GCD GWAS samples were genotyped on the Illumina HumanOmni1-Quad v1.0 microarray containing 988 306 autosomal SNPs, at the Center for Inherited Disease Research (CIDR) and the Yale Center for Genome Analysis. Genotypes were called using GenomeStudio software V2011.1 and genotyping module V1.8.4 (Illumina, San Diego, CA, USA). The SAGE samples were genotyped on the Illumina Human 1 M array containing 1 069 796 total SNPs. Follow-up genotyping in the replication sample was performed using a custom Illumina GoldenGate Genotyping Universal-32, 1536-plex microarray. Most SNPs included in the custom array were initially selected for studies of other phenotypes. A small number of additional SNPs were genotyped individually in our replication sample and in the German sample using TaqMan.18 In the primary GWAS data set, 44 644 SNPs on the microarray and 135 individuals with call rates <98% were excluded, and 62 076 additional SNPs were removed before imputation because of minor allele frequencies (MAF) <1%. After data cleaning and quality control, 5697 individuals and 889 659 SNPs remained for imputation. Further QC information and genotype imputation methods are found in Supplementary
