More of the gene sets that were nominally significantly enriched in the ALIGATOR analysis of the SNP data were also significantly enriched for case CNVs (Figure 2). Thus, of the 315 pathways with enrichment at p<0.05 from the SNP data, in the CNV data 13 were enriched at p<0.05, eight at p<0.01, and seven at p<0.001. These numbers are significantly higher than expected by chance (p=0.0080, p=0.0022, p<0.0001, respectively). The 13 pathways significantly enriched (p<0.05) in both the SNP data and the CNV data are listed in Table 3. Although there was strong evidence of SNP and CNV signal convergence at the level of pathways, this was not evident at the individual gene level. Within the 13 significantly enriched pathways, 63 genes for which there were gene-wide (Simes) p values from the GWAS were affected by at least one CNV in a case subject or a comparison subject. Among these, there was some correlation (r=0.236) between genes showing evidence for association (-log GWAS Simes p and -log CNV enrichment p) at the level of SNPs and CNVs, but this did not quite achieve statistical significance (p=0.063).
