A Monte Carlo test of linkage disequilibrium for single nucleotide polymorphisms.

ABSTRACT:

Background

Genetic association studies, especially genome-wide studies, make use of linkage disequilibrium(LD) information between single nucleotide polymorphisms (SNPs). LD is also used for studying genome structure and has been valuable for evolutionary studies. The strength of LD is commonly measured by r2, a statistic closely related to the Pearson's χ2 statistic. However, the computation and testing of linkage disequilibrium using r2 requires known haplotype counts of the SNP pair, which can be a problem for most population-based studies where the haplotype phase is unknown. Most statistical genetic packages use likelihood-based methods to infer haplotypes. However, the variability of haplotype estimation needs to be accounted for in the test for linkage disequilibrium.

Fin

SUBMITTER: Xu H 

PROVIDER: S-EPMC3096569 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature