A copy number variation morbidity map of developmental delay
Open accessAbstract
To understand the genetic heterogeneity underlying developmental delay, we compared copy number variants (CNVs) in 15,767 children with intellectual disability and various congenital defects (cases) to CNVs in 8,329 unaffected adult controls. We estimate that ∼14.2% of disease in these children is caused by CNVs >400 kb. We observed a greater enrichment of CNVs in individuals with craniofacial anomalies and cardiovascular defects compared to those with epilepsy or autism. We identified 59 pathogenic CNVs, including 14 new or previously weakly supported candidates, refined the critical interval for several genomic disorders, such as the 17q21.31 microdeletion syndrome, and identified 940 candidate dosage-sensitive genes. We also developed methods to opportunistically discover small, disruptive CNVs within the large and growing diagnostic array datasets. This evolving CNV morbidity map, combined with exome and genome sequencing, will be critical for deciphering the genetic basis of developmental delay, intellectual disability and autism spectrum disorders.
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About 0.25% of controls (n=66,462) are found with the 15q11.2 BP1-BP2 microdeletion.
“a review of reported data from control cohorts (n = 66,462 subjects) summarized to date show that about 0.25% of controls are found with the 15q11.2 BP1–BP2 microdeletion [18,27,28,29,30,31].”
From The 15q11.2 BP1–BP2 Microdeletion Syndrome: A Review (2015) · cites this paper as [27]
The Results (Locus-specific enrichments; page unavailable) identify the 15q11.2 deletion and report its enrichment in cases relative to controls. The Discussion identifies it as the BP1–BP2 deletion. Neither passage gives the claimed 0.25% control frequency or a control cohort of 66,462; searches for both figures found no supporting passage in our copy. (LLM, conf=0.82)
Experimental — accuracy not yet measuredDeletions and duplications of a chromosomal region including CYFIP1 have been linked to intellectual disability, autism spectrum disorder, and schizophrenia.
“Deletions and duplications of a chromosomal region including CYFIP1 have been linked to ID, ASD, and schizophrenia (Cooper et al., 2011, Doornbos et al., 2009, Leblond et al., 2012, Murthy et al., 2007, Nowicki et al., 2007, Tam et al., 2010, van der Zwaag et al., 2010, von der Lippe et al., 2010, Zhao et al., 2012).”
From CYFIP1 Coordinates mRNA Translation and Cytoskeleton Remodeling to Ensure Proper Dendritic Spine Formation (2013) · cites this paper as Cooper et al., 2011
The Results (Locus-specific enrichments; page unavailable) report that 15q11.2 deletions are enriched among individuals with intellectual disability or developmental delay. Our copy does not name CYFIP1 or establish the claimed links for duplications at that locus. Its discussion of autism and schizophrenia concerns a different deletion, at 15q25.2. (LLM, conf=0.84)
Experimental — accuracy not yet measuredThe 15q11.2 deletion is associated with developmental delay (OR 2.36).
“developmental delay (OR 2.36),3”
From Estimating the effect size of the 15Q11.2 BP1–BP2 deletion and its contribution to neurodevelopmental symptoms: recommendations for practice (2019) · cites this paper as [3]
CYFIP1 is implicated in intellectual disability, autism spectrum disorder, and schizophrenia.
“CYFIP1 is implicated in ID (Cooper et al., 2011, Napoli et al., 2008, Nowicki et al., 2007, Schenck et al., 2003), ASD (Cooper et al., 2011, Doornbos et al., 2009, Murthy et al., 2007, Nishimura et al., 2007, Sahoo et al., 2006, van der Zwaag et al., 2010, von der Lippe et al., 2010), and SCZ (Tam et al., 2010, Zhao et al., 2012).”
From CYFIP1 Coordinates mRNA Translation and Cytoskeleton Remodeling to Ensure Proper Dendritic Spine Formation (2013) · cites this paper as Cooper et al., 2011
The Discussion reports pathogenicity of 15q11.2 deletions in affected individuals, and the Methods describe an ID/DD cohort that includes autism cases. But searches for CYFIP1 and its proposed links to ID and ASD found no passage identifying that gene or linking it to either condition. The citing sentence attributes schizophrenia to other sources, not Cooper et al. (LLM, conf=0.73)
Experimental — accuracy not yet measured273 rare CNVs were identified in 206 affected offspring.
“we identified 273 rare CNVs (occurring with a carrier frequency of ≤1% of the 1379 individuals in the analysis and also appear <1% in 1000 Genomes population and healthy controls18) in 206 affected offspring.”
From Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes (2019) · cites this paper as [18]
The BP1-BP2 deletion is associated with phenotypic variability and has been reported in individuals with neurodevelopmental disorders, schizophrenia, ASD, and epilepsy.
“The BP1-BP2 deletion is associated with phenotypic variability and has been reported in individuals with neurodevelopmental disorders [20], schizophrenia [53], [60], ASD [44]–[46], [49], and epilepsy [61].”
From Genetic and Functional Analyses of SHANK2 Mutations Suggest a Multiple Hit Model of Autism Spectrum Disorders (2012) · cites this paper as [20]
In a recent screen for large CNVs (>400 kb) on 15,767 children with ID and various congenital defects and 8,329 unaffected adult controls, deletions affecting CYFIP1, NIPA1, NIPA2 and TUBGCP5 were associated with neurodevelopmental disorder, epilepsy, and autism.
“In a recent screen for large CNVs (>400 kb) performed on 15,767 children with ID and various congenital defects, and 8,329 unaffected adult controls [20], deletions affecting CYFIP1, NIPA1, NIPA2 and TUBGCP5 were associated with neurodevelopmental disorder (P = 4.73×10−6), epilepsy (P = 1.48×10−3) and autism (P = 1.99×10−2).”
From Genetic and Functional Analyses of SHANK2 Mutations Suggest a Multiple Hit Model of Autism Spectrum Disorders (2012) · cites this paper as [20]
Alterations of SNTG2 and MYT1L have been previously reported in patients with ASD and schizophrenia.
“Alterations of SNTG2 and MYT1L have been previously reported in patients with ASD [20], [63], [64] and schizophrenia [65], respectively.”
From Genetic and Functional Analyses of SHANK2 Mutations Suggest a Multiple Hit Model of Autism Spectrum Disorders (2012) · cites this paper as [20]
Virtually every CNV is associated with a wide variety of other neuropsychiatric or neurodevelopmental conditions.
“Virtually every CNV allele that is associated with a psychiatric disorder is present at a low frequency in populations of healthy controls, and virtually every CNV is also associated with a wide variety of other neuropsychiatric or neurodevelopmental conditions including bipolar disorder, seizure disorder, intellectual disability, attention deficit hyperactivity disorder (ADHD) etc (Cooper et al.,”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as Cooper et al., 2011
Virtually every CNV allele associated with a psychiatric disorder is present at low frequency in healthy controls.
“Virtually every CNV allele that is associated with a psychiatric disorder is present at a low frequency in populations of healthy controls, and virtually every CNV is also associated with a wide variety of other neuropsychiatric or neurodevelopmental conditions including bipolar disorder, seizure disorder, intellectual disability, attention deficit hyperactivity disorder (ADHD) etc (Cooper et al.,”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as Cooper et al., 2011
Deletions at EHMT1 are highly penetrant for phenotypes comprising developmental delay and a range of congenital anomalies.
“A recent study has also reported strong evidence that deletions at EHMT1 are highly penetrant for phenotypes comprising developmental delay and a range of congenital anomalies.32”
From De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia (2012) · cites this paper as [32]
Duplications at the WBS region have recently been identified increasing susceptibility for autism and developmental delay.
“given duplications at this locus have also recently been identified increasing susceptibility for autism25 and developmental delay,32”
From De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia (2012) · cites this paper as [32]
Deletions at the TAR region locus have very recently been strongly implicated in developmental delay.
“Again, deletions at this locus have very recently been strongly implicated in developmental delay.32”
From De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia (2012) · cites this paper as [32]
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.”
From Evidence for 28 genetic disorders discovered by combining healthcare and research data (2020) · cites this paper as [8]
Large de novo copy number variants are significantly enriched among ASD/ID probands compared with unaffected siblings or controls.
“By contrast, targeted and genome-wide microarray studies revealed that large de novo copy number variants (CNVs) were significantly enriched among probands when compared to unaffected siblings and/or controls [8–14]”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [13]
Rare large de novo CNVs are thought to account for up to 15% of disease burden among children with developmental delay and intellectual disability.
“Furthermore, among children with general developmental delay (DD) and ID, rare large de novo CNVs are thought to account for up to 15% of disease burden [13].”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [13]
The paper's prevalence of SHANK3 deletions in patients with ASD and ID is similar to that reported by Cooper et al. (2011) in 1379 patients with autism and developmental delay (0.87%).
“Our prevalence of SHANK3 deletions in patients with ASD and ID is similar to that reported by Cooper et al. (2011) in a large sample of 1 379 patients with autism and developmental delay (0.87%) [10].”
From Meta-analysis of SHANK Mutations in Autism Spectrum Disorders: A Gradient of Severity in Cognitive Impairments (2014) · cites this paper as [10]
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A general framework for estimating the relative pathogenicity of human genetic variants
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“…for common variants associated with ASD and genetically correlated traits, we ran competitive gene-set enrichment analyses on the set of 102 genes using MAGMA (de Leeuw et al., 2015) with brain-expressed genes from BrainSpan (see section below on developmental expression data) as background.”
MethodInfluentialSporadic autism exomes reveal a highly interconnected protein network of de novo mutations
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“For example, we identified a complex de novo mutation resulting in truncation of SETBP1 (SET binding protein 1), one of five genes in the critical region for del(18) (q12.”
Self-citationA genomic mutational constraint map using variation in 76,156 human genomes
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Self-citationMultiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders
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Self-citationGuidelines for investigating causality of sequence variants in human disease
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Self-citationLarge-scale discovery of novel genetic causes of developmental disorders
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CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics
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“32 With this additional evidence for the involvement of this gene in neurodevelopmental phenotypes, our data point to EHMT1 as a schizophrenia susceptibility gene.”
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Self-citationGenetic studies in intellectual disability and related disorders
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Evidence for 28 genetic disorders discovered by combining healthcare and research data
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“In particular, mutations in genes coding for synaptic cell adhesion molecules and scaffold proteins — such as neuroligins, neurexins and SHANK — have been repeatedly reported in individuals with ASD [5–10].”
BackgroundResultInfluentialPhenotypic Heterogeneity of Genomic Disorders and Rare Copy-Number Variants
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Self-citationInherited and de novo genetic risk for autism impacts shared networks
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Self-citationA de novo convergence of autism genetics and molecular neuroscience
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Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication
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Self-citationKCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number variant
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Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity
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Self-citationMapping and characterization of structural variation in 17,795 human genomes
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Heritability and genomics of gene expression in peripheral blood
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Segmental duplications and their variation in a complete human genome
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Self-citationGlobal diversity, population stratification, and selection of human copy-number variation
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Self-citationDevelopmental brain dysfunction: revival and expansion of old concepts based on new genetic evidence
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Genomics, Intellectual Disability, and Autism
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Evaluating historical candidate genes for schizophrenia
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Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes
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A High-Resolution Enhancer Atlas of the Developing Telencephalon
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Mutations in the chromatin modifier gene KANSL1 cause the 17q21.31 microdeletion syndrome
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Self-citationCopy number variation in obsessive-compulsive disorder and tourette syndrome: A cross-disorder study
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Self-citationAssociation of Rare Copy Number Variants With Risk of Depression
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- Authors
- Cooper, G. M., Coe, B. P., Girirajan, S., Rosenfeld, J. A., Vu, T. H., Baker, C., Williams, C., Stalker, H., Hamid, R., Hannig, V., Abdel-Hamid, H., Bader, P., McCracken, E., Niyazov, D., Leppig, K., Thiese, H., Hummel, M., Alexander, N., Gorski, J., Kussmann, J., Shashi, V., Johnson, K., Rehder, C., Ballif, B. C., Shaffer, L. G., & Eichler, E. E.
- Affiliations
- University of Washington (US)
- University of Florida (US)
- Vanderbilt University Medical Center (US)
- University of Pittsburgh (US)
- Children's Hospital of Pittsburgh (US)
- Ochsner Medical Center (US)
- Group Health Cooperative (US)
- West Virginia University (US)
- University of Missouri (US)
- Duke Medical Center (US)
- Duke University Health System (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Eichler, Evan E
- ORCID
- Venue
- Nature Genetics
- Published
- 2011-08-14
- Volume
- 43
- Issue
- 9
- Pages
- 838-846
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC3171215
- OpenAlex
- W2106650442
- Semantic Scholar
- 193f7fa4fdc0857775db94bf88ad03906baa6175
- Cited by
- 1,351
- References
- 62
- Citations by year
- 2026: 41 · 2025: 45 · 2024: 63 · 2023: 54 · 2022: 76 · 2021: 70 · 2020: 86 · 2019: 81 · 2018: 112 · 2017: 84 · 2016: 91 · 2015: 129 · 2014: 138 · 2013: 137 · 2012: 125
- FWCI
- 82.61
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- Wellcome Trust (085475, 076113)
- National Institutes of Health
- Canadian Institutes of Health Research
- National Heart, Lung, and Blood Institute (R01HL102020)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD065285, R01HD065285)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Keywords
- copy number variation, developmental delay, intellectual disability, congenital birth defects, craniofacial anomalies, cardiovascular defects, epilepsy, autism spectrum disorder, dosage-sensitive genes, genetic heterogeneity
- MeSH terms
- Congenital Abnormalities, Adult, Developmental Disabilities, Child, Preschool, Chromosome Mapping, Humans, Genetic Variation, Gene Dosage
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.
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