Chunk #18 — Materials and methods — Genotyping and CNV analysis — Gene set analyses — Statistical approaches

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De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia.

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Significance was assessed by one-sided test of an excess of genes hit in the gene set by case CNVs. The inclusion of CNV size allows for case de novo CNVs being larger than typical CNVs (and thus likely to hit more genes). Inclusion of the total number of genes hit outside the gene set in the regression corrects for case CNVs hitting more genes overall (regardless of function) than control CNVs. Although explicitly adjusted for in the above analysis, to confirm that the results are not due to the fact that de novo CNVs are more likely to hit genes, we also performed an analysis restricted to CNVs that hit genes.