Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads.

ABSTRACT:

Background

Recent technology advances have enabled sequencing of individual genomes, promising to revolutionize biomedical research. However, deep sequencing remains more expensive than microarrays for performing whole-genome SNP genotyping.

Results

In this paper we introduce a new multi-locus statistical model and computationally efficient genotype calling algorithms that integrate shotgun sequencing data with linkage disequilibrium (LD) information extracted from reference population panels such as Hapmap or the 1000 genomes project. Experiments on publicly available 454, Illumina, and ABI SOLiD sequencing datasets suggest that integration of LD information results in genotype calling accuracy comparable to that of microarray platforms from sequencing data of low-coverage.

SUBMITTER: Duitama J 

PROVIDER: S-EPMC3044311 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature