Abstract: Provided herein are methods for assessing a risk of a trait in a subject, by selecting a plurality of ancestry-informative SNP markers based on objective design criteria, measuring a genotype of the subject, obtaining trait-associated SNP markers, and calculating a global polygenic risk score for the risk of the trait in the subject based on the plurality of ancestry-informative SNP markers and the trait-associated SNP markers. The trait can be risk of cancer. Also provided are methods for assessing ancestry of a subject.

Abstract: A computer-implemented method is discussed that includes identifying, by a computer server system, stored electronic data that represents genetic sequencing for one or more genes for individuals in a population of patients who have submitted to genetic sequencing; generating, for each of multiple individuals and from the stored electronic data, probability data for the individuals and probability or weighting data, or both, for relatives of the individuals, the probability data representing likelihoods that a particular person corresponding to the probability data carries a deleterious mutation in a particular gene; and generating a score for a genetic variant, wherein the score is a function of probability or weighting data, or both, for the individuals and for relatives of the individuals, and the score represent a composite probability that a certain variant is a deleterious or benign variant.

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

Abstract: Provided herein are methods for determining polygenic traits and risks for medical use, such as cancer traits and risks, as well as treating diseases for which risk is identified and/or assessed. Methods of this invention can provide a polygenic score which takes into account local ancestry through the ancestral origin of the alleles of risk loci. A polygenic score can provide surprisingly increased accuracy in determining polygenic traits and risks for ancestrally admixed populations.

Abstract: Provided herein are 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: Provided herein are methods for determining a polygenic risk score and breast cancer estimated risk for medical use, as well as for treating breast cancer. Methods of this invention can provide a polygenic risk score which takes into account a plurality of breast cancer associated SNP markers. Also provide is a comprehensive breast cancer risk estimation with increased accuracy.

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: 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 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: 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: 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: 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: 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: 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.