The GWAS results from each site were uploaded to a centralized server for quality checking and processing. Results files from each cohort were free from genomic inflation in quantile–quantile plots and Manhattan plots (http://enigma.ini.usc.edu/publications/enigma-2/). Poorly imputed SNPs (with R2 < 0.5) and low minor allele count (< 10) were removed from the GWAS result files from each site. The resulting files were combined meta-analytically using a fixed-effect, inverse-variance-weighted model as implemented in the software package METAL37. The discovery cohorts were meta-analysed first, controlling for genomic inflation. The combined discovery data set (comprised of all meta-analysed SNPs with data from at least 5,000 subjects) was carried forward for the additional analyses detailed below.
