Common deletion polymorphisms in the human genome
Abstract
The locations and properties of common deletion variants in the human genome are largely unknown. We describe a systematic method for using dense SNP genotype data to discover deletions and its application to data from the International HapMap Consortium to characterize and catalogue segregating deletion variants across the human genome. We identified 541 deletion variants (94% novel) ranging from 1 kb to 745 kb in size; 278 of these variants were observed in multiple, unrelated individuals, 120 in the homozygous state. The coding exons of ten expressed genes were found to be commonly deleted, including multiple genes with roles in sex steroid metabolism, olfaction and drug response. These common deletion polymorphisms typically represent ancestral mutations that are in linkage disequilibrium with nearby SNPs, meaning that their association to disease can often be evaluated in the course of SNP-based whole-genome association studies.
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Many copy-number variations (CNVs) display tight LD with nearby SNPs and thus can be proxied by nearby SNPs in GWASs.
“Many CNVs display tight LD with nearby SNPs (56, 57) and thus can be proxied by nearby SNPs in GWASs.”
From Genetic Mapping in Human Disease (2008) · cites this paper as [57]
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- Authors
- McCarroll, S. A., Hadnott, T. N., Perry, G. H., Sabeti, P. C., Zody, M. C., Barrett, J. C., Dallaire, S., Gabriel, S. B., Lee, C., Daly, M. J., Altshuler, D. M., & The International HapMap Consortium
- Affiliations
- Massachusetts General Hospital (US)
- Brigham and Women's Hospital (US)
- Broad Institute (US)
- Corresponding author
- Altshuler, David M
- ORCID
- Venue
- Nature Genetics
- Published
- 2005-12-04
- Volume
- 38
- Issue
- 1
- Pages
- 86-92
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W2159091117
- Cited by
- 701
- References
- 19
- Citations by year
- 2026: 2 · 2025: 6 · 2024: 7 · 2023: 6 · 2022: 18 · 2021: 12 · 2020: 17 · 2019: 19 · 2018: 15 · 2017: 16 · 2016: 16 · 2015: 28 · 2014: 31 · 2013: 27 · 2012: 37
- FWCI
- 46.91
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- 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 › Forensic and Genetic Research
- Keywords
- deletion variants, human genome, HapMap, homozygous deletion, drug response genes, linkage disequilibrium, whole-genome association studies
- MeSH terms
- Exons, Genetic Techniques, Homozygote, Humans, Models, Genetic, Polymorphism, Genetic, Linkage Disequilibrium, Genome, Human, Polymerase Chain Reaction, Sequence Deletion, In Situ Hybridization, Fluorescence, Polymorphism, Single Nucleotide, Databases, Genetic, Racial Groups
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