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Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS, Devine SE. An initial map of insertion and deletion (INDEL) variation in the human genome. Genes Dev 2006; 16:1182-90. [PMID: 16902084 PMCID: PMC1557762 DOI: 10.1101/gr.4565806] [Citation(s) in RCA: 432] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2005] [Accepted: 07/12/2006] [Indexed: 01/22/2023]
Abstract
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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Affiliation(s)
- Ryan E. Mills
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
- Center for Bioinformatics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Christopher T. Luttig
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Christine E. Larkins
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Adam Beauchamp
- Genetics and Molecular Biology Graduate Program, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Circe Tsui
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
- Center for Bioinformatics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - W. Stephen Pittard
- Center for Bioinformatics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
- Bimcore, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Scott E. Devine
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
- Center for Bioinformatics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University School of Medicine, Atlanta, Georgia 30322, USA
- Genetics and Molecular Biology Graduate Program, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Miller RD, Phillips MS, Jo I, Donaldson MA, Studebaker JF, Addleman N, Alfisi SV, Ankener WM, Bhatti HA, Callahan CE, Carey BJ, Conley CL, Cyr JM, Derohannessian V, Donaldson RA, Elosua C, Ford SE, Forman AM, Gelfand CA, Grecco NM, Gutendorf SM, Hock CR, Hozza MJ, Hur S, In SM, Jackson DL, Jo SA, Jung SC, Kim S, Kimm K, Kloss EF, Koboldt DC, Kuebler JM, Kuo FS, Lathrop JA, Lee JK, Leis KL, Livingston SA, Lovins EG, Lundy ML, Maggan S, Minton M, Mockler MA, Morris DW, Nachtman EP, Oh B, Park C, Park CW, Pavelka N, Perkins AB, Restine SL, Sachidanandam R, Reinhart AJ, Scott KE, Shah GJ, Tate JM, Varde SA, Walters A, White JR, Yoo YK, Lee JE, Boyce-Jacino MT, Kwok PY. High-density single-nucleotide polymorphism maps of the human genome. Genomics 2005; 86:117-26. [PMID: 15961272 PMCID: PMC1885222 DOI: 10.1016/j.ygeno.2005.04.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2004] [Revised: 03/30/2005] [Accepted: 04/16/2005] [Indexed: 11/17/2022]
Abstract
Here we report a large, extensively characterized set of single-nucleotide polymorphisms (SNPs) covering the human genome. We determined the allele frequencies of 55,018 SNPs in African Americans, Asians (Japanese-Chinese), and European Americans as part of The SNP Consortium's Allele Frequency Project. A subset of 8333 SNPs was also characterized in Koreans. Because these SNPs were ascertained in the same way, the data set is particularly useful for modeling. Our results document that much genetic variation is shared among populations. For autosomes, some 44% of these SNPs have a minor allele frequency > or =10% in each population, and the average allele frequency differences between populations with different continental origins are less than 19%. However, the several percentage point allele frequency differences among the closely related Korean, Japanese, and Chinese populations suggest caution in using mixtures of well-established populations for case-control genetic studies of complex traits. We estimate that approximately 7% of these SNPs are private SNPs with minor allele frequencies <1%. A useful set of characterized SNPs with large allele frequency differences between populations (>60%) can be used for admixture studies. High-density maps of high-quality, characterized SNPs produced by this project are freely available.
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Affiliation(s)
| | | | - Inho Jo
- Department of Biomedical Sciences, National Institute of Health, Seoul, South Korea
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Soyoung Hur
- Department of Biomedical Sciences, National Institute of Health, Seoul, South Korea
| | | | | | - Sangmee Ahn Jo
- Department of Biomedical Sciences, National Institute of Health, Seoul, South Korea
| | - Sung-Chul Jung
- Department of Biomedical Sciences, National Institute of Health, Seoul, South Korea
| | - Sook Kim
- DNA Link, Inc., Seoul, South Korea
| | - Kuchan Kimm
- National Genome Research Institute, National Institute of Health, Seoul, South Korea
| | - Ellen F. Kloss
- Washington University, Division of Dermatology, St. Louis, MO, USA
| | | | | | | | | | - Jong-Keuk Lee
- National Genome Research Institute, National Institute of Health, Seoul, South Korea
| | | | | | | | | | - Sima Maggan
- Orchid BioSciences, Inc., Princeton, NJ, USA
| | - Matthew Minton
- Washington University, Division of Dermatology, St. Louis, MO, USA
| | | | | | | | - Bermseok Oh
- National Genome Research Institute, National Institute of Health, Seoul, South Korea
| | - Chan Park
- National Genome Research Institute, National Institute of Health, Seoul, South Korea
| | | | - Nicholas Pavelka
- Washington University, Division of Dermatology, St. Louis, MO, USA
| | | | | | | | | | | | | | | | | | - Amy Walters
- Orchid BioSciences, Inc., Princeton, NJ, USA
| | | | | | - Jong-Eun Lee
- DNA Link, Inc., Seoul, South Korea
- *Corresponding authors. Jong-Eun Lee is to be contacted at fax: +82 2 364 4778. Michael T. Boyce-Jacino, fax: +1 609 818 0054. Pui-Yan Kwok, fax: +1 415 476 2956. E-mail addresses: (J.-E. Lee), (M.T. Boyce-Jacinto), (P.-Y. Kwok)
| | - Michael T. Boyce-Jacino
- Orchid BioSciences, Inc., Princeton, NJ, USA
- *Corresponding authors. Jong-Eun Lee is to be contacted at fax: +82 2 364 4778. Michael T. Boyce-Jacino, fax: +1 609 818 0054. Pui-Yan Kwok, fax: +1 415 476 2956. E-mail addresses: (J.-E. Lee), (M.T. Boyce-Jacinto), (P.-Y. Kwok)
| | - Pui-Yan Kwok
- Washington University, Division of Dermatology, St. Louis, MO, USA
- *Corresponding authors. Jong-Eun Lee is to be contacted at fax: +82 2 364 4778. Michael T. Boyce-Jacino, fax: +1 609 818 0054. Pui-Yan Kwok, fax: +1 415 476 2956. E-mail addresses: (J.-E. Lee), (M.T. Boyce-Jacinto), (P.-Y. Kwok)
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