Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations
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Evidence for the etiology of autism spectrum disorders (ASDs) has consistently pointed to a strong genetic component complicated by substantial locus heterogeneity. We sequenced the exomes of 20 individuals with sporadic ASD (cases) and their parents, reasoning that these families would be enriched for de novo mutations of major effect. We identified 21 de novo mutations, 11 of which were protein altering. Protein-altering mutations were significantly enriched for changes at highly conserved residues. We identified potentially causative de novo events in 4 out of 20 probands, particularly among more severely affected individuals, in FOXP1, GRIN2B, SCN1A and LAMC3. In the FOXP1 mutation carrier, we also observed a rare inherited CNTNAP2 missense variant, and we provide functional support for a multi-hit model for disease risk. Our results show that trio-based exome sequencing is a powerful approach for identifying new candidate genes for ASDs and suggest that de novo mutations may contribute substantially to the genetic etiology of ASDs.
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ASD is polygenic, with recent studies of de novo exonic mutations suggesting involvement of as many as 400 to 1,000 genetic loci.
“ASD is polygenic in aetiology; recent studies of de novo exonic mutations suggest the involvement of as many as 400 to 1,000 genetic loci in ASD9.”
From Activity-dependent neuronal signalling and autism spectrum disorder (2013) · cites this paper as [9]
De novo mutations arising in the germline are a significant cause of ASD.
“Recent evidence suggests that de novo mutations that arise in the germline are a significant cause of ASD, although it is important to keep in mind that the genetic aetiology of about 70% of the forms of ASD is unknown and it remains perplexing why ASD is at least four times more prevalent in males than in females.”
From Activity-dependent neuronal signalling and autism spectrum disorder (2013) · cites this paper as [9]
ASD is often caused by newly arising CNVs or rare germline mutations, particularly in sperm of older fathers.
“ASD is often due to newly arising gene copy number variants (CNVs) — such as a deletion or duplication of a region of a chromosome — or a rare mutation that arises in the germ cell, particularly in sperm of older fathers5–10.”
From Activity-dependent neuronal signalling and autism spectrum disorder (2013) · cites this paper as [9]
Exome sequencing of parent-offspring trios has identified de novo exonic mutations in SCN2A, KATNAL2, CHD8, FOXP1, NTNG1, GRIN2B, and LAMC3, extending the number of genes for which mutation may contribute to ASD.
“In addition, very recent exome sequencing of parent-offspring trios has identified de novo exonic mutations in SCN2A, KATNAL2, CHD8, FOXP1, NTNG1, GRIN2B, LAMC3(refs 7–9), extending further the number of genes for which mutation may contribute to ASD.”
From Activity-dependent neuronal signalling and autism spectrum disorder (2013) · cites this paper as [9]
Those studies show that new sequencing technologies can greatly advance knowledge of the genetic basis of ASD.
“These studies demonstrate the ability of new sequencing technologies to significantly advance our understanding of the genetic basis of ASD.”
From Activity-dependent neuronal signalling and autism spectrum disorder (2013) · cites this paper as [9]
References 7-10 used exome and whole-genome sequencing to show the importance of rare mutations in ASD and to identify new genetic mutations linked to ASD.
“References 7– 10 use exome and entire genome sequencing to demonstrate the importance of rare mutations in ASD and identify new genetic mutations associated with ASD.”
From Activity-dependent neuronal signalling and autism spectrum disorder (2013) · cites this paper as [9]
Two recent exome sequencing studies of individuals with ASD found synonymous SNPs in the gene encoding IL-1R2.
“Two recent exome sequencing studies of individuals with ASD found synonymous SNPs in the gene encoding the IL-1β decoy receptor IL-1R2 (IL-1 receptor type 2)55,56.”
From Immune mediators in the brain and peripheral tissues in autism spectrum disorder (2015) · cites this paper as [56]
FOXP1 has been implicated in ASD aetiology based on observations of multiple de novo SNVs.
“FOXP1, a member of the Forkhead Box P family of transcription factors has been implicated in ASD aetiology based on observations of multiple de novo SNVs [65–67].”
Many studies of complex neuropsychiatric disorders have concluded that disease-causing variants are often clustered in protein-interaction networks with a high degree of connectivity among themselves and that these clustered networks are often enriched with functional pathways relevant to brain functions.
“Many studies of complex neuropsychiatric disorders have also concluded that disease-causing variants are often clustered in protein-interaction networks with a high degree of connectivity among themselves and that these clustered networks are often enriched with functional pathways relevant to brain functions [72–80].”
From An integrated analysis of genes and functional pathways for aggression in human and rodent models (2019) · cites this paper as [74]
There is a high rate of notable de novo mutations identified in probands from simplex families.
“the high rate of notable de novo mutations identified in probands from simplex families”
From Autism risk factors: genes, environment, and gene-environment interactions (2012) · cites this paper as [16]
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- Authors
- O'Roak, B. J., Deriziotis, P., Lee, C., Vives, L., Schwartz, J. J., Girirajan, S., Karakoc, E., MacKenzie, A. P., Ng, S. B., Baker, C., Rieder, M. J., Nickerson, D. A., Bernier, R., Fisher, S. E., Shendure, J., & Eichler, E. E.
- Affiliations
- Centre for Human Genetics (GB)
- University of Washington (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Shendure, Jay
- Eichler, Evan E
- ORCID
- Venue
- Nature Genetics
- Published
- 2011-05-15
- Volume
- 43
- Issue
- 6
- Pages
- 585-589
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC3115696
- OpenAlex
- W2127634492
- Cited by
- 1,203
- References
- 53
- Citations by year
- 2026: 14 · 2025: 30 · 2024: 35 · 2023: 24 · 2022: 39 · 2021: 54 · 2020: 53 · 2019: 66 · 2018: 79 · 2017: 93 · 2016: 89 · 2015: 101 · 2014: 138 · 2013: 153 · 2012: 153
- FWCI
- 84.23
- Type
- journal article
- Language
- en
- Update notices
- erratum (2012-03-28)
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Max Planck Digital Library (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- Wellcome Trust (075491/Z/04/Z, 075491/Z/04,)
- U.S. Public Health Service (273200800010C)
- National Heart, Lung, and Blood Institute (HL-102924, RC2HL102926, UC2HL102924, HL 1029230, R01HL094976, HL094976, RC2HL102924, UC2HL102926, HL-102926)
- National Human Genome Research Institute (RC2HG005608, HG 005608)
- National Institute of Environmental Health Sciences (HHSN273200800010C)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD065285, R01HD065285)
- Topics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- autism spectrum disorder, de novo mutations, exome sequencing, FOXP1, NR2B subunit, SCN1A, LAMC3, CNTNAP2, multi-hit model, disease risk, genetic etiology, conserved residues, frameshift mutation, splice site mutation, missense mutations
- MeSH terms
- Adult, Child, Child Development Disorders, Pervasive, Exons, Female, Humans, Male, Middle Aged, Mutation, Pedigree, Sequence Analysis, DNA, Genetic Predisposition to Disease
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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