It was also previously reported that there were no differences between cases and controls for rare CNVs greater than 100 kb that did not disrupt genes [21], however the International SNP Consortium found an excess of rare CNVs greater than 100 kb that do not disrupt genes in schizophrenia cases [22]. It should be noted that this dataset also included the Aberdeen samples. Our findings here, however, were similar to those of the gene-affecting CNVs: Aberdeen had significantly more rare deletions greater than 100 kb that did not affect a gene (two-tailed Fisher's p = 0.031), and no other comparisons were significantly different (Aberdeen duplications, Munich and US duplications and deletions). Overall, therefore, we cannot offer further support to the hypothesis that rare CNVs greater than 100 kb are present in excess in schizophrenia patients, although, as shown above, we report a trend for increased deletions greater than 1 Mb, and a significant excess of greater then 2 Mb deletions in cases.
