Extensive genetic quality control and filtering was performed on the contributed summary statistics from each cohort. We removed imputed variants with imputation quality less than 0.3 (the estimated squared correlation between the imputed dosage and true dosage). We compared the per-study allele labels and allele frequencies with those of the imputation reference panels, and removed or reconciled mismatches. For quantitative traits, we plotted the variance of the score statistics against the sample size, and tested whether the trait residuals in each study were properly normalized and whether the trait analyzed between studies was measured and analyzed using the same unit.
