Sensitive detection of chromosomal segments of distinct ancestry in admixed populations
Open accessAbstract
Identifying the ancestry of chromosomal segments of distinct ancestry has a wide range of applications from disease mapping to learning about history. Most methods require the use of unlinked markers; but, using all markers from genome-wide scanning arrays, it should in principle be possible to infer the ancestry of even very small segments with exquisite accuracy. We describe a method, HAPMIX, which employs an explicit population genetic model to perform such local ancestry inference based on fine-scale variation data. We show that HAPMIX outperforms other methods, and we explore its utility for inferring ancestry, learning about ancestral populations, and inferring dates of admixture. We validate the method empirically by applying it to populations that have experienced recent and ancient admixture: 935 African Americans from the United States and 29 Mozabites from North Africa. HAPMIX will be of particular utility for mapping disease genes in recently admixed populations, as its accurate estimates of local ancestry permit admixture and case-control association signals to be combined, enabling more powerful tests of association than with either signal alone.
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In simulation studies, the ARHMM achieves comparable accuracy as HapMix, but is more flexible and does not require information about the recombination rate.
“In simulation studies, the ARHMM achieves comparable accuracy as HapMix [49], but is more flexible and does not require information about the recombination rate.”
From Genetic Architecture of Skin and Eye Color in an African-European Admixed Population (2013) · cites this paper as [49]
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- Authors
- Price, A. L., Tandon, A., Patterson, N., Barnes, K. C., Rafaels, N., Ruczinski, I., Beaty, T. H., Mathias, R., Reich, D., & Myers, S.
- Affiliations
- Broad Institute (US)
- Johns Hopkins University (US)
- National Institutes of Health (US)
- Corresponding author
- Reich, David
- Myers, Simon
- ORCID
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2009-06-19
- Volume
- 5
- Issue
- 6
- Pages
- e1000519
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC2689842
- OpenAlex
- W2064902628
- Cited by
- 539
- References
- 28
- Citations by year
- 2026: 13 · 2025: 15 · 2024: 16 · 2023: 20 · 2022: 19 · 2021: 18 · 2020: 36 · 2019: 33 · 2018: 33 · 2017: 38 · 2016: 36 · 2015: 42 · 2014: 45 · 2013: 55 · 2012: 62
- FWCI
- 23.27
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Genetics (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- National Institutes of Health
- National Heart, Lung, and Blood Institute (R01HL087699)
- National Human Genome Research Institute (U01HG004168)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- local ancestry inference, admixture, population genetic models, African Americans, Mozabites, disease mapping, case-control association, ancestral populations
- MeSH terms
- Black or African American, Chromosomes, Human, Disease, Genetics, Population, Humans, Models, Genetic, Software, Evolution, Molecular, Black People
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