For SAGE, DNAs were genotyped on the Illumina Human 1 M beadchip (Illumina) by the Center for Inherited Diseases Research (CIDR) at the Johns Hopkins University; data are available at dbGaP phs000092. A total of 948 658 SNPs passed data-cleaning procedures and further within sample filtering for autosomal and X-chromosome markers yielded 948 142 markers. HapMap genotyping controls, duplicates, related subjects and outliers were removed from the sample set.17 The software package EIGENSTRAT25 was used to calculate principal components reflecting ancestral differences. Only genotyped SNPs were selected from SAGE, resulting in 669 984 overlapping SNPs which were further pruned for linkage disequilibrium (maximum pairwise r2=0.25 within sliding windows of 100 SNPs), resulting in 90 365 SNPs that were used for all subsequent analyses.
