Targeted Sequencing Identifies 90 Neurodevelopmental Disorder Risk Genes with Autism and Developmental Disability Biases

Background: De novo and rare, gene-disruptive mutations are known to contribute to the biology of neurodevelopmental disorders (NDDs), including autism spectrum disorders (ASD) and intellectual disability/developmental disability (ID/DD), but the pathogenicity of several hundred candidate genes that have emerged from whole-exome sequencing studies has yet to be established. Advances in next-generation sequencing technology have enabled systematic screening of tens of thousands of individuals to identify individually rare de novo events in the most important risk genes. Phenotypic follow-up of probands broadly drawn from NDDs has allowed us to explore specific clinical phenotypes in a genotype-first manner.

Objectives: Using a targeted sequencing approach, we aimed to screen over 10,000 NDD probands for disruptive variation in high-impact genes curated from published exome sequencing studies to identify individuals carrying novel de novo events, proving the statistical significance of specific genes. While disruptive genetic events may be individually rare, by leveraging samples and data from multiple comorbid conditions (e.g., ASD and ID/DD), we increase our sensitivity to identify the most important risk genes.

Methods:  We applied single-molecule molecular inversion probes to sequence 208 candidate genes from an international cohort of 13,475 NDD probands (n=6,410 with a primary diagnosis of ASD and n=7,065 with ID/DD) and 2,867 unaffected sibling controls. Samples were collected as part of an international consortium termed the ASID (Autism Spectrum/Intellectual Disability) network that involved 15 centers across seven countries and four continents where patients were largely consented for clinical follow-up.

Results:

We report 90 genes that show an excess of de novo mutations or an overall burden of private, disruptive mutations in 5.4% of patients screened in the study compared to unaffected controls. We identify 44 novel NDD genes that reach locus-specific significance (e.g., NAA15, KMT5B, ASH1L, KATNAL2 and NCKAP1) and confirm the importance of previously reported high-impact genes (e.g., SCN2A, ARID1B, ADNP, CHD8 and POGZ). Neuronal-based assays for a subset of genes in Drosophila as a model system add further evidence to bolster their involvement in NDDs, including genes at the cusp of statistical significance. While many genes are clearly risk factors for NDD broadly, secondary analyses of both the genetic burden and subsequent patient follow-up for 25 genes in 303 patients highlights genes with a statistical bias toward ASD versus ID/DD diagnosis. We find that patients with mutations in genes enriched for ASD show significantly lower rates of seizures (p = 1.20x10^-4), congenital abnormalities (p = 1.88x10^-2), and microcephaly (p = 1.79x10^-7) but higher rates of macrocephaly (p = 5.25x10^-3) compared to comorbid ASD and ID/DD genes and strong ID/DD genes. Clinical follow-up for specific genes—NAA15, KMT5B and ASH1L—reveals novel syndromic and non-syndromic forms of disease with variable penetrance.

Conclusions: In total, 43% (90/208) of our candidate genes reach locus-specific significance for disruptive mutations, closely matching empirical expectations based on the mutational differential between probands and unaffected siblings. We observe evidence of phenotypic bias (ASD versus ID/DD) for severe mutations in 25 genes, specifically highlighting a gene network associated with high-functioning autism (FSIQ > 100).