Abstract: The present disclosure provides methods for treating non-small cell lung cancer (NSCLC) in a subject in need thereof by obtaining a biological sample from the NSCLC from the subject; measuring the expression of the following genes associated with immune activation in the biological sample: IFNGR2, MICB, MICA, STATE, IFIT1, IFIT2, IFIT3, IFNGR1, IL16, STAT4, STAT5A, STAT2, SOCS5, STAT3, TNFSF4, TNFRSF18, CXCL9, IFNG, STAT1, TNFRSF9, CXCL10, SOCS1, TNFRSF4, SOCS3, CCL2, CD28, CD40, OX40, 4-1BB, GITR, CD27, ICOS, CD226, B7, CD226, TCR, and CD40L; measuring the expression of the following genes associated with immune inhibition in the biological sample: ES, CD86, HAVCR2, LAGS, PDCD1, TBX21, TNFRSF14, IDO1, PDCD1LG2, CD47, VTCN1, CD274, MIF, CD276, LGALS3, CTLA4, PD1, TIM3, BTLA, TIGIT, CD96, H3, VISTA, CD112R, and GITR; determining that the NSCLC is responsive to an immunotherapy where the expression of fifteen or more of the genes associated with immune activation are upregulated and ten or less of the genes ass

Abstract: The present disclosure provides method for determining an immune response score (irScore), the method comprising: determining a number of differentially expressed genes that have are implicated in anti-tumor immune cell signaling/activation; determining a number of differentially expressed genes that are implicated in immunosuppression, wherein the irScore=X(low, medium, or high), wherein X is the number of differentially expressed genes that are implicated in anti-tumor immune cell signaling/activation, and wherein low refers to 1-4 differentially expressed genes that are implicated in immunosuppression, medium refers to 5-9 differentially expressed genes that are implicated in immunosuppression, and high refers to 10 or more differentially expressed genes that are implicated in immunosuppression.

Abstract: This invention provides methods for determining or predicting response to HER2-directed therapy in an individual.

Abstract: The present disclosure provides method for determining an immune response score (irScore), the method comprising: determining a number of differentially expressed genes that have are implicated in anti-tumor immune cell signaling/activation; determining a number of differentially expressed genes that are implicated in immunosuppression, wherein the irScore=X(low, medium, or high), wherein X is the number of differentially expressed genes that are implicated in anti-tumor immune cell signaling/activation, and wherein low refers to 1-4 differentially expressed genes that are implicated in immunosuppression, medium refers to 5-9 differentially expressed genes that are implicated in immunosuppression, and high refers to 10 or more differentially expressed genes that are implicated in immunosuppression.

Abstract: This invention provides methods for determining or predicting response to HER2-directed therapy in an individual.

Abstract: This invention provides methods for determining or predicting response to cancer therapy in an individual using differential image analysis of immunohistochemically stained tumor samples.

Abstract: This invention provides methods for determining or predicting response to HER2-directed therapy in an individual.

Abstract: This invention provides methods for determining or predicting response to HER2-directed therapy in an individual.

Abstract: This invention provides methods for determining or predicting response to HER2-directed therapy in an individual.

Abstract: This invention provides methods for determining or predicting response to HER2-directed therapy in an individual.

Abstract: Methods are disclosed for determining whether organ toxicity, particularly cardiotoxicity, will occur in a patient selected for treatment with various kinase inhibitors, such as tyrosine kinase inhibitors, more particularly erbB inhibitors such as Herceptin. In addition, methods are disclosed for determining whether a potential drug is likely to produce a cardiotoxic effect. The methods involve analyzing lipid levels or the expression fatty acid oxidation enzymes, pAMP activated protein kinase, glucose uptake, to determine whether a fatty acid oxidation disorder is present. The identification of a fatty acid oxidation disorder can be used as a predictor of toxicity, especially cardiac toxicity, and as an indication that organ function should be carefully monitored if a drug such as a tyrosine kinase inhibitor is administered. Methods are also disclosed for protecting organs from metabolic stress and for the treatment of cells, such as adipocytes, to reduce their lipid content.

Abstract: This invention provides methods for determining or predicting response to HER2-directed therapy in an individual.

Abstract: The present disclosure provides methods for predicting the sensitivity (e.g., responsiveness) of a cell and/or biological sample obtained from a subject (e.g., a human) to a drug (e.g., a DHFR inhibitor). Such methods may comprise determining the presence or absence of one or more Ras mutations and/or determining the presence or absence of an amplification of the Ras gene in the cell and/or biological sample. The methods may be used to predict the responsiveness of a subject to treatment with a drug.

Abstract: This invention provides methods for determining or predicting response to HER2-directed therapy in an individual.

Abstract: This invention provides methods for determining or predicting response to HER2-directed therapy in an individual.

Abstract: The present invention relates to a panel of targeted therapy markers that can be used in assessing a particular subject's sensitivity to various therapeutic agents and cancer treatments as a means of prognosticating whether a treatment or use of a particular therapeutic agent will result in a clinically positive outcome. Cellular receptors, ligands to those receptors and molecules involved in the programmed cell death pathway are examples of targeted therapy markers that might be used in the present invention.

Abstract: The present disclosure relates generally to methods for the detection and quantitation of the p95 component of HER2/neu (ERbB2). Such methods may comprise assaying the biological sample for expression of HER2 ICD; assaying the biological sample for expression of a HER2 ECD; quantitating an expressed amount of the HER2 ICD and an expressed amount of the HER2 ECD in the biological sample; and determining the amount of p95 expressed in the biological sample based on a difference between the expressed amount of the HER2 ICD and the expressed amount of the HER2 ECD. The methods of the present disclosure may be used to predict whether a subject will be responsive to a receptor tyrosine kinase inhibitor and/or may be used to select subjects for inclusion/exclusion in a clinical trial.

Abstract: The present disclosure provides methods for determining if PTEN is elevated or reduced in one or more tumor cells relative to one or more normal cells in the same biological sample by obtaining a biological sample comprising one or more tumor cells and one or more normal cells; assaying the biological sample for expression of PTEN; quantitating an amount of PTEN expression in the one or more tumor cells and an amount of PTEN expression in the one or more normal cells; comparing the amount of PTEN expression in the tumor cells to the amount of PTEN expression in the normal cells; and determining that PTEN is elevated in the tumor cells where the amount of expression of PTEN is greater in the tumor cells as compared to the normal cells or determining that PTEN is reduced in the tumor cells where the amount of expression of PTEN is less in the tumor cells than in the normal cells.

Abstract: The invention relates to a method for determining the response to cancer therapy in an individual using image analysis.

Abstract: This invention provides methods for determining or predicting response to cancer therapy in an individual.