Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders

Nat Commun. 2020 Oct 1;11(1):4932. doi: 10.1038/s41467-020-18723-y.

Abstract

Most genes associated with neurodevelopmental disorders (NDDs) were identified with an excess of de novo mutations (DNMs) but the significance in case-control mutation burden analysis is unestablished. Here, we sequence 63 genes in 16,294 NDD cases and an additional 62 genes in 6,211 NDD cases. By combining these with published data, we assess a total of 125 genes in over 16,000 NDD cases and compare the mutation burden to nonpsychiatric controls from ExAC. We identify 48 genes (25 newly reported) showing significant burden of ultra-rare (MAF < 0.01%) gene-disruptive mutations (FDR 5%), six of which reach family-wise error rate (FWER) significance (p < 1.25E-06). Among these 125 targeted genes, we also reevaluate DNM excess in 17,426 NDD trios with 6,499 new autism trios. We identify 90 genes enriched for DNMs (FDR 5%; e.g., GABRG2 and UIMC1); of which, 61 reach FWER significance (p < 3.64E-07; e.g., CASZ1). In addition to doubling the number of patients for many NDD risk genes, we present phenotype-genotype correlations for seven risk genes (CTCF, HNRNPU, KCNQ3, ZBTB18, TCF12, SPEN, and LEO1) based on this large-scale targeted sequencing effort.

Publication types

  • Multicenter Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Basic Helix-Loop-Helix Transcription Factors / genetics
  • CCCTC-Binding Factor / genetics
  • Case-Control Studies
  • Cohort Studies
  • DNA Mutational Analysis
  • DNA-Binding Proteins / genetics
  • Female
  • Genetic Association Studies
  • Genetic Predisposition to Disease*
  • Heterogeneous-Nuclear Ribonucleoprotein U / genetics
  • High-Throughput Nucleotide Sequencing
  • Humans
  • KCNQ3 Potassium Channel / genetics
  • Male
  • Mutation
  • Neurodevelopmental Disorders / genetics*
  • RNA-Binding Proteins / genetics
  • Repressor Proteins / genetics
  • Transcription Factors / genetics

Substances

  • Basic Helix-Loop-Helix Transcription Factors
  • CCCTC-Binding Factor
  • CTCF protein, human
  • DNA-Binding Proteins
  • HNRNPU protein, human
  • Heterogeneous-Nuclear Ribonucleoprotein U
  • KCNQ3 Potassium Channel
  • KCNQ3 protein, human
  • LEO1 protein, human
  • RNA-Binding Proteins
  • Repressor Proteins
  • SPEN protein, human
  • Transcription Factors
  • ZBTB18 protein, human
  • TCF12 protein, human