Each study performed its own genotyping using Illumina (San Diego, CA, USA) or Affymetrix GWAS arrays (Santa Clara, CA, USA). Supplementary Tables 1 and 2 present the details of the arrays, genotyping quality control procedures and sample exclusions (i.e., sex mismatch, call rate failure, relatedness, missing smoking and ancestry outliers) for each study. The quality control filters applied by each study were comparable; single-nucleotide polymorphisms (SNPs) with call rates <95% (except the Genetic Study of Atherosclerosis Risk, <90%), <1% minor allele frequency or significant (P<10−6) departure from Hardy–Weinberg equilibrium were excluded, as were individuals with excess autosomal heterozygosity, mismatch between reported and genetically determined sex, or first- or second-degree relatedness. Genome-wide imputation24 was carried out in each study using the software MACH, IMPUTE, BEAGLE or BIMBAM v0.99,25, 26, 27, 28, 29, 30, 31, 32 to infer genotypes for SNPs that were not genotyped directly on the platforms, but were genotyped on the HapMap phase 2 CEU and YRI samples.33 SNPs with imputation quality scores <0.5 were excluded.
