Cited by 1,546Genomics and Rare DiseasesGenetics and Neurodevelopmental DisordersDown syndrome and intellectual disability research

Diagnostic exome sequencing in persons with severe intellectual disability

Open access
de Ligt, Joep, Willemsen, Marjolein H., van Bon, Bregje W.M., Kleefstra, Tjitske, Yntema, Helger G., Kroes, Thessa, Vulto-van Silfhout, Anneke T., Koolen, David A. +9 more·2012·New England Journal of Medicine

Abstract

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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Crossref · 10.1056/nejmoa1206524

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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).”
  • 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”
  • 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.”

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Research works printed but not linked: 1

  1. Prasad C, Rupar T, Prasad AN. Pyru- vate dehydrogenase deficiency and epi- lepsy. Brain Dev 2011;33:856-65.

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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)
Venue
New England Journal of Medicine
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
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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