The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Population Stratification of a Common APOBEC Gene Deletion Polymorphism
Open accessAbstract
The APOBEC3 gene family plays a role in innate cellular immunity inhibiting retroviral infection, hepatitis B virus propagation, and the retrotransposition of endogenous elements. We present a detailed sequence and population genetic analysis of a 29.5-kb common human deletion polymorphism that removes the APOBEC3B gene. We developed a PCR-based genotyping assay, characterized 1,277 human diversity samples, and found that the frequency of the deletion allele varies significantly among major continental groups (global FST = 0.2843). The deletion is rare in Africans and Europeans (frequency of 0.9% and 6%), more common in East Asians and Amerindians (36.9% and 57.7%), and almost fixed in Oceanic populations (92.9%). Despite a worldwide frequency of 22.5%, analysis of data from the International HapMap Project reveals that no single existing tag single nucleotide polymorphism may serve as a surrogate for the deletion variant, emphasizing that without careful analysis its phenotypic impact may be overlooked in association studies. Application of haplotype-based tests for selection revealed potential pitfalls in the direct application of existing methods to the analysis of genomic structural variation. These data emphasize the importance of directly genotyping structural variation in association studies and of accurately resolving variant breakpoints before proceeding with more detailed population-genetic analysis.
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Cites
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The Structure of Haplotype Blocks in the Human Genome
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Detection of large-scale variation in the human genome
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Detecting recent positive selection in the human genome from haplotype structure
Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z. P., Richter, D. J., Schaffner, S. F., Gabriel, S. B., Platko, J. V., Patterson, N. J., McDonald, G. J., et al. (2002) · Nature · doi:10.1038/nature01140 · Cited by 2,106
Common deletion polymorphisms in the human genome
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., et al. (2006) · Nature Genetics · doi:10.1038/ng1696 · Cited by 701
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Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G
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When Less Is More: Gene Loss as an Engine of Evolutionary Change
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Common deletions and SNPs are in linkage disequilibrium in the human genome
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Integrated detection and population-genetic analysis of SNPs and copy number variation
McCarroll, S. A., Kuruvilla, F. G., Korn, J. M., Cawley, S., Nemesh, J., Wysoker, A., Shapero, M. H., de Bakker, P. I. W., Maller, J. B., Kirby, A., et al. (2008) · Nature Genetics · doi:10.1038/ng.238 · Cited by 936
LINE-1 elements in structural variation and disease
Beck, C. R., Garcia-Perez, J. L., Badge, R. M., & Moran, J. V. (2011) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082509-141802 · Cited by 615
Harris, R. S., & Dudley, J. P. (2015) · Virology · doi:10.1016/j.virol.2015.03.012 · Cited by 551
Rules of engagement: molecular insights from host–virus arms races
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Metadata
- Authors
- Kidd, J. M., Newman, T. L., Tuzun, E., Kaul, R., & Eichler, E. E.
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2007-04-20
- Volume
- 3
- Issue
- 4
- Pages
- e63
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- OpenAlex
- W2027613370
- Cited by
- 249
- References
- 10
- FWCI
- 8.37
- Type
- journal article
- Language
- en
- Open access
- gold
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