17 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.

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.

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 detecting loss of HLA allele heterozygosity is provided. The method may include accessing a trained machine learning model, the model being trained using a training dataset, the training dataset including at least the following training datasets: an adjusted B allele frequency, it represents a ratio between a first B allele frequency of a heterozygous allele corresponding to the genomic region in the tumor sample and a second B allele frequency of a heterozygous allele associated with one or more control samples in the genomic region. The method may also include using the machine learning model to generate a result corresponding to a probability of whether a loss of heterozygosity exists in HLA alleles identified in a biological sample of a particular subject by processing sequence data using the machine learning model.

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.

The application provides application of a ZNF652 gene as a marker in preparation of a kit for evaluating cancer occurrence risk and / or prognosis, wherein the ZNF652 gene as the marker comprises transcription of ZNF652 and / or loss of heterozygosity (LOH) of ZNF652. Further provided is use of a ZNF652 gene expression detection reagent in preparation of a kit for guiding anti-PD-L1 immunotherapy and guiding combination use of an anti-PD-L1 antibody. Further provided is use of an HDAC inhibitor romidepsin combined with an anti-PD-L1 antibody in preparation of a breast cancer treatment drug. The application provides an important theoretical basis for evaluating occurrence risk, treatment and prognosis of clinical triple-negative breast cancer.

Disclosed are systems and methods for predicting the prevalence of loss of heterozygosity (LOH) in a target cell population, the system including a memory and a processor configured to receive genetic data for a first reference cell population, the processor configured to sequence the genetic data of the first reference cell population to obtain first reference data, identify and remove heterozygous mutation locations with imbalanced allelic expression in the first reference data to generate second reference data, map an identifier for each cell of the target cell population to the second reference data, and apply the mapped identifier for each cell of the target cell population to a supervised machine learning model, the processor further configured to receive one or more outputs from the model, at least one of the one or more outputs including LOH for the target cell population.

Disclosed is a method of detecting signatures of genetic instability within a nucleic acid sample, comprising: (a) identifying a plurality of single nucleotide polymorphism (SNPs) at one or more pre-determined intervals across (i) one or more target chromosome arms and / or (ii) one or more target genes; (b) performing a plurality of multiplexed PCR reactions using a plurality of forward and reverse primer pairs that are capable of capturing the plurality of SNPs, wherein each primer comprises a target-specific sequence, a barcode sequence, and an adapter-specific sequence, thereby generating a plurality of amplicons; and (c) sequencing and analysing the plurality of amplicons. In particular, the signature of genetic instability is loss of heterozygosity (LOH). Also disclosed is a method of predicting and / or monitoring the response of a subject having a disorder associated with signatures of genetic stability towards treatment. In particular, the disorder is Homologous Recombination Deficiency (HRD).

This present disclosure relates to systems and methods for detecting HLA alterations (e.g., HLA loss of heterozygosity or HLA copy number alterations) in a sample from a subject. The disclosed methods may comprise, for example, receiving sequence read data derived from a tumor sample and a normal sample from the subject; receiving a subject-specific reference sequence for an HLA region of the subject's genome; determining, based on the sequence read data and the subject-specific reference sequence, a number of unique tumor-derived sequence reads and unique normal-derived sequence reads for each of a first allele and a second allele of an HLA gene; and detecting an HLA alteration for the HLA gene based on a tumor allelic ratio and a normal allelic ratio that are determined based on the number of unique tumor-derived sequence reads and unique normal-derived sequence reads for the first allele and second alleles of the HLA gene.

Provided herein are methods of determining loss of heterozygosity and damaging mutations in human immune-related genes in liquid biopsies and applications thereof in cancer treatment.

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