# US 12,595,513 B2 · Methods and materials for assessing loss of heterozygosity > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 12,595,513 B2 - Document ID: US12595513B2 - Status: Granted - Kind: B2 - Application number: 16/799,797 - Filed: 2020-02-24 - Published: 2020-06-18 - Granted: 2026-04-07 - Earliest claimed: 2011-12-21 - Assignees: Myriad Genetics, Inc.; Board of Regents, The University of Texas System - Applicants: Myriad Genetics, Inc. - Inventors: Victor Abkevich; Alexander Gutin; Kirsten Timms; Jerry Lanchbury - Web page: https://patentgrep.com/patent/US12595513B2 ## CPC - C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575) - A61K 31/282: Platinum compounds - A61K 33/243: Platinum; Compounds thereof - A61P 35/00: Antineoplastic agents - A61P 43/00: Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00 - G16B 20/10: Ploidy or copy number detection - G16B 20/20: Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection - C12Q 2600/106: Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism - C12Q 2600/154: Methylation markers - C12Q 2600/156: Polymorphic or mutational markers - C12Q 2600/158: Expression markers - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES - A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D) - A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS - G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY ## 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. ## Claims ### Claim 1 A method, comprising: assaying a sample of DNA extracted from a cancer cell to genotype a plurality of single nucleotide polymorphism (SNP) loci in at least one pair of human chromosomes other than a human X/Y chromosome pair of the cancer cell by: (i) enriching the sample for test DNA molecules each comprising at least one locus from the plurality of SNP loci using capture probes, thereby obtaining an enriched sample; and (ii) sequencing the test DNA molecules to detect either a homozygous genotype or heterozygous genotype at SNP loci spaced about 25 kb to about 100 kb apart on one or more chromosome pairs other than a human X/Y sex chromosome pair; and wherein the test DNA molecules comprise a loss of heterozygosity (LOH) Region, wherein each LOH Region is characterized by loss of heterozygosity with a length of about 1.5 or more megabases but shorter than the length of the whole chromosome containing the LOH Region. ### Claim 2 (depends on 1) The method of claim 1, wherein the plurality of SNP loci are present on at least 10 pairs of human chromosomes. ### Claim 3 (depends on 1) The method of claim 1, wherein the plurality of SNP loci are present on at least 21 pairs of human chromosomes. ### Claim 4 (depends on 1) The method of claim 1, wherein each LOH Region is equal to or longer than 5 megabases. ### Claim 5 (depends on 1) The method of claim 1, wherein each LOH Region is equal to or longer than 15 megabases. ### Claim 6 A method, comprising: assaying a cancer cell sample obtained from a breast or ovarian cancer patient to detect DNA comprising a loss of heterozygosity (LOH) Region in at least one pair of human chromosomes other than the human X/Y sex chromosome pair, wherein assaying comprises genotyping a plurality of single nucleotide polymorphism (SNP) loci by (i) enriching the sample for test DNA molecules each comprising at least one locus from the plurality of SNP loci using capture probes, thereby obtaining an enriched sample, and (ii) sequencing the test DNA molecules to determine whether SNP loci spaced about 25 kb to about 100 kb apart on one or more chromosome pairs other than a human X/Y sex chromosome pair are homozygous or heterozygous, and wherein the test DNA molecules comprise a LOH Region, wherein the LOH Region is defined as a genomic region wherein all SNP loci genotyped are homozygous, 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. ### Claim 7 (depends on 6) The method of claim 6, wherein the plurality of SNP loci are present on at least 10 pairs of human chromosomes. ### Claim 8 (depends on 6) The method of claim 6, wherein the length of the first length is at least 5 megabases. ### Claim 9 (depends on 6) The method of claim 6, wherein the length of the first length is at least 15 megabases. ### Claim 10 (depends on 1) The method of claim 1, wherein the plurality of SNP loci comprises at least 1,000 SNP loci. ### Claim 11 (depends on 1) The method of claim 1, wherein the plurality of SNP loci comprises at least 10,000 SNP loci. ### Claim 12 (depends on 1) The method of claim 1, wherein the plurality of SNP loci comprises at least 25,000 SNP loci. ### Claim 13 (depends on 1) The method of claim 1, wherein the plurality of SNP loci comprises at least 50,000 SNP loci. ### Claim 14 (depends on 1) The method of claim 1, wherein the cancer cell is a breast cancer cell or an ovarian cancer cell. ### Claim 15 (depends on 6) The method of claim 6, wherein the plurality of SNP loci comprises at least 1,000 SNP loci. ### Claim 16 (depends on 6) The method of claim 6, wherein the plurality of SNP loci comprises at least 10,000 SNP loci. ### Claim 17 (depends on 6) The method of claim 6, wherein the plurality of SNP loci comprises at least 25,000 SNP loci. ### Claim 18 (depends on 6) The method of claim 6, wherein the plurality of SNP loci comprises at least 50,000 SNP loci. ### Claim 19 (depends on 1) The method of claim 1, wherein the plurality of SNP loci are present on at least 5 pairs of human chromosomes. ### Claim 20 (depends on 6) The method of claim 6, wherein the plurality of SNP loci are present on at least 5 pairs of human chromosomes.