Genotype imputation for African Americans using data from HapMap phase II versus 1000 genomes projects.

ABSTRACT: Genotype imputation provides imputation of untyped single nucleotide polymorphisms (SNPs) that are present on a reference panel such as those from the HapMap Project. It is popular for increasing statistical power and comparing results across studies using different platforms. Imputation for African American populations is challenging because their linkage disequilibrium blocks are shorter and also because no ideal reference panel is available due to admixture. In this paper, we evaluated three imputation strategies for African Americans. The intersection strategy used a combined panel consisting of SNPs polymorphic in both CEU and YRI. The union strategy used a panel consisting of SNPs polymorphic in either CEU or YRI. The merge strategy merged results from two separate imputations, one u

SUBMITTER: Sung YJ 

PROVIDER: S-EPMC3703942 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature