Schizophrenia data used in this study is summarized in Supplementary Table 16. PGC wave 2 schizophrenia GWAS summary statistics34 were used as the European discovery dataset. Except for one cohort (TMIM1), EAS samples used as discovery and target datasets were described in Lam et al.15 TMIM1 was recruited from multiple university hospitals and local hospitals in Japan. Patients were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM-IV) with consensus from at least two experienced psychiatrists. All patients agreed to participate in the study and provided written informed consent. The study was approved by the Institutional Review Boards of the Tokyo Metropolitan Institute of Medical Science and all affiliated institutions. DNA samples were genotyped on the Illumina Infinium Global Screening Array-24 v1.0 (GSA) BeadChip at the Broad Institute, using standard reagents and HTS workflow procedures. GWAS QC and imputation were performed using Ricopili50 with default parameters. When used as a target cohort, SNPs were further filtered by imputation INFO score <0.9 and MAF <0.01.
