The Illumina 1 M array covers all of the SNPs on the Illumina 550 K array. We started with all SAGE subjects genotyped on the Illumina 1 M array and extracted the 545,966 SNPs that are present on the Illumina 550 K SNPs. We used these Illumina 550 K SNPs to impute to the full Illumina 1 M array. We imputed 262,864 autosomal SNPs in 2597 European Americans (EA), and 304,425 autosomal SNPs in 1264 African Americans (AA). We compared imputed SNPs to the genotyping results from the Illumina 1 M array. The remaining SNPs could not be evaluated due to the absence of those SNPs in either the Illumina 1 M array or reference panel.
