As an example of Scenario A, we used the 120 HapMap CEU parental haplotypes as a reference panel to impute genotypes in the WTCCC 1958 Birth Cohort (58 C) controls [1]. The 58 C samples were genotyped on the Affymetrix 500 K SNP chip, and the data were subjected to the SNP and sample filters specified in the WTCCC study [1]. Of the 1,502 58 C individuals, 1,407 were also genotyped on the Illumina 550 K chip, and 1,377 passed filtering in both datasets. We supplied only the latter set of individuals to the imputation methods, and we asked them to impute the 22,270 CEU HapMap SNPs on chromosome 10 that were represented on the Illumina chip but not the Affymetrix chip. We then used the imputed Illumina genotypes to evaluate the success of imputation based on the Affymetrix data.
