Groups used dosage based imputed SNP sets using CEU reference panels hg19/build 37 from 1000 genomes phase1 or phase3. Imputation followed ENIGMA imputation protocols (Thompson et al., 2014; http://enigma.usc.edu/wp-content/uploads/2012/07/ENIGMA2_1KGP_cookbook_v3.pdf). Association analyses accounted for family relatedness using various validated modeling techniques (Merlin, GEE, RFGLS). Sex, Age and age2 and/or age‐group/wave were used as covariates plus ancestry Principal Components plus disease status (when applicable). See supplementary materials for more group specific methods and/or deviance from these standard analyses protocols, and covariate analysis results.
