SummaryWe present the largest exome sequencing study of autism spectrum disorder (ASD) to date (n=35,584 total samples, 11,986 with ASD). Using an enhanced Bayesian framework to integrate de novo and case-control rare variation, we identify 102 risk genes at a false discovery rate ≤ 0.1. Of these genes, 49 show higher frequencies of disruptive de novo variants in individuals ascertained for severe neurodevelopmental delay, while 53 show higher frequencies in individuals ascertained for ASD; comparing ASD cases with mutations in these groups reveals phenotypic differences. Expressed early in brain development, most of the risk genes have roles in regulation of gene expression or neuronal communication (i.e., mutations effect neurodevelopmental and neurophysiological changes), and 13 fall within loci recurrently hit by copy number variants. In human cortex single-cell gene expression data, expression of risk genes is enriched in both excitatory and inhibitory neuronal lineages, consistent with multiple paths to an excitatory/inhibitory imbalance underlying ASD.

Corresponding authors, satterst@broadinstitute.org (FKS) and mjdaly@atgu.mgh.harvard.edu (MJD). Main Text Introductory paragraphAutism spectrum disorder (ASD) and attention-deficit/hyperactivity disorder (ADHD) are substantially heritable 1-4 , but individuals with psychiatric diagnoses often do not have blood drawn as part of routine medical procedure, making it difficult to collect large cohorts for genetic study. To overcome this challenge, we drew upon two Danish national resources: the Danish Neonatal Screening Biobank (DNSB) and the Danish national psychiatric registry. We have previously validated the use of archived bloodspots from the DNSB for genotyping 5 and sequencing 6,7 , and we recently performed common variant analysis on dried bloodspot material in both ASD 8 and ADHD 9 . Here, we present exome sequences from over 13,000 DNSB samples, finding that ASD and ADHD show a strikingly similar burden of rare protein-truncating variants, both significantly higher than controls. Additionally, the distributions of genes hit by these variants are not distinguishable between the two disorders, suggesting that many risk genes may be shared between them. These results motivate a combined analysis across ASD and ADHD, which-in conjunction with incorporation of the gnomAD reference database as additional population controls-leads to the identification of genes conferring general risk for childhood psychiatric disorders, including the novel gene MAP1A. Sample overviewExome sequences for individuals included in the iPSYCH research initiative 10 were obtained from archived dried blood samples stored by the DNSB. Individuals in this

Background: Copy number variants (CNVs) and single nucleotide variants (SNVs) are sources of risk for autism spectrum disorder (ASD). The distribution of such pathogenic variants in individuals with ASD and the characterization of those who carry such variants versus those who do not are understudied at the population level. We describe a population sample from Sweden, evaluating the distribution of likely pathogenic variants and their impact on medical, neurological, and psychiatric phenotypes.Methods: The genotyped sample consisted of 1,236 children born in Sweden with autistic disorder, a severe form of ASD (International Classification of Diseases, Tenth Revision, code F84.0.) Of these individuals, CNVs were called from 997, while SNVs were called from 808. Results: Out of 997 individuals from whom CNVs were called, 104 (10.4 %) carried one or more likely pathogenic CNV, including 15q11q13 (n=8), 15q13.3 (n=5), 16p13.11 (n=5), 16p11.11 (n=5), 22q11.2 (n=5). Of 808 individuals assessed by whole-exome sequencing, 69 (8.5%) had a likely pathogenic SNV, including in GRIN2B (n = 6), POGZ (n = 5), SATB1 (n=4), DYNC1H1 (n=4), and CREBBP (n=3). Fourteen individuals carried two likely pathogenic CNVs, and 5 carried a likely pathogenic CNV and SNV. Carriers of likely pathogenic CNVs or SNVs were more likely to have intellectual disability (ID), scholastic skill disorders, and epilepsy, with odds ratios of 2.31 (95%CI, 1.55,3.47), 1.98 (95%CI, 1.19,3.21), and 1.63 (95%CI, 1.08,2.44) respectively. Carriers of likely pathogenic CNVs also showed significant increased rates of congenital anomalies. We compared rates of likely pathogenic CNVs, SNVs, and phenotypes from genotyped AD subjects with and without ID: rates were not significantly different between groups. Limitations: As a case-control cohort, we did not have de novo information to aid in classification. More broadly, there were judgment calls involved in identifying likely pathogenic variants. For these reasons, some misclassification is possible. In addition, phenotypes are defined from medical registers, which may lead to underestimates of milder findings.Conclusions: People with ASD who carry likely pathogenic CNVs or SNVs show increased rates of various comorbidities, most prominently ID. Despite the strong association with ID, conditioning on its presence explains little of the variation for other comorbidities and physical traits.