Cited by 876Genetic Associations and EpidemiologyForensic and Genetic ResearchGenetic diversity and population structure

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The effects of human population structure on large genetic association studies

Marchini, Jonathan, Cardon, Lon R, Phillips, Michael S, Donnelly, Peter·2004·Nature Genetics

DOI 10.1038/ng1337

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Abstract

Large-scale association studies hold substantial promise for unraveling the genetic basis of common human diseases. A well-known problem with such studies is the presence of undetected population structure, which can lead to both false positive results and failures to detect genuine associations. Here we examine approximately 15,000 genome-wide single-nucleotide polymorphisms typed in three population groups to assess the consequences of population structure on the coming generation of association studies. The consequences of population structure on association outcomes increase markedly with sample size. For the size of study needed to detect typical genetic effects in common diseases, even the modest levels of population structure within population groups cannot safely be ignored. We also examine one method for correcting for population structure (Genomic Control). Although it often performs well, it may not correct for structure if too few loci are used and may overcorrect in other settings, leading to substantial loss of power. The results of our analysis can guide the design of large-scale association studies.

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Authors: Marchini, J., Cardon, L. R., Phillips, M. S., & Donnelly, P.
Affiliations: University of Oxford (GB)
Centre for Human Genetics (GB)
McGill Genome Centre (CA)
Corresponding author: Donnelly, Peter
ORCID: Marchini, Jonathan
Donnelly, Peter
Venue: Nature Genetics
Publisher: Springer Science and Business Media LLC
Published: 2004-03-28
Volume: 36
Issue: 5
Pages: 512-517
ISSN: 1061-4036 (ISSN-L)
1546-1718
DOI: 10.1038/ng1337
OpenAlex: W1986265706
Cited by: 869
References: 31
Citations by year: 2026: 11 · 2025: 13 · 2024: 14 · 2023: 19 · 2022: 29 · 2021: 34 · 2020: 16 · 2019: 30 · 2018: 38 · 2017: 35 · 2016: 33 · 2015: 39 · 2014: 28 · 2013: 46 · 2012: 48
FWCI: 31.50
Type: journal article
Language: en
Open access: closed
Licence: www.springer.com/tdm (tdm)
Locations: Nature Genetics (publishedVersion)
PubMed (publishedVersion)
Funders: Wellcome Trust
National Institutes of Health
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Keywords: population structure, genetic association studies, single nucleotide polymorphisms, genomic control, false positives, statistical power, common diseases
MeSH terms: Genetic Markers, Genetics, Population, Humans, Models, Genetic, Genetic Variation, Linkage Disequilibrium, Quantitative Trait, Heritable, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide

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The effects of human population structure on large genetic association studies

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