All 11 GWAS summary data files were delivered to the co-ordinating site via secure file-sharing services. Imputation quality control procedures were centrally imposed. Specifically, variants were excluded if: a) MAF < 1%, and/or b) info score < 0.4 or r2 < 0.3. Once the quality of each data file was confirmed, files were imported into METAL (March 2011 Release) (http://www.sph.umich.edu/csg/abecasis/metal/index.html), a software tool for meta-analysis of whole genome association data. Genomic control was enabled (appropriate genomic control correction applied to input files) to correct for population structure. A fixed-effects meta-analysis was then performed for each SNP by combining allelic effects weighted by the inverse of their variance. Secondary correction for population structure via genomic control of summary statistics was not performed as the genomic control parameter (λGC) for meta-analysis summary statistics was 0.992. The fixed threshold for genome-wide significance was set at p < 5 × 10−8. The meta-analysis was completed for ~11 M variants. Results were limited to the ~7 M variants which had been genotyped/imputed in at least 3,000 individuals. The meta-analysis was also repeated using GWAMA 2.125 assuming random effects and an additive model, and the same results were obtained.
