Imputation in African Americans has typically relied on some composition of the YRI, CEU, and CHB+JPT populations from HapMap [3], [4]. The 1000 Genomes project [18] now offers a wider range of reference populations that provide a better match of allele frequencies and linkage disequilibrium patterns for admixed populations, such as African Americans from the Southwest United States (ASW). However, there has been limited evaluation of the imputation performance of the newer reference populations in admixed study populations [8]. The present study offers a thorough evaluation of SNP genotype imputation performance in African Americans, by comparing imputation results using four different imputation software programs (IMPUTE2, BEAGLE, MaCH, and MaCH-Admix) and three reference panels consisting of different combinations of 1000 Genomes (February 2012 release) populations that are either closely or more broadly related to African Americans.
