For analysis of copy number variation, we used the three cohorts with genome-wide SNP genotype data, namely Aberdeen, Munich, and an American cohort that has not yet been studied (for copy number variation) in any previous publications. All samples that passed SNP-QC procedures (see Methods) were entered into the CNV analysis, whereupon further QC was performed to determine if accurate CNV calling could be expected (see Methods). In Aberdeen, 12 samples (10 cases and 2 controls) failed CNV QC, in Munich 39 samples (9 cases and 31 controls) and in the American 49 samples (29 cases and 14 controls) failed CNV QC. These samples were excluded from further analysis, leaving a final dataset of 422 cases and 381 controls from Munich, 441 cases and 439 controls from Aberdeen and 150 cases and 264 controls from the US (European origin), a total of 1,013 cases and 1,084 controls. We also examined both previously implicated regions, and regions newly implicated here in 60 African-American schizophrenia patients and 64 African American controls (after excluding 8 and 1 respectively for CNV QC failure).
