Imputation of missing genotypes within LD-blocks relying on the basic coalescent and beyond: consideration of population growth and structure.

ABSTRACT:

Background

Genotypes not directly measured in genetic studies are often imputed to improve statistical power and to increase mapping resolution. The accuracy of standard imputation techniques strongly depends on the similarity of linkage disequilibrium (LD) patterns in the study and reference populations. Here we develop a novel approach for genotype imputation in low-recombination regions that relies on the coalescent and permits to explicitly account for population demographic factors. To test the new method, study and reference haplotypes were simulated and gene trees were inferred under the basic coalescent and also considering population growth and structure. The reference haplotypes that first coalesced with study haplotypes were used as templates for genotype imputation. Com

SUBMITTER: Kabisch M 

PROVIDER: S-EPMC5646149 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature