Losing balance: Hardy-Weinberg disequilibrium as a marker for recurrent loss-of-heterozygosity in cancer.

ABSTRACT: Identifying regions of loss-of-heterozygosity (LOH) in a tumor sample is a challenging problem. State-of-the-art computational approaches can infer LOH from single-nucleotide polymorphism (SNP) array data, but calling precise boundaries is complicated by normal-cell contamination and markers that are homozygous in the germline and therefore non-informative. More recently, the focus has shifted to pinpointing the loci recurrently affected by LOH events across multiple tumors. Recurrent LOH regions often harbor genes important for tumor suppression. Here, we propose a method that infers LOH rates across an entire sample set on an SNP-by-SNP basis. Our method achieves this by leveraging the straightforward principle that, by definition, LOH depletes heterozygotes, thereby disrupting Hardy-Wei

SUBMITTER: Wilkins K 

PROVIDER: S-EPMC3221535 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature