Journal Article

The contribution of de novo coding mutations to autism spectrum disorder

Ye, Kenny, Hakker, Inessa, Gonzalez, Luis E., Shendure, Jay, Murtha, Michael T., Grabowska, Ewa, Marks, Steven, Ronemus, Michael, Dalkic, Ertugrul, Stessman, Holly A., Yoon, Seungtai, Dea, Jeanselle, Lee, Yoon-ha, Paeper, Bryan, Yamrom, Boris, Rosenbaum, Julie, Ma, Beicong, Leotta, Anthony, Wei, Liping, Wigler, Michael, Schatz, Michael C., Troge, Jennifer, Levy, Dan, Sanders, Stephan J., Rodgers, Linda, Walker, Michael F., Iossifov, Ivan, Patterson, Karynne E., Witherspoon, Kali T., Sullivan, Catherine A., Kendall, Jude, Nickerson, Deborah A., Mane, Shrikant M., Dong, Shan, McCombie, W. Richard, State, Matthew W., Krumm, Niklas, Vives, Laura, Mandell, Jeffrey D., Eichler, Evan E., Willsey, A. Jeremy, Wang, Zihua, Smith, Joshua D., O’Roak, Brian J., Narzisi, Giuseppe, Waqar, Zainulabedin, Andrews, Peter

2014

Overview

Whole exome sequencing has proven to be a powerful tool for understanding the genetic architecture of human disease. Here we apply it to more than 2,500 simplex families, each having a child with an autistic spectrum disorder. By comparing affected to unaffected siblings, we show that 13% of de novo missense mutations and 43% of de novo likely gene-disrupting (LGD) mutations contribute to 12% and 9% of diagnoses, respectively. Including copy number variants, coding de novo mutations contribute to about 30% of all simplex and 45% of female diagnoses. Almost all LGD mutations occur opposite wild-type alleles. LGD targets in affected females significantly overlap the targets in males of lower intelligence quotient (IQ), but neither overlaps significantly with targets in males of higher IQ. We estimate that LGD mutation in about 400 genes can contribute to the joint class of affected females and males of lower IQ, with an overlapping and similar number of genes vulnerable to contributory missense mutation. LGD targets in the joint class overlap with published targets for intellectual disability and schizophrenia, and are enriched for chromatin modifiers, FMRP-associated genes and embryonically expressed genes. Most of the significance for the latter comes from affected females. Family-based exome sequencing in a large autism study has identified 27 high-confidence gene targets and accurately estimates the contribution of both de novo gene-disrupting and missense mutations to the incidence of simplex autism, with target genes in affected females overlapping those in males of lower but not higher IQ; targets also overlap known targets for intellectual disability and schizophrenia, and are enriched for chromatin modifiers, FMRP-associated genes and embryonically expressed genes. Autism-linked genetic factors analysed Autism spectrum disorder (ASD) is a broad group of brain development disorders, including autism, childhood disintegrative disorder and Asperger's syndrome, characterized by impaired social interaction and communication, repetitive behaviour and restricted interests. Two groups reporting in this issue of Nature have used large-scale whole-exome sequencing to examine the contribution of inherited and germline de novo mutations to ASD risk. Silvia De Rubeis et al . analysed DNA samples from 3,871 autism cases and 9,937 ancestry-matched or parental controls and identify more than 100 autosomal genes that are likely to affect risk for the disease. De novo loss-of-function mutations were detected in more than 5% of autistic subjects. Many of the associated gene products appear to function in synaptic, transcriptional, and chromatin remodelling pathways. Ivan Iossifov et al . sequenced exomes from more than 2,500 families, each with one child with ASD. They identify 27 high-confidence gene targets and estimate that 13% of de novo missense mutations and 43% of de novo 'likely gene-disrupting' (LGD) mutations contribute to 12% and 9% of diagnoses, respectively.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 45 / 45/23 / 631/114/2785 / 631/208/212/2301 / 631/208/366 / 631/378/1689/1373 / Analysis / Autism / Child / Child Development Disorders, Pervasive - genetics / Cluster Analysis / DNA sequencing / Exome - genetics / Female / Gene mutations / Genes / Genetic Predisposition to Disease - genetics / Health aspects / Humanities and Social Sciences / Humans / Intelligence Tests / Male / Mental disorders / multidisciplinary / Mutation / Mutation - genetics / Nucleotide sequencing / Open Reading Frames - genetics / Pervasive developmental disorders / Reproducibility of Results / Science / Siblings