DNA was extracted from blood at the General Clinical Research Center at the University of Chicago. Genotyping was performed using the Affymetrix 6.0 array at the Functional Genomics Core Facility (Vanderbilt University, Memphis, TN, USA). The arrays were passed through the Affymetrix apt-geno-qc package, and DM call rate, contrast QC metric, and genotypic gender were computed. Genotypes were called with the Birdseed [41] and CRLMM [42] algorithms. We imputed missing and non-genotyped SNPs with the IMPUTE2 software package [43], using the 1000 Genomes [44] and HapMap 3 [45] genotypes as reference panels. Imputation brought the total number of SNPs to 7,573,542 SNPs per individual. We removed SNPs that had a MAF<0.05 in our sample because they had low power to identify associations; this left each individual with 5,476,100 SNPs. The SNPs presented in the Results section were re-genotyped using an Applied Biosystems TaqMan® SNP Genotyping Assay (Table S4).
