Methods and materials for assessing loss of heterozygosity

• US 10,612,098 B2
• Filed: 06/24/2016
• Issued: 04/07/2020
• Est. Priority Date: 12/21/2011
• Status: Active Grant

• Current Assignee: Myriad Genetics, Board of Regents of the University of Texas System (University of Texas System)
• Original Assignee: Myriad Genetics
• Inventors: Abkevich, Victor, Gutin, Alexander, Timms, Kirsten, Lanchbury, Jerry
• Primary Examiner(s): Johannsen, Diana B
• Application Number:
  US15/192,497
• Publication Number:
  US 20170022569A1
• Time in Patent Office: 1,383 Days
• CPC Class Codes: A61K 31/282 Platinum compounds
• CPC Class Codes: A61K 33/243 Platinum; Compounds thereof
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/154 Methylation markers
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: G16B 20/10 Ploidy or copy number detection
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

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

1. A system for detecting a homologous recombination deficiency in a cancer cell obtained from a patient, comprising:

(a) a sample analyzer configured to assay a sample of DNA extracted from or derived from the cancer cell to genotype a plurality of single nucleotide polymorphism loci in at least five pairs of human chromosomes of the cancer cell by

(i) enriching the sample for test DNA molecules each comprising at least one locus from the plurality of single nucleotide polymorphism loci, wherein the plurality of single nucleotide polymorphism loci comprises at least 1,000 single nucleotide polymorphism loci and wherein there is at least one single nucleotide polymorphism locus located on average every 500 kb within each chromosome of the at least five pairs of human chromosomes; and

(ii) assaying the test DNA molecules to detect either a homozygous or heterozygous genotype at each locus in the plurality of single nucleotide polymorphism loci;

(b) a computer sub-system programmed to

(i) calculate, based on the genotypes detected in (a)(ii), a test value equal to or derived from the number of Indicator LOH Regions in the at least five pairs of human chromosomes, wherein an Indicator LOH Region is equal to or longer than a first length but shorter than the length of the whole chromosome containing the Indicator LOH Region, and wherein the first length is at least 1.5 megabases;

(ii) determine whether the test value calculated in (b)(i) exceeds a reference value equal to or derived from a reference number of Indicator LOH Regions in at least five pairs of human chromosomes in cancer cell samples of a population of reference patients; and

either

(iii)(A) detect a homologous recombination deficiency in the cancer cell if the test value exceeds the reference value;

or

(iii)(B) detect no homologous recombination deficiency in the cancer cell if the test value does not exceed the reference value.

2. The system of claim 1, wherein the computer sub-system in (b) is programmed to

(i) receive data from the analysis performed by the sample analyzer in (a) indicating either a homozygous or heterozygous genotype detected at each locus in the plurality of single nucleotide polymorphism loci in (a)(ii);

(ii) calculate, based on the data received in (b)(i), a test value equal to or derived from the number of Indicator LOH Regions in the at least five pairs of human chromosomes, wherein an Indicator LOH Region is equal to or longer than a first length but shorter than the length of the whole chromosome containing the Indicator LOH Region, and wherein the first length is at least 1.5 megabases;

(iii) determine whether the test value calculated in (b)(ii) exceeds a reference value equal to or derived from a reference number of Indicator LOH Regions in at least five pairs of human chromosomes in cancer cell samples of a population of reference patients; and

either

(iv)(A) detect a homologous recombination deficiency in the cancer cell if the test value exceeds the reference value;

or

(iv)(B) detect no homologous recombination deficiency in the cancer cell if the test value does not exceed the reference value.

3. The system of claim 1, wherein the sample analyzer in (a) is configured to assay a sample of DNA extracted from or derived from the cancer cell to genotype a plurality of single nucleotide polymorphism loci in at least 10 pairs of human chromosomes and the computer sub-system is programmed in (b)(ii) to determine whether the test value calculated in (b)(i) exceeds a reference value equal to or derived from a reference number of Indicator LOH Regions in at least 10 pairs of human chromosomes in cancer cell samples of a population of reference patients.

4. The system of claim 1, wherein the sample analyzer in (a) is configured to assay a sample of DNA extracted from or derived from the cancer cell to genotype a plurality of single nucleotide polymorphism loci in at least 15 pairs of human chromosomes and the computer sub-system is programmed in (b)(ii) to determine whether the test value calculated in (b)(i) exceeds a reference value equal to or derived from a reference number of Indicator LOH Regions in at least 15 pairs of human chromosomes in cancer cell samples of a population of reference patients.

5. The system of claim 1, wherein the sample analyzer in (a) is configured to assay a sample of DNA extracted from or derived from the cancer cell to genotype a plurality of single nucleotide polymorphism loci in at least 21 pairs of human chromosomes and the computer sub-system is programmed in (b)(ii) to determine whether the test value calculated in (b)(i) exceeds a reference value equal to or derived from a reference number of Indicator LOH Regions in at least 21 pairs of human chromosomes in cancer cell samples of a population of reference patients.

6. The system of claim 1, wherein the first length is at least 10 megabases.

7. The system of claim 1, wherein the first length is at least 12 megabases.

8. The system of claim 1, wherein the first length is at least 15 megabases.

9. The system of claim 1, wherein the reference number of Indicator LOH Regions is at least five.

10. The system of claim 1, wherein the reference number of Indicator LOH Regions is at least 10.

11. The system of claim 1, wherein the reference number of Indicator LOH Regions is at least 12.

12. The system of claim 1, wherein the reference number of Indicator LOH Regions is at least 15.

13. The system of claim 1, wherein the plurality of single nucleotide polymorphism loci comprises at least 10,000 single nucleotide polymorphism loci.

14. The system of claim 1, wherein the plurality of single nucleotide polymorphism loci comprises at least 25,000 single nucleotide polymorphism loci.

15. The system of claim 1, wherein the plurality of single nucleotide polymorphism loci comprises at least 50,000 single nucleotide polymorphism loci.