Genome-wide association analyses for the 11 PGC samples and the 23 waves in iPSYCH were performed using logistic regression model with the imputed marker dosages in PLINK v1.9116,117. Principal components were included as covariates to control for population stratification35,118, along with relevant study-specific covariates where applicable (Supplementary Information, Supplementary Table 1). Subsequently the results were meta-analysed using an inverse-variance weighted fixed effects model, implemented in METAL (version 2011–03–25)36. Variants were filtered and included if imputation quality (INFO score) was > 0.8 and MAF > 0.01. Only markers supported by an effective sample size Neff = 4/(1/Ncases + 1/Ncontrols)119 greater than 70% were included. After filtering, the meta-analysis included results for 8,047,421 markers.
