(PCs) were generated using genotyped SNPs in each cohort separately using EIGENSTRAT v6.1.495. Based on visual inspection of plots of PCs for each dataset (which were all of European descent according to self-report/clinical data), we excluded samples to obtain more clearly homogeneous datasets. Genotype imputation was performed using the pre-phasing/ imputation stepwise approach implemented in Eagle v2.3.596 and Minimac397 to the Haplotype Reference Consortium (HRC) reference panel v1.098. Data on the X chromosome were available for 50 cohorts internal to the PGC and one external cohort (HUNT), and the X chromosome was imputed to the HRC reference panel in males and females separately within each cohort. The five external cohorts were processed by the collaborating research teams using comparable procedures and imputed to the HRC or a custom reference panel as appropriate. Full details of the genotyping, quality control and imputation for each of these cohorts are available in the Supplementary Note. Identical individuals between PGC cohorts and the Estonian Biobank and UK Biobank cohorts were detected using genotype-based checksums (https://personal.broadinstitute.org/sripke/share_links/zpXkV8INxUg9bayDpLToG4g58TMtjN_PGC_SCZ_w3.0718d.76) and removed from PGC cohorts.
