Diagnostic exome sequencing in persons with severe intellectual disability
Open accessAbstract
BACKGROUND: The causes of intellectual disability remain largely unknown because of extensive clinical and genetic heterogeneity. METHODS: We evaluated patients with intellectual disability to exclude known causes of the disorder. We then sequenced the coding regions of more than 21,000 genes obtained from 100 patients with an IQ below 50 and their unaffected parents. A data-analysis procedure was developed to identify and classify de novo, autosomal recessive, and X-linked mutations. In addition, we used high-throughput resequencing to confirm new candidate genes in 765 persons with intellectual disability (a confirmation series). All mutations were evaluated by molecular geneticists and clinicians in the context of the patients' clinical presentation. RESULTS: We identified 79 de novo mutations in 53 of 100 patients. A total of 10 de novo mutations and 3 X-linked (maternally inherited) mutations that had been previously predicted to compromise the function of known intellectual-disability genes were found in 13 patients. Potentially causative de novo mutations in novel candidate genes were detected in 22 patients. Additional de novo mutations in 3 of these candidate genes were identified in patients with similar phenotypes in the confirmation series, providing support for mutations in these genes as the cause of intellectual disability. We detected no causative autosomal recessive inherited mutations in the discovery series. Thus, the total diagnostic yield was 16%, mostly involving de novo mutations. CONCLUSIONS: De novo mutations represent an important cause of intellectual disability; exome sequencing was used as an effective diagnostic strategy for their detection. (Funded by the European Union and others.).
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The prevalence of ASD in several ID/DD-ascertained cohorts is not quantified, and the prevalence of ID in ASD-ascertained cohorts is known only for a minority subset of participants.
“Because of this bias, the phenotypic overlap between the groups is unclear; the prevalence of ASD in several of the ID/DD-ascertained cohorts is not quantified,13, 14, 15,18,19 and the prevalence of ID in the ASD-ascertained cohorts is known only for a minority subset of participants.11,12”
From Insufficient Evidence for “Autism-Specific” Genes (2020) · cites this paper as [14]
The ID/DD cohorts evaluated in the Satterstrom and Coe studies overlapped almost completely; each study used samples from five previously published studies, and four of the five were the same studies, accounting for 99% of the samples.
“In fact, the ID/DD cohorts evaluated in these two studies overlapped almost completely; each study used samples from five previously published studies, and four of the five were the same studies, accounting for 99% of the samples.11, 12, 13, 14, 15, 16”
From Insufficient Evidence for “Autism-Specific” Genes (2020) · cites this paper as [14]
CTNNB1 mutations appear among suggestive de novo ASD risk mutations, and about 40% of 126 mutations map to a β-catenin/chromatin remodeling network.
“Mutation of the gene encoding β-catenin, CTNNB1, has been found among suggestive de novo ASD risk contributing mutations (de Ligt et al., 2012; O'Roak et al., 2012b); furthermore, ∼40% of those 126 mutations map to a highly interconnected β-catenin/chromatin remodeling network (O'Roak et al., 2012b).”
From Unifying Views of Autism Spectrum Disorders: A Consideration of Autoregulatory Feedback Loops (2016) · cites this paper as de Ligt et al., 2012
CHD2, SYNGAP1, and SYNCRIP are also affected by LoF de novo SNVs in ID, and SYNGAP1 and DPYD are altered in schizophrenia.
“Three other genes affected by de novo CNVs (also picked by NETBAG)—CHD2, SYNGAP1, and SYNCRIP—are also affected by LoF de novo SNVs in ID,50,52 and two (SYNGAP1 and DPYD [MIM 612779]) are altered in schizophrenia.53”
From Convergence of genes and cellular pathways dysregulated in autism spectrum disorders (2014) · cites this paper as [52]
Genetic approaches have identified causes for more than 1,000 Mendelian and fewer non-Mendelian forms of neurodevelopmental disorders, including intellectual disability, ASD, epilepsy, and schizophrenia.
“Various genetic approaches have been successful in identifying the causes of more than 1,000 Mendelian, and fewer non-Mendelian, forms of neurodevelopmental disorders: prototypical examples are intellectual disability62–68, autism spectrum disorder (ASD)69–77, epilepsy78,79 and schizophrenia80–82.”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [66]
Only three genes, CHD8, SCN2A, and SYNGAP1, had two independent truncating de novo mutations in any single study, and no gene had more than three mutations.
“In summary, only three genes [CHD8, SCN2A, and synaptic Ras GTPase activating protein 1 (SYNGAP1)] had two independent truncating de novo mutations in any single study, and no gene had more than three mutations.”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [28]
SCN2A mutations have highly variable phenotypic outcomes, as only one of five cases had a history of seizures.
“Lastly, only one of the five cases had a history of seizures [28], suggesting that mutations in SCN2A have highly variable phenotypic outcomes.”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [28]
Exome sequencing of ASD/ID families has revealed a significant excess of de novo mutations in probands compared with unaffected siblings and has identified novel candidate genes.
“Exome sequencing of ASD/ID families has revealed a significant excess of de novo mutations in probands when compared to unaffected siblings and has identified novel candidate genes contributing to the neurological deficits.”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [28]
The strongest effects are observed for de novo loss-of-function or truncating mutations.
“We note that the strongest effects are observed for de novo loss-of-function (or truncating) mutations”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [28]
Many strong neurobiological candidates have emerged from genes disrupted by de novo mutations, including previously identified ASD/ID genes.
“Many strong neurobiological candidates have emerged from the genes disrupted by de novo mutations in these studies, including mutations in previously identified ASD/ID genes.”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [28]
Sporadic cases of autism spectrum disorder and intellectual disability are enriched for disruptive de novo mutations.
“New exome sequencing technology has identified novel rare variants and has found that sporadic cases of ASD/ID are enriched for disruptive de novo mutations.”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [28]
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 [28]
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“Unsurprisingly, many ASD 14 genes are also associated with NDD (22-26).”
Background
- Authors
- de Ligt, J., Willemsen, M. H., van Bon, B. W. M., Kleefstra, T., Yntema, H. G., Kroes, T., Vulto-van Silfhout, A. T., Koolen, D. A., de Vries, P., Gilissen, C., del Rosario, M., Hoischen, A., Scheffer, H., de Vries, B. B. A., Brunner, H. G., Veltman, J. A., & Vissers, L. E. L. M.
- Affiliations
- Radboud University Nijmegen (NL)
- ORCID
- Venue
- New England Journal of Medicine
- Publisher
- Massachusetts Medical Society
- Published
- 2012-11-15
- Volume
- 367
- Issue
- 20
- Pages
- 1921-1929
- ISSN
- 0028-4793 (ISSN-L)
- 1533-4406
- OpenAlex
- W2115558586
- Cited by
- 1,546
- References
- 31
- Citations by year
- 2026: 37 · 2025: 61 · 2024: 88 · 2023: 71 · 2022: 97 · 2021: 101 · 2020: 108 · 2019: 111 · 2018: 151 · 2017: 173 · 2016: 149 · 2015: 133 · 2014: 163 · 2013: 93 · 2012: 6
- FWCI
- 74.90
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- New England Journal of Medicine (publishedVersion)
- PubMed (publishedVersion)
- Radboud Repository (Radboud University) (submittedVersion)
- Zenodo (CERN European Organization for Nuclear Research) (submittedVersion, other-oa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Down syndrome and intellectual disability research
- Keywords
- intellectual disability, exome sequencing, de novo mutations, X-linked mutations, autosomal recessive mutation, candidate genes, diagnostic yield, genetic heterogeneity, molecular diagnosis
- MeSH terms
- Adolescent, Child, Female, Genes, Recessive, Humans, Male, Intellectual Disability, Mutation, Sequence Analysis, DNA, Genetic Diseases, X-Linked, Genes, X-Linked, Young Adult, Exome
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