SNP genotyping is described in the Supplementary Methods and summarized in Supplementary Table S2. Briefly, all samples were genotyped with SNP arrays intending to provide genome-wide coverage of common variation. Imputation was performed within each study in batches of 300 individuals. Batches were randomly assigned to keep the same case–control ratios as in the primary studies. We used Beagle 3.0.4 [ref. 49] with the CEU+TSI HapMap3 data as reference (410 phased haplotypes)50 to impute 1 235 109 autosomal SNP allele dosages. We had previously evaluated this approach by masking and then imputing genotyped loci and found a high correlation between the genotyped and imputed allele dosages (Pearson r > 0.999).37
