Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder. M. Uddin1, K. Tammimies1,2, G. Pellecchia1, B. Alipanahi3, P. Hu1, Z. Wang1, D. Pinto4,5,6, L. Lau1, T. Nalpathamkalam1, C. Marshall1,7, B. Blencowe8,9, B. Frey3, D. Merico1, R. Yuen1, S. Scherer1,7,9 1) Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; 2) Neuropsychiatric Unit, Department of Womens and Childrens Health, Karolinska Institutet, Stockholm, Sweden.Center of Neurodevelopmental Disorders (KIND),; 3) Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada; 4) Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA; 5) Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA; 6) Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA; 7) McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada; 8) Donnelly Centre, University of Toronto, Toronto, Ontario, Canada; 9) Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

   A universal challenge in genetic studies of autism spectrum disorders (ASD) is determining whether a given DNA sequence alteration will manifest as disease. Among different population controls, we observed, for specific exons, an inverse correlation between exon expression level in brain and burden of rare missense mutations. For genes that harbor de novo mutations predicted to be deleterious, we found that specific critical exons were significantly enriched in individuals with ASD relative to their siblings without ASD (P < 1.13 10-38; odds ratio (OR) = 2.40). Spatio-temporal analyses reveal the most significant association is observed from prenatal samples and for prefrontal cortex region. The analysis of genes impacted by de novo CNVs also showed significant enrichment of critical exons with a similar spatio-temporal pattern. Furthermore, our analysis of genes with high exonic expression only in brain and low burden of rare mutations demonstrated enrichment for known ASD-associated genes (P < 3.40 10-11; OR = 6.08) and ASD-relevant fragile-X protein targets (P < 2.91 10-157; OR = 9.52). Gene set enrichment analysis for brain-critical exon genes showed enrichment in specific biological pathways involving synapse regulation, neuron differentiation, signaling complexes and synaptic vesicles. Our results suggest that brain-expressed exons under purifying selection should be prioritized in genotype-phenotype studies for ASD and related neurodevelopmental conditions.