For gene set enrichment analysis, we used 39 de novo CNVs including nine in SCZ, ten in BD, four in our controls, and an additional 16 CNVs detected in a previous study by Levy et al. (2011) in an independent set of control subjects using the same array platform. We prefer to use only de novo CNVs as a control set. Naturally occurring variants in the population do not make the ideal control set for this analysis because the gene content of these CNVs is shaped by natural selection and is not likely to be representative of random mutation.
