN-Y. The methods may comprise treating inflammatory bowel disease by administering a therapeutically effective amount of a therapeutic agent to a subject. Described further herein are processes for patient identification and/or stratification.

Abstract: The present invention provides methods for measuring translation rates of RNA associated with a ribosome (e.g., mRNA) in a rapid, cost-effective, and targeted manner.

Abstract: The present invention relates to compositions and methods for diagnosing and treating arrhythmias. In particular, the present invention provides IL-18 markers and uses thereof.