We used four large publicly available data sets to which we also had access to the raw data. (1) The International Schizophrenia Consortium (ISC),2 which included 3391 cases and 3181 controls genotyped with Affymetrix 6.0 or 5.0 arrays (Affymetrix, Santa Clara, CA, USA). Note that 328 Bulgarian cases from that study are probands in our trios (although their parents were not genotyped for de novo calling in the ISC study). We excluded those subjects from the ISC data. The ISC also included 605 unrelated controls recruited by us in Bulgaria (details in ref. 2) and those publicly available data were included in the present study. (2) The Molecular Genetics of Schizophrenia (MGS) Consortium,4 which included 3192 cases and 3437 controls genotyped with Affymetrix 6.0 arrays. (3) A UK case–control study of 471 schizophrenia and 2792 controls genotyped using the Affymetrix (Affymetrix) GeneChip500K Mapping Array (see ref. 3 for details of the sample and CNV calling). (4) CNV data reported by Ikeda et al.26 comprising a Japanese sample of 519 cases and 513 controls. Including the data from the current study
