Differential expression of long non-coding RNAs (lncRNAs) and enhancer RNAs (eRNAs) are used to diagnose diseases including neurological diseases, inflammatory diseases, rheumatic diseases, and autoimmune diseases. Machine learning systems are used to identify lncRNAs or eRNAs having differential expression correlated with certain disease states.

Disclosed are methods for treating Set1/COMPASS-associated cancers characterized by expression of Set1B/COMPASS. The methods typically include administering a therapeutic amount of an inhibitor of the Set1B/COMPASS pathway and/or an agonist for a target that is negatively regulated by the Set1B/COMPASS pathway.

Certain embodiments of the invention provide a method of detecting and/or quantitating nonsense mediated RNA decay (NMD) activity in a cell, comprising 1) detecting an altered level of RNA expression of a NMD-sensitive isoform in a cell, as compared to a control cell; and 2) detecting an unaltered level of RNA expression of a corresponding NMD-insensitive isoform in the cell, as compared to a control cell, wherein the isoforms are derived from an endogenously expressed, alternatively spliced gene.

Methods and compositions for in situ detection of circular RNA in a tissue sample are provided.

The present invention is related to an improved method for HER2 gene test by using quantitative real-time PCR (Polymerase Chain Reaction) technique. Our invention streamlines test process, and incorporates quality control for each major step, including sample, reagent, operation, and data report. We eliminate the need for reference genes which is hard to standardize in HER2 PCR test. We develop a cutoff reference point by using the statistical mean of tumor tissue population, and adopt a simplified scoring scheme for evaluation of HER2 status. Our invention produces consistent result across machines and labs, and has proven to be clinically successful in HER2 test.

The present invention provides methods and compositions involving microbiome signatures and their association with oral complications of cancer therapy.

Provided is a method of diagnosing lymphoma by analyzing an increase or decrease in contents of specific bacterial extracellular vesicles by performing bacterial metagenomic analysis using normal individual and subject-derived samples, wherein a lymphoma risk group may be diagnosed and predicted early to delay the time of onset or prevent the onset of lymphoma with proper cure, and after onset, early diagnosis may be performed, thereby reducing the incidence of lymphoma and increasing a therapeutic effect.

The subject invention pertains to methods of treating colorectal cancer by administering an atypical PKC inhibitor. The inhibitors of aPKC useful in the methods of the instant invention include ACPD, ICA-1, DNDA and ζ-Stat. Also provided are methods of measuring the susceptibility of colon cancer cells of a subject to inhibitors of aPKCs.

Disclosed herein are assays and methods for the identification of premalignant lesions, as well as methods of determining the likelihood that such premalignant lesions will progress to lung cancer. Also disclosed are methods and assays that are useful for monitoring the progression of premalignant lesions to lung cancer. The assays and methods disclosed herein provide minimally invasive means of accurately detecting and monitoring the presence or absence of premalignant lesions, thus providing novel insights into the earliest stages of lung cancer and facilitating early detection and early intervention.

The present invention is based on the discovery of genetic polymorphisms that are associated with cardiovascular disorders, particularly acute coronary events such as myocardial infarction and stroke, and genetic polymorphisms that are associated with responsiveness of an individual to treatment of cardiovascular disorders with statin. In particular, the present invention relates to 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.