Brain-expressed genes showed significant excess in affected versus control subjects for deletions only (OR = 1.89, 95% CI = 1.51–2.37, Fisher’s exact test p = 2.6 × 10−8; Figures 3A and 3B). Similarly, deletions (and not duplications) overlapping genes implicated in dominant neurological diseases and orthologous genes associated with abnormal phenotypes in heterozygous knockout mice conferred significant increase in ASD risk (OR = 2.94, 95% CI = 1.76–4.93, p = 2.5 × 10−5). Many of the genes implicated in dominant diseases have been related to loss of function or haploinsufficiency, previously suggested to be more frequent and penetrant when deletions rather than duplications are involved.46 Accordingly, we detected an excess of affected subjects carrying deletions overlapping genes with a high pHI (>0.35) (OR = 1.41, 95% CI = 1.13–1.76, p = 0.002).