Methods for the large scale identification of post-translational modification states of proteins and enzyme activities for carrying out post-translational modification reactions involve the analysis of functional extracts from fresh and frozen samples using protein arrays. The methods and kits of the present invention can be used to analyze and characterize compounds for their effects on post-translational modifications and their pathways. The methods and kits can also be used to diagnose and characterize a wide variety of diseases and medical conditions, including cancer, neurodegenerative diseases, immune diseases, infectious diseases, genetic diseases, metabolic conditions, and drug effects using cells or body fluids of a patient.

The present disclosure provides methods for determining prognosis of cancer and/or infection in a subject based on the number of viable blast-transformed mononuclear cells and/or the number of viable large granular lymphocytes in a blood sample obtained from the subject.

Provided herein are methods for simultaneously determining the functional status of multiple signaling pathways in a diseased cell sample obtained from a subject to thereby select for therapeutic use in the subject a targeted therapeutic agent that affects the signaling pathway with the highest level of aberrant activity in the subject's cells. Also provided are methods for determining whether a signaling pathway is ultrasensitive in a diseased cell sample from a subject, also allowing for selection of an effective targeted therapeutic agent for therapeutic use in the subject. Methods of administering a selected targeted therapeutic agent to the subject are also provided.

A method of data interpretation from a multiplex cancer assay is described. The aggregate normalized score from the assay is transformed to a quantitative risk score quantifying a human subject's increased risk for the presence of cancer as compared to the known prevalence of the cancer in the population before testing the subject.

A method of data interpretation from a multiplex cancer assay is described. The aggregate normalized score from the assay is transformed to a quantitative risk score quantifying a human subject's increased risk for the presence of cancer as compared to the known prevalence of the cancer in the population before testing the subject.

This disclosure relates generally to methods and agents for assessing T-cell function and for predicting responses to therapy. More particularly, the present invention relates to methods and agents for detecting different forms of Eomesodermin (EOMES) in T-cells, which are useful for assessing the function of a T-cell, for assessing the immune function of a subject, for predicting the likelihood of response of a cancer patient to therapy including immunotherapy, for stratifying a cancer patient as a likely responder or non-responder to a therapy, and for managing treatment of a cancer patient.

The present invention aims to provide a humanized antibody or an antigen-binding fragment thereof having stable physical property, superior in tumor accumulation, and capable of binding to mucin subtype 5AC.

The above-mentioned problem is solved by the present invention that provides a humanized antibody or an antigen-binding fragment thereof having a heavy chain variable region consisting of the amino acid sequence shown in SEQ ID NO: 1-4 or a mutated amino acid sequence thereof, and a light chain variable region consisting of the amino acid sequence shown in SEQ ID NO: 5-8 or a mutated amino acid sequence thereof, and capable of binding to mucin subtype 5AC.

A bioinformatics process which provides an improved means to detect NFkB cellular signaling pathway in a subject, such as a human, based on the expression levels of at least six unique target genes of the NFkB cellular signaling pathway measured in a sample. The invention includes an apparatus comprising a digital processor configured to perform such a method, a non-transitory storage medium storing instructions that are executable by a digital processing device to perform such a method, and a computer program comprising program code means for causing a digital processing device to perform such a method. Kits are also provided for measuring expression levels of unique sets of NFkB cellular signaling pathway target genes.

Heritable mutations in the BRCA1 and BRCA2 and other genes in the DNA double-strand break (DSB) repair pathway increase risk of breast, ovarian and other cancers. In response to DNA breaks, the proteins encoded by these genes bind to each other and are transported into the nucleus to form nuclear foci and initiate homologous recombination. Flow cytometry-based functional variant analyses (FVAs) were developed to determine whether variants in BRCA1 or other DSB repair genes disrupted the binding of BRCA1 to its protein partners, the phosphorylation of p53 or the transport of the BRCA1complex to the nucleus in response to DNA damage. Each of these assays distinguished high-risk BRCA1 mutations from low-risk BRCA1 controls. Mutations in other DSB repair pathway genes produced molecular phenocopies with these assays. FVA assays may represent an adjunct to sequencing for categorizing VUS or may represent a stand-alone measure for assessing breast cancer risk.

The invention provides for the early detection, diagnostic, and prognostic assays and assay kits for breast cancer and other cancers, based upon the detection of human endogenous retroviruses (HERVs) as cancer biomarkers.