Methods and materials for assessing loss of heterozygosity

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.