Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders
Open accessAbstract
Autism Genes, Again and Again: Despite recent advances in sequencing technologies and their lowered costs—effective, highly sensitive, and specific sequencing of multiple genes of interest from large cohorts remains expensive. O'Roak et al. (p. 1619 ; published online 15 November) modified molecular inversion probe methods for target-specific capture and sequencing to resequence candidate genes in thousands of patients. The technique was applied to 44 candidate genes to identify de novo mutations in a large cohort of individuals with and without autism spectrum disorder. The analysis revealed several de novo mutations in genes that together contribute to 1% of sporadic autism spectrum disorders, supporting the notion that multiple genes underlie autism-spectrum disorders.
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Targeted sequencing of genes in that subnetwork in a larger cohort found more risk variants than expected by chance, showing PPI connectivity can predict ASD risk mutations.
“Genes in this subnetwork were evaluated in a larger cohort in a targeted sequencing study120, which identified more risk variants compared with chance and demonstrated that PPI connectivity can be a predictor of ASD risk mutations.”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [120]
CHD8 is the gene most frequently affected by ASD-associated rare de novo variation.
“chromodomain helicase DNA-binding protein 8 (CHD8)118, which is the gene most frequently affected by ASD-associated rare de novo variation72,119–121.”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [120]
DYRK1A has three truncating mutations in autism probands and de novo structural variants in ID probands.
“Another striking candidate is DYRK1A (dual-specificity tyrosine phosphorylation-regulated kinase 1A), for which three truncating mutations have been discovered in autism probands [24,44] and de novo structural variants in ID probands [54,55].”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [44]
MIP resequencing of 44 candidate genes in 2446 ASD probands yielded 27 new de novo mutations across 16 genes, of which 17 were disruptive SNVs, a fraction higher than expected by chance.
“Altogether, this assay yielded 27 new de novo mutations across 16 genes; of these mutations, 17 were disruptive SNVs, a fraction higher than expected by chance.”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [44]
CHD8 has the strongest overall association, with eight de novo truncating mutations observed across 2597 cases and none in control siblings or over 6500 ESP exomes.
“Overall, eight de novo truncating mutations were observed across 2597 cases in this gene; by contrast, no such mutations were observed in control siblings, or in over 6500 exomes in the ESP.”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [44]
MIP resequencing confirmed ASD association for CHD8 and DYRK1A and provided statistical support for GRIN2B, TBR1, PTEN, and TBL1XR1.
“The discovery of these mutations confirmed the association with ASD for CHD8 and DYRK1A and provided significant statistical support for four novel genes: GRIN2B (glutamate receptor, ionotropic, N-methyl d-aspartate 2B), TBR1 (T-box brain gene 1), PTEN (phosphatase and tensin homolog), and TBL1XR1 [transducin (beta)-like 1 X-linked receptor 1].”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [44]
ASD cases with truncating CHD8 mutations have significant macrocephaly, whereas all three cases with truncating beta-catenin mutations have microcephaly.
“Strikingly, ASD cases with truncating mutations in CHD8 have significant macrocephaly [44], whereas all three cases with truncating mutations in beta-catenin have microcephaly ([28]; B.J. O’Roak, unpublished).”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [44]
Low-cost/high-throughput MIP-based resequencing strongly implicated a half-dozen novel genes accounting for 1% of disease in a 44-gene survey.
“the development of low-cost/high-throughput MIP-based resequencing has strongly implicated a half-dozen novel genes accounting for 1% of disease based on a limited survey of 44 genes [44].”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [44]
Among eight truncating de novo CHD8 mutations in ASD probands, five had ID and three had IQ above 90.
“of eight truncating de novo CHD8 mutations in ASD probands, five had ID and three had IQs above 90 [44].”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [44]
Using a probabilistic model based on human-chimpanzee fixed differences and sequence context, and assuming a de novo rate of 1.2 non-synonymous coding variants per individual, the probability of detecting eight or more de novo truncating ADNP events in the cohort was p = 2.65e-18 by binomial test.
“Under a de novo rate of 1.2 non-synonymous coding variants per individual, we estimate the probability of detecting eight or more de novo truncating events in ADNP within our cohort as p = 2.65e-18 (binomial test).”
From A SWI/SNF-related autism syndrome caused by de novo mutations in ADNP (2014) · cites this paper as [16]
De novo loss-of-function mutations in ADNP had previously been reported in two autism spectrum disorder patients by whole-exome sequencing and targeted resequencing, but those studies did not establish locus-specific significance for causality.
“De novo loss of function mutations in this gene had previously been identified in two patients by WES2 and targeted resequencing16 of patients with ASD. In those studies however, causal relationship did not reach locus-specific significance.”
From A SWI/SNF-related autism syndrome caused by de novo mutations in ADNP (2014) · cites this paper as [16]
An inherited p.Gly1094Profs*5 ADNP mutation identified by molecular inversion probe sequencing is located nine amino acids from the C-terminal end and is not associated with any protein domains.
“An inherited p.Gly1094Profs*5 mutation was identified by MIP sequencing16 but the reported frameshift is the ninth amino acid from the C-terminal end of the protein and not associated with any protein domains.”
From A SWI/SNF-related autism syndrome caused by de novo mutations in ADNP (2014) · cites this paper as [16]
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 [75]
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- Authors
- O’Roak, B. J., Vives, L., Fu, W., Egertson, J. D., Stanaway, I. B., Phelps, I. G., Carvill, G., Kumar, A., Lee, C., Ankenman, K., Munson, J., Hiatt, J. B., Turner, E. H., Levy, R., O’Day, D. R., Krumm, N., Coe, B. P., Martin, B. K., Borenstein, E., Nickerson, D. A., Mefford, H. C., Doherty, D., Akey, J. M., Bernier, R., Eichler, E. E., & Shendure, J.
- Affiliations
- University of Washington (US)
- Seattle Children's Hospital (US)
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA.
- Santa Fe Institute (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Eichler, Evan E.
- Shendure, Jay
- ORCID
- O’Roak, Brian J.
- Egertson, Jarrett D.
- Stanaway, Ian B.
- Carvill, Gemma
- Kumar, Akash
- Lee, Choli
- Ankenman, Katy
- Hiatt, Joseph B.
- Turner, Emily H.
- O’Day, Diana R.
- Krumm, Niklas
- Coe, Bradley P.
- Martin, Beth K.
- Borenstein, Elhanan
- Nickerson, Deborah A.
- Mefford, Heather C.
- Doherty, Dan
- Akey, Joshua M.
- Bernier, Raphael
- Eichler, Evan E.
- Shendure, Jay
- Venue
- Science
- Published
- 2012-12-21
- Volume
- 338
- Issue
- 6114
- Pages
- 1619-1622
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3528801
- OpenAlex
- W1988670106
- Cited by
- 1,240
- References
- 93
- Citations by year
- 2026: 24 · 2025: 32 · 2024: 55 · 2023: 61 · 2022: 85 · 2021: 101 · 2020: 91 · 2019: 111 · 2018: 96 · 2017: 124 · 2016: 124 · 2015: 117 · 2014: 133 · 2013: 78 · 2012: 1
- FWCI
- 53.93
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health (1rc2hl103010-01)
- National Heart, Lung, and Blood Institute (HL 102923, RC2HL102925, HL-102924, HL-102925, RC2HL102926, RC2HL102923, UC2HL102924, RC2HL-103010, UC2HL102925, HL 103010, UC2HL102923, UC2HL103010, RC2HL102924, UC2HL102926, HL-102926)
- National Institute of Neurological Disorders and Stroke (R56NS069605, R01NS064077, R01NS069605, NS069605)
- 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, recurrent mutations, de novo mutations, molecular inversion probes, CHD8, DYRK1A, NR2B subunit, Tbr1, PTEN, TBL1XR1, macrocephaly, microcephaly, β-catenin, chromatin remodeling, gene disruption, splicing disruption
- MeSH terms
- Dyrk Kinases, Cephalometry, Child, Child Development Disorders, Pervasive, Child, Preschool, DNA-Binding Proteins, Female, Humans, Male, Microcephaly, Mutation, Nuclear Proteins, Protein-Tyrosine Kinases, Repressor Proteins, Transcription Factors, Cohort Studies, DNA Probes, Receptors, N-Methyl-D-Aspartate, Protein Serine-Threonine Kinases, Sequence Analysis, DNA, Receptors, Cytoplasmic and Nuclear, Genetic Predisposition to Disease, T-Box Domain Proteins, Chromatin Assembly and Disassembly, PTEN Phosphohydrolase, beta Catenin, Genetic Association Studies, Megalencephaly, Exome
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