9 results about "Heterozygosity Loss" patented technology

Disclosed herein are systems, methods, and compositions for treating a subject diagnosed with, or suffering from cancer. In some embodiments, the method comprises determining whether a tumor sample from the subject includes a cytotoxic gene signature, and treating the subject based on the determination. In some embodiments, the subject has or is suspected of having a loss of heterozygosity in human leukocyte antigen (HLA) class I genes. In some embodiments, the therapy comprises one or more checkpoint inhibitors. In some embodiments, the cancer is colorectal, uterine, stomach, lung, skin, head or neck, or non-small cell lung carcinoma.

The application provides a calculation method and system for accurately identifying loss of heterozygosity in prenatal diagnosis, and is applied to the technical field of medical data processing. Bam files and variation information are obtained through whole genome library construction and sequencing analysis through data processing. SNP sites are screened, allele mutation frequency is calculated, and effective sites are screened. The genome window is divided, the homozygosity rate HR value is calculated, and the nonlinear weight reference is constructed based on normal samples. Finally, the improved CBS algorithm is used to identify significant AOH segments combined with the weight reference, generate a table containing position and HR average information, complete the identification of loss of heterozygosity, and do not need additional CMA detection, which is accurate and efficient.

Methods, systems, and software are provided for determining a homologous recombination pathway status of a cancer in a test subject, e.g., to improve cancer treatment predictions and outcomes. In some embodiments, classifiers using one or more of (i) a heterozygosity status for DNA damage repair genes in a cancerous tissue, (ii) a measure of the loss of heterozygosity across the genome of the cancerous tissue, (iii) a measure of variant alleles detected in a second plurality of DNA damage repair genes in the genome of the cancerous tissue, (iv) a measure of variant alleles detected in the second plurality of DNA damage repair genes in the genome of a non-cancerous tissue, and (v) tumor sample purity are provided.

The application discloses a method for detecting glioma chromosome abnormalities based on targeted sequencing, and belongs to the technical field of biological medicine. The method first acquires the allele frequency of a to-be-detected sample at preset SNP sites (covering 1p, 1q, 19p, 19q, chromosome 7 and chromosome 10), and then calculates and determines whether specific chromosome arms or chromosomes have loss of heterozygosity. Meanwhile, the copy number of the region where each SNP site is located is calculated based on the sequencing depth, and the total copy number of the above-mentioned chromosomes is obtained by integration. Finally, the loss of heterozygosity determination result and the chromosome copy number information are comprehensively combined, so that the simultaneous identification of 1p / 19q co-deletion, gain of chromosome 7 (+7) and deletion of chromosome 10 (-10) is realized. The method does not require paired samples, can accurately quantify the copy number, avoid false positives, and only needs to detect part of the SNP sites, that is, can be combined with hot spot mutation detection, thereby saving cost and improving detection efficiency.

A method of determining a therapeutic regimen in a patient with cancer comprising determining in a sample from the patient the tumor mutation burden (TMB) and loss of heterozygosity (LOH), wherein high TMB in combination with no LOH is indicative of a positive outcome when treated with a checkpoint inhibitor and high TMB with LOH is indicative of a poor outcome, is provided herein.

This disclosure relates to methods of determining the loss of heterozygosity (LOH) status of a tumor and to methods of determining the homologous recombination repair deficiency (HRD) status of a tumor. Such methods further translate into ways of predicting the response of a subject having cancer to treatments or therapies comprising DNA damaging agents and / or agents inhibiting or impairing DNA repair; and into use of such treatments or therapies when the LOH or HRD status of the subject having cancer is positive.

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.

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.

To provide methods for assessing LOH in a cancer cell or genomic DNA thereof.SOLUTION: Provided are methods and materials involved in assessing samples (e.g. cancer cells) for the presence of a loss of heterozygosity (LOH) signature. For example, provided are methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an LOH signature. Also provided are 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.SELECTED DRAWING: None