A cross-population extended haplotype-based homozygosity score test to detect positive selection in genome-wide scans.

ABSTRACT: In this article, we developed a cross-population comparison test statistic to detect chromosome regions in which there is no significant excess homozygosity in one population but homozygosity remains high in the other. We treated an extended stretch of homozygosity as a surrogate indicator of a recent positive selection. Conditioned on existing linkage disequilibrium, we proposed to test the haplotype version of the Hardy-Weinberg equilibrium (HWE). For each population, we assumed that a random sample of unrelated individuals were typed on a large number of single nucleotide polymorphisms (SNPs). A pooled-test statistic was constructed by comparing the measurements of homozygosity of the two samples around a core SNP. In the chromosome regions where HWE is roughly true in one population an

SUBMITTER: Zhong M 

PROVIDER: S-EPMC4470573 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature