GWAS genotyping was done by each study following standard manufacturer protocols followed by imputation to ~2.5 million SNPs from HapMap37 Phase II release 22 using Genome Build 36. Quality control was performed independently for each study. To facilitate meta-analysis, each group performed genotype imputation with BIMBAM38, IMPUTE39, or MACH40 software using genotypes from the HapMapPhase II release 22 (CEU or CHB/JPT as appropriate). HapMap release 21 was used as reference for SNPs residing on the X chromosome and IMPUTE software was used for imputation. Overall imputation quality scores for each SNP were obtained from IMPUTE (proper_info) and MACH (rsq_hat) statistics. Details on the genotyping platform used, genotype quality control procedures and software for imputation employed for each study are presented in the Supplementary Tables 18D and 19D.
