The consortium was formed after individual studies had finalized their GWAS platforms, which differed across studies. All studies used their genotype data to impute to the 2.5 million non-monomorphic, autosomal SNPs described in HapMap's CEU panel. Extensive quality control (QC) analyses were performed in each cohort. Because the top SNP was imputed in all of the cohorts, we directly genotyped it in studies where the quality of imputation was judged to be poor. Details on the genotyping, imputation, and QC efforts can be found in the Appendix, Section 3.
