Cited by 621Genomic variations and chromosomal abnormalitiesGenetic Associations and EpidemiologyGenomics and Rare Diseases

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Population Analysis of Large Copy Number Variants and Hotspots of Human Genetic Disease

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Itsara, Andy, Cooper, Gregory M., Baker, Carl, Girirajan, Santhosh, Li, Jun, Absher, Devin, Krauss, Ronald M., Myers, Richard M., Ridker, Paul M., Chasman, Daniel I., Mefford, Heather, Ying, Phyllis, Nickerson, Deborah A., Eichler, Evan E.·2009·The American Journal of Human Genetics

DOI 10.1016/j.ajhg.2008.12.014PMC PMC2668011

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Abstract

Copy number variants (CNVs) contribute to human genetic and phenotypic diversity. However, the distribution of larger CNVs in the general population remains largely unexplored. We identify large variants in approximately 2500 individuals by using Illumina SNP data, with an emphasis on "hotspots" prone to recurrent mutations. We find variants larger than 500 kb in 5%-10% of individuals and variants greater than 1 Mb in 1%-2%. In contrast to previous studies, we find limited evidence for stratification of CNVs in geographically distinct human populations. Importantly, our sample size permits a robust distinction between truly rare and polymorphic but low-frequency copy number variation. We find that a significant fraction of individual CNVs larger than 100 kb are rare and that both gene density and size are strongly anticorrelated with allele frequency. Thus, although large CNVs commonly exist in normal individuals, which suggests that size alone can not be used as a predictor of pathogenicity, such variation is generally deleterious. Considering these observations, we combine our data with published CNVs from more than 12,000 individuals contrasting control and neurological disease collections. This analysis identifies known disease loci and highlights additional CNVs (e.g., 3q29, 16p12, and 15q25.2) for further investigation. This study provides one of the first analyses of large, rare (0.1%-1%) CNVs in the general population, with insights relevant to future analyses of genetic disease.

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Self-citation

Authors: Itsara, A., Cooper, G. M., Baker, C., Girirajan, S., Li, J., Absher, D., Krauss, R. M., Myers, R. M., Ridker, P. M., Chasman, D. I., Mefford, H., Ying, P., Nickerson, D. A., & Eichler, E. E.
Affiliations: University of Washington (US)
University of Michigan (US)
HudsonAlpha Institute for Biotechnology (US)
Brigham and Women's Hospital (US)
Howard Hughes Medical Institute (US)
Corresponding author: Eichler, Evan E.
ORCID: Cooper, Gregory M.
Girirajan, Santhosh
Li, Jun
Absher, Devin
Krauss, Ronald M.
Myers, Richard M.
Ridker, Paul M.
Chasman, Daniel I.
Mefford, Heather
Nickerson, Deborah A.
Eichler, Evan E.
Venue: The American Journal of Human Genetics
Publisher: Elsevier BV
Published: 2009-02
Volume: 84
Issue: 2
Pages: 148-161
ISSN: 0002-9297 (ISSN-L)
DOI: 10.1016/j.ajhg.2008.12.014
PMC: PMC2668011
OpenAlex: W2148095347
Cited by: 591
References: 59
Citations by year: 2026: 7 · 2025: 7 · 2024: 23 · 2023: 15 · 2022: 27 · 2021: 24 · 2020: 25 · 2019: 19 · 2018: 19 · 2017: 26 · 2016: 25 · 2015: 43 · 2014: 40 · 2013: 57 · 2012: 74
FWCI: 42.23
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 1663 d)
Locations: The American Journal of Human Genetics (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: Howard Hughes Medical Institute
U.S. Department of Health and Human Services
Donald W. Reynolds Foundation
National Institutes of Health
National Institute on Aging (Z01AG000932)
National Heart, Lung, and Blood Institute (HL01069757)
National Human Genome Research Institute (P01HG004120, HG004120, T32HG000035)
National Institute of General Medical Sciences (T32GM007266)
National Institute of Neurological Disorders and Stroke
Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD043569, R01HD043569)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
Keywords: copy number variation, population genetics, recurrent mutations, allele frequency, gene density, neurological disorders, disease loci, rare variants
MeSH terms: Genetics, Population, Genotype, Geography, Humans, Polymorphism, Genetic, Genetic Variation, Genome, Human, Sequence Deletion, Gene Dosage, Oligonucleotide Array Sequence Analysis, Gene Duplication, Polymorphism, Single Nucleotide, Genetic Diseases, Inborn

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Population Analysis of Large Copy Number Variants and Hotspots of Human Genetic Disease

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