A method for identifying and enumerating candidate target cells within a biological fluid specimen is described. The method includes obtaining a biological fluid specimen, preparing the biological fluid specimen by staining cell features in the biological fluid specimen, capturing a digital image having a plurality of color channels of the biological fluid specimen, and applying image analysis to the digital image. A computer program product for identifying candidate target cells within a biological fluid specimen is also described. The computer program comprises instructions to cause a processor to carry out the image analysis.

The present invention relates inter alia to methods for determining whether a subject with squamous cell carcinoma (SCC) has an increased risk of metastasis. The invention further relates to methods of treating such subjects, diagnostic assays and kits. In certain embodiments, the invention relates to identifying whether a subject suffering from SCC has an increased risk of metastasis by determining the expression of Ambra-1 and p62 in a SCC tissue sample obtained from the subject.

The present invention relates to a population of cells with an increased proportion of left ventricular cardiomyocytes, and uses thereof, for example in treatment of disorders of the left ventricle and use in screening for drugs which may be used to treat disorders of the left ventricle.

Embodiments described herein provide methods of determining a risk of progression of Barrett's esophagus in a subject, classifying Barrett's esophagus in a subject, and detecting a field effect associated with malignant transformation of an esophagus of a subject suffering from Barrett's esophagus. The disclosure also provides kits for determining a risk of progression of Barrett's esophagus in a subject and classifying Barrett's esophagus in a subject.

This disclosure is directed, in part, to a method of determining whether a subject having cancer is at risk for developing metastasis of the cancer. In one embodiment, the method comprises (a) obtaining a biological sample from the subject having cancer; (b) determining CCR5 expression level and/or expression level of at least one of CCR5 ligands in the biological sample; and (c) if the expression level of CCR5 and/or of at least one of CCR5 ligands determined in step (b) is increased compared to CCR5 expression level and/or expression level of at least one of CCR5 ligands in a control sample, then the subject is identified as likely at risk for developing metastasis of the cancer.

Disclosed are compositions and methods for identifying neoantigens and using neoantigens in the use of treating cancer, as well as autoimmune diseases, where antigens causing tissue destruction.

Compositions and methods are provided for measuring population size for a plurality of clonal cell populations in the same individual, e.g., for measuring tumor size for a plurality of clonally independent tumors within the same individual. A subject method can include: (a) contacting an individual with a plurality of cell markers that are heritable and distinguishable from one another, to generate a plurality of distinguishable lineages of heritably marked cells; (b) after sufficient time has passed for the heritably marked cells to undergo at least one round of division, detecting and measuring quantities of at least two of the plurality of cell markers present in the contacted tissue, thereby generating a set of measured values: and (c) using the set of measured values to calculate the number of heritably marked cells that are present (e.g., for at least two of the distinguishable lineages of heritably marked cells).

Provided herein are methods and kits for the detection of solid tumor cancers by measuring expression levels of at least one biomarker of solid tumor microenvironment potential or solid state tumor mass potential.

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.

A system and method for using new biomarkers to assess individual diseases is provided. In one embodiment of the present invention, absolute quantification of annotated metabolites by mass spectrometry is used to identify certain biomarkers and derivatives thereof (i.e., signatures), which are then used to screen for, diagnose, predict, prognose, and treat various diseases, including, but not limited to, breast cancer, ovarian cancer, colorectal cancer, pancreatic cancer, and acute graft-versus-host disease.