First looking at the Aberdeen cohort, which has been included in a previous study replicating the Walsh et al. effect [22] we found that 91 of the 441 Aberdeen cases that passed QC (21%) contained one or more rare deletions >100 kb that affected a gene, compared to 66/439 controls (15%), and that 61/441 (14%) cases contained rare, greater than 100 kb, gene-affecting duplications, compared to 49/439 (11%) of controls. Fisher's exact test indicated that this was a significant excess of deletions in cases (p = 0.03), but only a trend for duplications (p = 0.26). In contrast, neither the Munich nor the US cohort (which have not been assessed in previous publications) showed an excess of deletions in cases (Table 5), although the Munich cohort had significantly more duplications in cases (p = 0.03) and US cohort showed a trend in the same direction for deletions (p = 0.08).
