Methods and materials for assessing loss of heterozygosity
AssigneesMyriad Genetics, Inc., Board of Regents, The University of Texas System
InventorsVictor Abkevich, Alexander Gutin, Kirsten Timms, Jerry Lanchbury
Life of this patent
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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.
Claims9
A method for detecting DNA from a cancer cell, comprising:
- (A) extracting DNA from a sample comprising a cancer cell,
- (B) genotyping a plurality of single nucleotide polymorphism (SNP) loci in at least five pairs of human chromosomes other than a human X/Y sex chromosome pair in DNA from the sample, wherein the SNP loci are spaced about 25 kb to about 100 kb apart on one or more of the at least five pairs of human chromosomes, wherein genotyping comprises
- (i) enriching the sample for DNA molecules each comprising at least one locus from the plurality of SNP loci, and wherein the enriching is achieved using at least 500 oligonucleotide capture probes, and
- (ii) detecting either a homozygous genotype or heterozygous genotype at each locus from the plurality of SNP loci, wherein the plurality of SNP loci comprises at least 1,000 SNP loci,
- wherein the homozygous genotype indicates the presence of a loss of heterozygosity (LOH) Region, wherein the LOH Region is defined as a genomic region wherein all SNP loci in the genotyped region are homozygous, and wherein such genomic region is equal to or longer than a first length but shorter than the length of the whole chromosome containing the genomic region, and wherein the first length is at least 1.5 megabases;
- thereby detecting DNA from the sample comprising the presence of a LOH region.
Dependencies are inferred from the claim text.