Genotyping of GWAS samples was performed at the Center for Inherited Disease Research using 1 μg of genomic DNA on Affymetrix Genome-wide Human SNP array 6.0. DNA from cohorts 1 and 2 were equally interleaved on 96-well master plates for genotyping. Genotypes were called using Birdseed version 2, APT 1.10.0 and samples were grouped by DNA plate to determine the genotype cluster boundaries. Among 868,157 autosomal single-nucleotide polymorphisms (SNPs) genotyped, 746,626 SNPs passed quality controls with call rate ≥95%, Hardy–Weinberg Equilibrium P value ≥ 0.0001 and minor allele frequency ≥0.05 were included in subsequent data analysis. The average sample call rate was 99.16% for all autosomal SNPs. The genotype concordance rates of 46 blind duplicates and 90 HapMap control samples were 99.59 and 99.76%, respectively. One individual was discordant for gender call from X chromosome genotype data when compared to the patient record and was excluded from the analysis. Cryptic relatedness was estimated by pairwise identity-by-descent (IBD) analysis implemented in PLINK (http://pngu.mgh.harvard.edu/purcell/plink/). Two pairs of duplicate samples and 104 cryptic first degree relative samples were identified and only one unrelated
