COGA samples were generated on four arrays: Illumina Human1M array (Illumina, San Diego, CA, USA) genotyped at the Center for Inherited Disease Research (CIDR), Johns Hopkins University; Illumina Human OmniExpress 12V1 array (Illumina, San Diego, CA, USA) genotyped at the Genome Technology Access Center, Washington University School of Medicine in St. Louis; Illumina 2.5M array (Illumina, San Diego, CA, USA) at CIDR; and Smokescreen genotyping array (Biorealm LLC, Walnut, CA, USA) genotyped at Rutgers University. Two to 127 samples were genotyped on at least two different arrays and pairwise concordance rates within subjects typed on more than one array exceeded 99.18% for those common SNPs, confirming limited batch or array effects. Sex and heterogeneity checks were performed and any discrepancies were removed.
