Cited by 720Genomic variations and chromosomal abnormalitiesGenetics and Neurodevelopmental DisordersGenomics and Rare Diseases

Refining analyses of copy number variation identifies specific genes associated with developmental delay

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Coe, Bradley P, Witherspoon, Kali, Rosenfeld, Jill A, van Bon, Bregje W M, Vulto-van Silfhout, Anneke T, Bosco, Paolo, Friend, Kathryn L, Baker, Carl +31 more·2014·Nature Genetics

Abstract

Copy number variants (CNVs) are associated with many neurocognitive disorders; however, these events are typically large, and the underlying causative genes are unclear. We created an expanded CNV morbidity map from 29,085 children with developmental delay in comparison to 19,584 healthy controls, identifying 70 significant CNVs. We resequenced 26 candidate genes in 4,716 additional cases with developmental delay or autism and 2,193 controls. An integrated analysis of CNV and single-nucleotide variant (SNV) data pinpointed 10 genes enriched for putative loss of function. Follow-up of a subset of affected individuals identified new clinical subtypes of pediatric disease and the genes responsible for disease-associated CNVs. These genetic changes include haploinsufficiency of SETBP1 associated with intellectual disability and loss of expressive language and truncations of ZMYND11 in individuals with autism, aggression and complex neuropsychiatric features. This combined CNV and SNV approach facilitates the rapid discovery of new syndromes and genes involved in neuropsychiatric disease despite extensive genetic heterogeneity.

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  • Previous studies of pathogenic copy number variation found that healthcare data were key to achieving larger sample sizes than research data alone.

    “In previous studies of pathogenic Copy Number Variation, utilising healthcare data has been key to achieve larger sample sizes than would be possible in a research setting alone8,9.”

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Authors
Coe, B. P., Witherspoon, K., Rosenfeld, J. A., van Bon, B. W. M., Vulto-van Silfhout, A. T., Bosco, P., Friend, K. L., Baker, C., Buono, S., Vissers, L. E. L. M., Schuurs-Hoeijmakers, J. H., Hoischen, A., Pfundt, R., Krumm, N., Carvill, G. L., Li, D., Amaral, D., Brown, N., Lockhart, P. J., Scheffer, I. E., Alberti, A., Shaw, M., Pettinato, R., Tervo, R., de Leeuw, N., Reijnders, M. R. F., Torchia, B. S., Peeters, H., Thompson, E., O'Roak, B. J., Fichera, M., Hehir-Kwa, J. Y., Shendure, J., Mefford, H. C., Haan, E., Gécz, J., de Vries, B. B. A., Romano, C., & Eichler, E. E.
Affiliations
  • University of Washington (US)
  • PerkinElmer (United States) (US)
  • Oasi Maria SS (IT)
  • South Australia Pathology (AU)
  • Radboud University Medical Center (NL)
  • University of California, Davis (US)
  • Barwon Health (AU)
  • Royal Children's Hospital (AU)
  • Mayo Clinic (US)
  • KU Leuven (BE)
  • Howard Hughes Medical Institute (US)
Corresponding author
Eichler, Evan E
Venue
Nature Genetics
Published
2014-09-14
Volume
46
Issue
10
Pages
1063-1071
ISSN
  • 1061-4036 (ISSN-L)
  • 1546-1718
OpenAlex
W1964512314
Cited by
720
References
61
Citations by year
2026: 40 · 2025: 40 · 2024: 54 · 2023: 57 · 2022: 51 · 2021: 53 · 2020: 96 · 2019: 72 · 2018: 83 · 2017: 62 · 2016: 59 · 2015: 43 · 2014: 7
FWCI
37.34
Type
journal article
Language
en
Open access
Locations
  • Nature Genetics (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
  • Minerva Access (University of Melbourne) (submittedVersion)
  • Lirias (submittedVersion)
  • Radboud Repository (Radboud University) (submittedVersion)
Funders
  • Howard Hughes Medical Institute
  • Paul G. Allen Family Foundation
  • Allen Foundation
  • Wellcome Trust
  • National Institutes of Health
  • National Institute of Mental Health (MH101221,, R01MH101221)
  • National Institute of General Medical Sciences (T32GM007266)
  • National Institute of Neurological Disorders and Stroke (K99NS089858)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
  • 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
copy number variation, developmental delay, autism spectrum disorder, SETBP1, ZMYND11, haploinsufficiency, intellectual disability, neuropsychiatric disorders, single nucleotide variants, loss of function, candidate genes, genetic heterogeneity, pediatric syndromes
MeSH terms
Autistic Disorder, Base Sequence, Carrier Proteins, Child, Developmental Disabilities, Chromosome Mapping, DNA-Binding Proteins, Female, Humans, Male, Intellectual Disability, Molecular Sequence Data, Nuclear Proteins, Sequence Analysis, DNA, Cell Cycle Proteins, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Comparative Genomic Hybridization, Genetic Association Studies, DNA Copy Number Variations, Co-Repressor Proteins, Haploinsufficiency

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