We found that the associated SNPs rs950169 and rs2135551 showed a highly significant correlation with the use of an alternative splice acceptor site, resulting in a truncated PLAC (protease and lacunin) domain in the ADAMTSL3 protein (p<0.0001, Figure S2 ).
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).
The most strongly associated SNP in NOTCH4 (rs3134942, a synonymous coding SNP in very high LD with rs8192585, a nonsynonymous coding SNP) was actually the top hit in the Aberdeen cohort (p = 0.000016), but has not itself been implicated in other schizophrenia studies, and was not even marginally significant in the Munich dataset (p = 0.93).