In the first experiment, we used genotype data generated by the International HapMap Consortium. We considered each of the HapMap samples in turn and masked available genotypes so as to mimic an experiment using one of several commercially available chips. For example, to evaluate the Affymetrix 500K SNP chip, we marked genotypes for all markers that are not on the chip as missing for the individual being considered. We then used haplotypes for the remaining individuals on the same HapMap analysis panel (either YRI, CEU, or JPT+CHB) to impute the missing genotypes. The results are summarized in Table III and clearly show that a large number of SNPs can be imputed very accurately using any of the commercially available panels (e.g. with r2>0.80 to experimental genotypes) and that, compared to relying on single marker tagging, imputation results in improved coverage of the genome.
