Accurate local-ancestry inference in exome-sequenced admixed individuals via off-target sequence reads.

ABSTRACT: Estimates of the ancestry of specific chromosomal regions in admixed individuals are useful for studies of human evolutionary history and for genetic association studies. Previously, this ancestry inference relied on high-quality genotypes from genome-wide association study (GWAS) arrays. These high-quality genotypes are not always available when samples are exome sequenced, and exome sequencing is the strategy of choice for many ongoing genetic studies. Here we show that off-target reads generated during exome-sequencing experiments can be combined with on-target reads to accurately estimate the ancestry of each chromosomal segment in an admixed individual. To reconstruct local ancestry, our method SEQMIX models aligned bases directly instead of relying on hard genotype calls. We evaluate

SUBMITTER: Hu Y 

PROVIDER: S-EPMC3824118 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature