The samples were genotyped in two genotyping rounds referred to as iPSYCH1 and iPSYCH2. iPSYCH1 samples were genotyped using Illumina’s PsychArray and iPSYCH2 samples using Illumina´s GSA v.2 (Illumina). QC and GWAS were performed using the Ricopili pipeline67. More details can be found in ref. 68. GWAS were performed separately for iPSYCH1 (2,117 cases and 13,238 controls) and iPSYCH2 (1,024 cases and 5,732 controls) using dosages for imputed genotypes and additive logistic regression with the first five PCs (from the final PCAs) as covariates using PLINK v1.9 (ref. 69). Only variants with a MAF >0.01 and imputation score >0.8 were included in the final summary statistics.
