Samples were genotyped using the Illumina HumanHap550 quad genome-wide SNP genotyping platform as previously described [35]. Individuals were excluded from analyses on the basis of excessive or minimal heterozygosity, gender mismatch, individual missingness (3%), cryptic relatedness as measured by identity by descent (genome-wide IBD 10%) and sample duplication. Individuals were assessed for population stratification using multi-dimensional scaling modeling seeded with HapMap Phase II release 22 reference populations, and those of non-European ancestry were excluded from further analysis [35]. SNPs with a final call rate of <95%, minor allele frequency <1% and evidence of departure from Hardy–Weinberg equilibrium (p<5 × 10−7) were also excluded from analyses. Individuals were imputed to 1000 Genomes Phase 1 Version 3, using MACH for phasing and Minimac for imputation. Imputed polymorphisms with an r-square imputation quality metric of <.5 were excluded from further analyses. The genome-wide association analysis was conducted using MACH2QTL [36], including sex as a covariate. After quality controls were applied, genetic data were available for 4304 of the individuals with phenotypic data (42.9% male).
