Next, we investigated general CNV load between cases and controls. It was recently shown that schizophrenia patients were more likely to have rare CNVs greater than 100 kb that disrupted genes (that is, began or ended within a gene) or that deleted or duplicated entire genes [21],[22], although this was not replicated in a Chinese population [41]. Following Walsh et al. [21], we selected all CNVs greater than 100 kb that had not been previously reported in the DGV and compared the frequencies of those that did and did not affect genes between cases and controls, separating cases and controls, and deletions and duplications. Since our CNVs are identified based on SNP data, we are not able to precisely determine where each event begins and ends. Therefore, we did not attempt to distinguish between “disrupted” (Walsh et al. define this as a gene that is interrupted by a CNV [21]) and “included” genes (genes completely encompassed by a CNV) - instead we counted all gene-including and apparently gene-disrupting CNVs together as “gene-affecting”.
