Identification of allelic imbalance with a statistical model for subtle genomic mosaicism.

ABSTRACT: Genetic heterogeneity in a mixed sample of tumor and normal DNA can confound characterization of the tumor genome. Numerous computational methods have been proposed to detect aberrations in DNA samples from tumor and normal tissue mixtures. Most of these require tumor purities to be at least 10-15%. Here, we present a statistical model to capture information, contained in the individual's germline haplotypes, about expected patterns in the B allele frequencies from SNP microarrays while fully modeling their magnitude, the first such model for SNP microarray data. Our model consists of a pair of hidden Markov models--one for the germline and one for the tumor genome--which, conditional on the observed array data and patterns of population haplotype variation, have a dependence structure ind

SUBMITTER: Xia R 

PROVIDER: S-EPMC4148184 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature