Genotyping was performed with Illumina HumanOmniExpress-12v1.0 BeadChip with coverage of 733,202 separate markers. PLINK (54) was used for initial genotyping quality control (QC), including identity by descent (IBD) analysis to ensure individuals were unrelated, and heterozygosity testing and multidimensional scaling to identify population outliers compared to HapMap populations. For SNP filtering, we used sample and SNP call rates >98%. We used a MAF of 4% and a Hardy-Weinberg equilibrium threshold set at 1 × 10−6. We removed 11 individuals because of failure in one or more QC criteria, resulting in 421 individuals for further analysis with genotyping data available at 609,704 SNPs. Genotyping files were subsequently converted from PLINK output for use in MatrixEQTL.
