Table 4.

Role of one-gene de novo CNVs in simplex autism.

	SSC unaffected		SSC affected
effect	CNV number	CNV rate	CNV number	CNV rate	expected CNVs number	delta	p-value	AD	PC
all	53	0.028	75	0.040	52.9	22.1	0.027	1.18% (−0.03–2.34)	29.5% (−0.7–50.9)
coding	31	0.017	41	0.022	30.9	10.1	0.12	0.54% (−0.28–1.42)	24.6% (−16.4–53.7)
intercoding intronic	11	0.006	26	0.014	11.0	15.0	0.0068	0.80% (0.22–1.47)	57.8% (20.7–82.3)
peripheral	4	0.002	5	0.003	4.0	1.0	0.34	0.05% (−0.27–0.37)	20.2% (−304.9–100.0)

The increased power for CNV detection through whole-genome sequencing allowed us to examine the role small CNVs that affect a single gene. We analyzed all de novo CNVs including the ones smaller than 4KB and focused on the 1,874 unaffected and the 1,869 affected children from SSC. We quantified the role of all single-gene de novo CNVs (labeled as ‘all’) in the effect columns and separately for the non-overlapping subsets labeled as ‘coding’, ‘intercoding intronic’ and ‘peripheral’ (see Fig. 2 for definition of these terms). The format of the table and the analysis was identical to what is described in the Table 2’s legend.