Genotyping was performed on a 1,536-plex GoldenGate Custom Panel (GS0007064-OPA, Illumina, San Diego, CA). 1350 SNPs were selected from 130 candidate genes (Hodgkinson et al., 2008). In addition, the array included 186 ancestry informative markers (AIMs) that were selected based on allele frequencies in the European, African and Chinese population of the HapMap project (Enoch et al., 2006, Hodgkinson et al., 2008). Genotyping was performed at the Rockefeller University Genomics Resource Center according to the manufacturer's protocol (Illumina). Analysis was performed using BeadStudio genotyping software (Illumina). Genotype data was filtered based on SNP call rates (>99.5%), MAF>0.01, cluster separation score, and deviation from Hardy-Weinberg Equilibrium (HWE). Random samples (~10%) were genotyped in duplicate and two identical samples were genotyped on each of the arrays for reproducibility control purposes.
