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De novo rates and selection of large copy number variation
Open accessAbstract
While copy number variation (CNV) is an active area of research, de novo mutation rates within human populations are not well characterized. By focusing on large (>100 kbp) events, we estimate the rate of de novo CNV formation in humans by analyzing 4394 transmissions from human pedigrees with and without neurocognitive disease. We show that a significant limitation in directly measuring genome-wide CNV mutation is accessing DNA derived from primary tissues as opposed to cell lines. We conservatively estimated the genome-wide CNV mutation rate using single nucleotide polymorphism (SNP) microarrays to analyze whole-blood derived DNA from asthmatic trios, a collection in which we observed no elevation in the prevalence of large CNVs. At a resolution of ∼30 kb, nine de novo CNVs were observed from 772 transmissions, corresponding to a mutation rate of μ = 1.2 × 10−2 CNVs per genome per transmission (μ = 6.5 × 10−3 for CNVs >500 kb). Combined with previous estimates of CNV prevalence and assuming a model of mutation-selection balance, we estimate significant purifying selection for large (>500 kb) events at the genome-wide level to be s = 0.16. Supporting this, we identify de novo CNVs in 717 multiplex autism pedigrees from the AGRE collection and observe a fourfold enrichment (P = 1.4 × 10−3) for de novo CNVs in cases of multiplex autism versus unaffected siblings, suggesting that many de novo CNV mutations contribute a subtle, but significant risk for autism. We observe no parental bias in the origin or transmission of CNVs among any of the cohorts studied.
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“The over-representation of large de novo CNVs in ASD has been replicated in studies ranging from 60 to 393 simplex trios (Itsara et al., 2010; Marshall et al., 2008; Pinto et al., 2010)”
From Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism (2011) · cites this paper as Itsara et al., 2010
In the citing paper
“Subsequent studies in larger samples have confirmed a high (5–10%) rate of de novo CNVs in ASD and further elucidated the extent of genetic heterogeneity in ASD (Itsara et al., 2010; Levy et al., 2011; Marshall et al., 2008; Pinto et al., 2010; Sanders et al., 2011).”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as Itsara et al., 2010
In the citing paper
“CNVs >10 Kb in size occur at a rate of ~0.01–0.02 per generation.(Itsara et al., 2010; Levy et al., 2011; Marshall et al., 2008; Sanders et al., 2011; Sebat et al., 2007).”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as Itsara et al., 2010
In the citing paper
“This rate is consistent with estimates from previous studies ranging from 0.5% to 3% (Conrad et al., 2010, Itsara et al., 2010, Levy et al., 2011, Sebat et al., 2007 and Xu et al., 2008).”
From High frequencies of de novo CNVs in bipolar disorder and schizophrenia (2011) · cites this paper as Itsara et al., 2010
In the citing paper
“Notably, the median size of SD and non-SD-mediated de novo CNVs was 722 kb and 67 kb respectively, consistent with previous studies that have found differences in CNV size related to the underlying mutational mechanism (Itsara et al., 2010 and Stefansson et al., 2008).”
From High frequencies of de novo CNVs in bipolar disorder and schizophrenia (2011) · cites this paper as Itsara et al., 2010
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Strauss, B. S. (2010) · Elsevier eBooks · doi:10.1016/b978-0-12-374430-2.00001-8
Chromosomal Disorders of Sex Development
Gardner, R. J. M., & Amor, D. J. (2018) · Oxford University Press eBooks · doi:10.1093/med/9780199329007.003.0023
Transient structural variations alter gene expression and quantitative
Jeffares, D. C., Jolly, C., Hoti, M., Speed, D., Charalampos, Dessimoz, C., Bähler, J., & Sedlazeck, F. J. (2016)
Identification of Thrombosis Modifier Genes Using ENU Mutagenesis in the Mouse.
Tomberg, K. (2016) · Deep Blue (University of Michigan)
Discovering Patterns of Structural Variation by Mining Molecular Fossils
Poot, M. (2016) · Molecular Syndromology · doi:10.1159/000450807
“CNVs larger than 100 kb arise de novo at an estimated rate of ∼ 1.2 × 10 –2 CNVs per meiosis [Itsara et al., 2010].”
BackgroundInfluentialAl-Sukhni, W. (2012) · TSpace (University of Toronto)
СОВРЕМЕННЫЕ ПРЕДСТАВЛЕНИЯ О МОЛЕКУЛЯРНОЙ ГЕНЕТИКЕ И ГЕНОМИКЕ АУТИЗМА
Vorsanova, S. G., Yurov, Y. B., Silvanovich, A. P., Ia, D., & Yurov, Y. B. (2013)
Willard, H. F. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-800681-8.00001-3
Sahli, A., Giguère, I., Bousquet, J., & MacKay, J. J. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/103796
“CNVs are among the least studied genetic variations despite their abundance in natural populations (Blackburn et al. 2013; Chain et al. 2014; Jakobsson et al. 2008; Kato et al. 2010; Mills et al. 2011; Tan et al. 2012), the considerable proportion of the genome they affect (12-15% of the human…”
BackgroundWhat Mutagenic Events Contribute to Human Cancer and Genetic Disease?
Waters, M. D. (2017) · John Wiley & Sons, Inc. eBooks · doi:10.1002/9781119023647.ch2
Gardner, R. J. M., & Amor, D. J. (2018) · Oxford University Press eBooks · doi:10.1093/med/9780199329007.003.0017
Autosomal Structural Rearrangements
Gardner, R. J. M., & Amor, D. J. (2018) · Oxford University Press eBooks · doi:10.1093/med/9780199329007.003.0014
Gardner, R. J. M., & Amor, D. J. (2018) · Oxford University Press eBooks · doi:10.1093/med/9780199329007.003.0020
Down Syndrome, Other Full Aneuploidies, Polyploidy, and the Influence of Parental Age
Gardner, R. J. M., & Amor, D. J. (2018) · Oxford University Press eBooks · doi:10.1093/med/9780199329007.003.0013
Complex Chromosomal Rearrangements
Gardner, R. J. M., & Amor, D. J. (2018) · Oxford University Press eBooks · doi:10.1093/med/9780199329007.003.0010
Gardner, R. J. M., & Amor, D. J. (2018) · Oxford University Press eBooks · doi:10.1093/med/9780199329007.003.0012
Computational insights into the generation of chromosomal copy number changes
Liu, Y. (2018) · Digital Commons-TMC (Texas Medical Center)
The human genome as a foundation for genomic and precision health
Willard, H. F. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-801496-7.00002-2
Detection of Copy Number Variation (CNV) and its characterization in Brazilian population
Ciconelle, A. C. M. (2019) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/d.95.2019.tde-08102019-094508
Genomics of autism spectrum disorders
Raygada, M. J., Grant, P., & Rennert, O. M. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-813176-3.00014-6
Genetics of autism spectrum disorders
Gupta, A. R., Fernandez, T. V., & Hoffman, E. J. (2020) · doi:10.1093/med/9780198713005.003.0028
Copy Number Variation in the Human Genome
Ferreira, E. N., & Quaio, C. R. D. C. (2021) · Springer eBooks · doi:10.1007/978-3-030-73151-9_9
Prunier, J., Carrier, A., Gilbert, I., Poisson, W., Albert, V., Taillon, J., Bourret, V., Côté, S. D., Droit, A., & Robert, C. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.22.453386
“…that CNVs in human genomes involve more nucleotides than single-nucleotide polymorphisms (Carson et al. 2006; Redon et al. 2006; Sebat et al. 2004; Itsara et al. 2010; Conrad et al. 2010), an increasing number of studies even suggested that CNVs have a greater impact than SNPs on phenotypic…”
Background
Metadata
- Authors
- Itsara, A., Wu, H., Smith, J. D., Nickerson, D. A., Romieu, I., London, S. J., & Eichler, E. E.
- Affiliations
- University of Washington (US)
- National Institutes of Health (US)
- Instituto Nacional de Salud Pública (MX)
- Howard Hughes Medical Institute (US)
- ORCID
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2010-09-14
- Volume
- 20
- Issue
- 11
- Pages
- 1469-1481
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC2963811
- OpenAlex
- W2158959870
- Cited by
- 328
- References
- 65
- Citations by year
- 2026: 4 · 2025: 5 · 2024: 9 · 2023: 9 · 2022: 8 · 2021: 14 · 2020: 16 · 2019: 10 · 2018: 43 · 2017: 19 · 2016: 30 · 2015: 25 · 2014: 25 · 2013: 36 · 2012: 43
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- U.S. Department of Health and Human Services
- Autism Speaks
- Simons Foundation
- Simons Foundation Autism Research Initiative (137578)
- Consejo Nacional de Ciencia y Tecnología (26206-M)
- National Institutes of Health (26206-M)
- National Institute of Mental Health (U24MH081810)
- National Institute of General Medical Sciences (T32GM007266)
- National Institute of Environmental Health Sciences (26206-M, ES049019, ES025045, ZIAES049019, ZIAES025045)
- 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 › Genome Rearrangement Algorithms
- Keywords
- copy number variation, de novo mutations, mutation rate, purifying selection, mutation-selection balance, autism spectrum disorder, human pedigrees, SNP array, parental bias
- MeSH terms
- Adolescent, Asthma, Autistic Disorder, Base Sequence, Child, Child, Preschool, Female, Gene Frequency, Humans, Male, Pedigree, Selection, Genetic, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Genome-Wide Association Study, DNA Copy Number Variations
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