Genome-wide characteristics of de novo mutations in autism

De novo mutations (DNMs) are important in autism spectrum disorder (ASD), but so far analyses have mainly been on the ~ 1.5% of the genome encoding genes. Here, we performed whole-genome sequencing (WGS) of 200 ASD parent-child trios and characterised germline and somatic DNMs. We confirmed that the majority of germline DNMs (75.6%) originated from the father, and these increased significantly with paternal age only (P = 4.2 × 10^-10). However, when clustered DNMs (those within 20 kb) were found in ASD, not only did they mostly originate from the mother (P = 7.7 × 10- 13), but they could also be found adjacent to de novo copy number variations where the mutation rate was significantly elevated (P = 2.4 × 10- 24). By comparing with DNMs detected in controls, we found a significant enrichment of predicted damaging DNMs in ASD cases (P = 8.0 × 10^-9; odds ratio = 1.84), of which 15.6% (P = 4.3 × 10^-3) and 22.5% (P = 7.0 × 10^-5) were non-coding or genic non-coding, respectively. The non-coding elements most enriched for DNM were untranslated regions of genes, regulatory sequences involved in exon-skipping and DNase I hypersensitive regions. Using microarrays and a novel outlier detection test, we also found aberrant methylation profiles in 2/185 (1.1%) of ASD cases. These same individuals carried independently identified DNMs in the ASD-risk and epigenetic genes DNMT3A and ADNP. Our data begins to characterize different genome-wide DNMs, and highlight the contribution of noncoding variants, to the aetiology of ASD.