QIMR was analyzed using GEMMA89 v0.96, including the first five PCs as covariates. RCOG was analyzed using the generalized disequilibrium test90. UKBB was analyzed using BOLT-LMM91 including 6 PCs, and batch and center indicator variables as covariates. VETS was analyzed using BOLT-LMM including 5 PCs as covariates. EHR-based studies that included related individuals were analyzed using saddle point approximation methods to account for case/control imbalances. AGDS and QIM2 were analyzed using SAIGE92 including 4 PCs and study-specific covariates. BIOV was analyzed using SAIGE including 10 PCs and age of record. ESBB, FING, HUNT, and SWED were analyzed using SAIGE including 5 PCs. UKB2 was analyzed using REGENIE93 including 6 PCs, assessment center, and genotyping batch covariates. GWAS was additionally performed stratified by sex. For the X chromosome analysis, sex was added as a covariate.
