The SNPs chosen for inclusion were based on two large sets of previous genotyping results in our laboratory (Tian, et al., 2007; Tian, et al., 2006) were limited to those SNPs that overlapped with the 300K genome-wide Illumina SNP array. 250 SNPs were chosen selecting the best SNP in each 10 cM deCODE bin that met the criteria of a large allele frequency differences (>45%) between EURA and AMI groups and small allele frequency differences (<5%) between two disparate AMI groups (Pima and Mayan). Similarly, 250 SNPs with large frequency differences (>45%) between African and European groups were selected. From these 500 SNPs we reduced the number for testing to 184 based on the following criteria: 1) in silico design criteria for TaqMan assays; 2) genome-wide distribution pattern (minimum inter-marker distance = 8 cM on deCODE map); and 3) EAS differences based on HapMap results in JPT and CHB. TaqMan® SNP genotyping assays were designed for the 184 SNPs and tested using DNA panels. Of these, 128 SNPs passed our quality filters demonstrating reproducible genotyping results in population samples of
