As the bench mark, imputation with SNPs available on the 1M array resulted in the highest quality (average R2 = 0.91 in European Americans and average R2 = 0.89 in African Americans). As the number of different arrays increased and the number of genotyped SNPs in the intersecting set decreased, the resulting quality of imputed SNPs also decreased. However, decreases in quality were not as rapid as might be expected. In European Americans (Fig. 3a), imputation quality remained reasonable for input genotyped SNP sets derived from the intersection of up to four Illumina arrays even though only 30 % of the original 1M SNPs were used in the imputation: average R2 = 0.79 across the MAF spectrum and several higher MAF bins having average R2 ≥ 0.9. Imputation quality was further reduced with the inclusion of an older Illumina array (HumanHap300-Duo version 2): average R2 < 0.9 for each MAF bin and average R2 = 0.71 across the MAF spectrum. Imputation quality resulting from the intersection of the Illumina 1M and Affymetrix 6.0 arrays was comparable to the imputation quality
