Sample and SNP quality control assessments were performed using PLINK, version 1.07 (23). Sample quality control assessment was performed separately for case and comparison subjects. Full details are provided in the data supplement that accompanies the online edition of this article. In brief, case and comparison subjects were excluded if there was a call rate less than 0.99, low or high heterozygosity, evidence of relatedness, duplication, or non-European ancestry. Exclusions included one member of related pairs. Also, SNPs were excluded if they had a call rate less than 0.99, had a minor allele frequency less than 0.01, deviated from Hardy-Weinberg equilibrium at p<1×10–5, or had more than 1% discordant genotypes between the Illumina 550K and the Illumina Human 1.2M BeadChip arrays. After all the quality control, 502,702 SNPs were tested for association in 727 case subjects and 5,081 comparison subjects.
