Imputation is often used to infer genotypes at untyped markers in association studies. Widely used genotype imputation algorithms, such as IMPUTE [Howie et al., 2009], MACH [Li et al., 2010], and fastPHASE [Scheet and Stephens, 2007], match genotype data at typed SNPs in a sample of individuals to haplotypes from suitable reference panels. Huang and Tseng [2013] examined the accuracy of genotype imputation in admixed population samples using different reference panels with the IMPUTE2 software [Howie et al., 2012]. A subset of 345 individuals with both WGS and SNP genotype data on chromosome 3 was chosen for the imputation analysis. SNPs on chromosome 3 that are represented in the 1000 Genomes Project (1kGP) [The 1000 Genomes Project Consortium, 2010] but are not typed in the GAW18 SNP data were imputed. The following subsets from the 1kGP were used as reference panels: (1) all 1,094 individuals; (2) 120 randomly selected individuals; (3) 246 individuals with African ancestry; (4) 286 individuals with Asian ancestry; (5) 381 individuals with European ancestry; and (6) 181 individuals from the Americas (comprised of Colombian, Mexican, and
