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 imputation, average r2 increased from 0.22 to 0.66 in the set of SNPs whose best genotyped proxy had r2<0.30 and from 0.33 to 0.75 in the set of SNPs whose best genotyped proxy had r2<0.5 [for specific examples of disease susceptibility loci that would be missed without imputation, see Li et al., 2009b].
