HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations.

ABSTRACT:

Motivation

Identifying somatic changes from tumor and matched normal sequences has become a standard approach in cancer research. More specifically, this requires accurate detection of somatic point mutations with low allele frequencies in impure and heterogeneous cancer samples. Although haplotype phasing information derived by using heterozygous germ line variants near candidate mutations would improve accuracy, no somatic mutation caller that uses such information is currently available.

Results

We propose a Bayesian hierarchical method, termed HapMuC, in which power is increased by using available information on heterozygous germ line variants located near candidate mutations. We first constructed two generative models (the mutation model and the error model). In the gen

SUBMITTER: Usuyama N 

PROVIDER: S-EPMC4816033 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature