Here, we evaluate whether pre-phased haplotypes can be used to accurately impute missing genotypes in three GWAS datasets sampled from diverse populations: the WTCCC2 data described above, a European-American case-control dataset from a psoriasis study by the Genetic Association Information Network (GAIN)18, and a set of African Americans from the Women’s Health Initiative (WHI)19. In each dataset we masked and imputed a subset of the genotyped SNPs, as detailed in Table 2. We measured imputation accuracy at these SNPs as the average squared correlation (mean R2) between masked array genotypes and imputed allele dosages (posterior mean genotypes).
