Abstract: This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of homologous recombination deficiency (HRD) or an HRD signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an HRD signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

Abstract: This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of a loss of heterozygosity (LOH) signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an LOH signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

Abstract: Provided herein are methods for predicting chemotherapy benefit. The invention predicts chemotherapy benefit based on the expression analysis of biomarkers, e.g., RNA biomarker transcription analysis, taken from a tumor sample. The biomarker expression data can be combined with clinical variables, e.g., tumor size and nodal status, to generate a profile that predicts the benefit of including chemotherapy as a treatment decision.

Abstract: This disclosure generally relates to a molecular classification of cancer and particularly to molecular markers for predicting response to cancer therapy, including cancer immune therapy, and methods of use thereof.

Abstract: Provided herein are methods for predicting chemotherapy benefit. The invention predicts chemotherapy benefit based on the expression analysis of biomarkers, e.g., RNA biomarker transcription analysis, taken from a tumor sample. The biomarker expression data can be combined with clinical variables, e.g., tumor size and nodal status, to generate a profile that predicts the benefit of including chemotherapy as a treatment decision.

Abstract: Biomarkers and methods using the biomarkers for the prediction of the recurrence risk of cancer in a patient are provided.

Abstract: Methods and compositions involving molecular markers for the detection and characterization of cancer in a patient are provided.

Abstract: This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of a loss of heterozygosity (LOH) signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an LOH signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

Abstract: The present disclosure relates to methods, kits, and systems for assessing the risk of a human subject for developing a cancer, including genetic risk assessment, clinical risk assessment, and combinations of both to improve risk analysis.

Abstract: Methods and systems for detecting allelic imbalance using nucleic acid sequencing are provided.

Abstract: Biomarkers and methods using the biomarkers for classifying cancer in a patient (e.g., predicting the risk of cancer-specific death or cancer recurrence) are provided.

Abstract: Direct targeted sequencing (DTS) methods and a hidden Markov model (HMM) can be used to call the copy number of a segment of interest within a region of interest. Described herein are methods for calling a copy number variant or a copy number variant abnormality using an HMM, and methods for determining a copy number based on a copy number likelihood model, in a test sequencing library that has be sequenced using DTS methods. Also described herein are methods for determining a copy number of a segment, including accounting for spurious capture probes that may arise from the DTS methods.

Abstract: Methods and systems for detecting allelic imbalance using nucleic acid sequencing are provided.

Abstract: This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of a loss of heterozygosity (LOH) signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an LOH signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

Abstract: Biomarkers and methods using the biomarkers for classifying cancer in a patient (e.g., predicting the risk of cancer-specific death or cancer recurrence) are provided.

Abstract: The invention generally relates to a molecular classification of disease predisposition and particularly to molecular markers for cancer predisposition and methods of use thereof.

Abstract: This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of homologous recombination deficiency (HRD) or an HRD signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an HRD signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

Abstract: The invention generally relates to a molecular classification of disease predisposition and particularly to molecular markers for cancer predisposition and methods of use thereof.

Abstract: This invention provides methods and compositions for detecting somatic mutations in cancer cells. The methods can be used for measuring tumor mutation burden. Provided are methods for identifying and treating subjects who benefit from treatment with anticancer agents such as immune checkpoint inhibitors, methods for treating cancer in a subject, and methods for monitoring and prognosing a subject having cancer.

Abstract: Panels of biomarkers, methods and systems are disclosed for determining gene expression, and diagnosing and treating melanoma.