Cited by 701Genomic variations and chromosomal abnormalitiesGenetic Associations and EpidemiologyForensic and Genetic Research

Common deletion polymorphisms in the human genome

McCarroll, Steven A, Hadnott, Tracy N, Perry, George H, Sabeti, Pardis C, Zody, Michael C, Barrett, Jeffrey C, Dallaire, Stephanie, Gabriel, Stacey B +4 more·2006·Nature Genetics

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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Crossref · 10.1038/ng1696

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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
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
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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