Measuring and using admixture to study the genetics of complex diseases
Open accessAbstract
Admixture is an important evolutionary force that can and should be used in efforts to apply genomic data and technology to the study of complex disease genetics. Admixture linkage disequilibrium (ALD) is created by the process of admixture and, in recently admixed populations, extends for substantial distances (of the order of 10 to 20 cM). The amount of ALD generated depends on the level of admixture, ancestry information content of markers and the admixture dynamics of the population, and thus influences admixture mapping (AM). The authors discuss different models of admixture and how these can have an impact on the success of AM studies. Selection of markers is important, since markers informative for parental population ancestry are required and these are uncommon. Rarely does the process of admixture result in a population that is uniform for individual admixture levels, but instead there is substantial population stratification. This stratification can be understood as variation in individual admixtures and can be both a source of statistical power for ancestry--phenotype correlation studies as well as a confounder in causing false-positives in gene association studies. Methods to detect and control for stratification in case/control and AM studies are reviewed, along with recent studies showing individual ancestry--phenotype correlations. Using skin pigmentation as a model phenotype, implications of AM in complex disease gene mapping studies are discussed. Finally, the article discusses some limitations of this approach that should be considered when designing an effective AM study.
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Global ancestry was included as a covariate to correct for ancestry stratification and any environmental variables that might covary with ancestry.
“Global ancestry, calculated from the mean of local ancestry across all SNPs, was included as a covariate to correct for ancestry stratification and any environmental variables that might covary with ancestry [16,72].”
From Investigating the case of human nose shape and climate adaptation (2017) · cites this paper as [72]
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- Authors
- Halder, I., & Shriver, M. D.
- Affiliations
- Pennsylvania State University (US)
- Corresponding author
- Shriver, Mark D
- ORCID
- Shriver, Mark D
- Venue
- Human Genomics
- Published
- 2003
- Volume
- 1
- Issue
- 1
- Pages
- 52
- ISSN
- 1473-9542 (ISSN-L)
- 1479-7364
- PMC
- PMC3525000
- OpenAlex
- W2122294028
- Cited by
- 93
- References
- 82
- Citations by year
- 2025: 3 · 2024: 3 · 2022: 1 · 2021: 1 · 2020: 2 · 2019: 1 · 2018: 2 · 2017: 3 · 2016: 2 · 2015: 2 · 2014: 1 · 2013: 3 · 2012: 6
- FWCI
- 4.42
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Human Genomics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (R01HG002154, HG-02154)
- National Institute of Diabetes and Digestive and Kidney Diseases (DK53958, R01DK053958)
- 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 › Race, Genetics, and Society
- Keywords
- admixture, admixture mapping, complex disease genetics, population stratification, ancestry informative markers, genetic association studies, skin pigmentation
- MeSH terms
- Alleles, Black or African American, Chromosome Mapping, Ethnicity, Forecasting, Genetic Markers, Genetics, Population, Hispanic or Latino, Humans, Indians, North American, Models, Genetic, Population Dynamics, Skin Pigmentation, United States, Genetic Variation, Linkage Disequilibrium, Case-Control Studies, Genetic Diseases, Inborn, Black People, White People, Asian People
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