The results summarized so far compare a variety of imputed genotypes with experimentally derived counterparts. However, a more interesting comparison focuses on imputed genotypes that appear to show strong evidence for association, as those might motivate further downstream experiments. To evaluate the accuracy of imputed genotypes for these “strongly associated SNPs,” we compared imputed and experimental genotypes in regions that were only selected for follow-up genotyping after imputation (for example, because imputed genotypes resulted in strong evidence for association but nearby genotyped markers did not). Table II summarizes the comparison of allele frequencies, association test statistics, and individual genotype calls between imputed genotypes and actual genotypes later determined by genotyping. Overall, it is clear that even among these strongly associated SNPs imputation provided accurate estimates of the true P-values. The largest observed discrepancies were for rs17384005, rs11646114, and rs4812831, which were also the three markers for which our imputation approach estimated lower r2 with actual genotypes. Imputation is particularly useful because it allows evidence for association at SNPs with no reliable proxies to be evaluated more accurately. For instance, after
