An initial map of insertion and deletion (INDEL) variation in the human genome
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Although many studies have been conducted to identify single nucleotide polymorphisms (SNPs) in humans, few studies have been conducted to identify alternative forms of natural genetic variation, such as insertion and deletion (INDEL) polymorphisms. In this report, we describe an initial map of human INDEL variation that contains 415,436 unique INDEL polymorphisms. These INDELs were identified with a computational approach using DNA re-sequencing traces that originally were generated for SNP discovery projects. They range from 1 bp to 9989 bp in length and are split almost equally between insertions and deletions, relative to the chimpanzee genome sequence. Five major classes of INDELs were identified, including (1) insertions and deletions of single-base pairs, (2) monomeric base pair expansions, (3) multi-base pair expansions of 2–15 bp repeat units, (4) transposon insertions, and (5) INDELs containing random DNA sequences. Our INDELs are distributed throughout the human genome with an average density of one INDEL per 7.2 kb of DNA. Variation hotspots were identified with up to 48-fold regional increases in INDEL and/or SNP variation compared with the chromosomal averages for the same chromosomes. Over 148,000 INDELs (35.7%) were identified within known genes, and 5542 of these INDELs were located in the promoters and exons of genes, where gene function would be expected to be influenced the greatest. All INDELs in this study have been deposited into dbSNP and have been integrated into maps of human genetic variation that are available to the research community.
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Deletion discovery sensitivity was assessed against a gold standard assembled from four earlier surveys.
“We further assessed the sensitivity of deletion discovery methods by collating data from four earlier surveys1,13,22,28 into a gold standard”
From Mapping copy number variation by population-scale genome sequencing (2011) · cites this paper as [28]
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- Authors
- Mills, R. E., Luttig, C. T., Larkins, C. E., Beauchamp, A., Tsui, C., Pittard, W. S., & Devine, S. E.
- Affiliations
- Emory University (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2006-08-10
- Volume
- 16
- Issue
- 9
- Pages
- 1182-1190
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC1557762
- OpenAlex
- W1998120162
- Cited by
- 673
- References
- 37
- Citations by year
- 2026: 16 · 2025: 23 · 2024: 26 · 2023: 24 · 2022: 34 · 2021: 43 · 2020: 34 · 2019: 47 · 2018: 31 · 2017: 21 · 2016: 30 · 2015: 35 · 2014: 33 · 2013: 39 · 2012: 45
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- University of California, Santa Cruz
- National Institutes of Health
- National Human Genome Research Institute (R01HG002898)
- 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
- insertion/deletion polymorphism, indels, human genetic variation, single nucleotide polymorphisms, transposon insertion, dbSNP
- MeSH terms
- Animals, Pan troglodytes, Humans, Polymorphism, Genetic, Genome, Human, Sequence Deletion, Computational Biology, Polymorphism, Single Nucleotide
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