Demonstrating stratification in a European American population
Abstract
Population stratification occurs in case-control association studies when allele frequencies differ between cases and controls because of ancestry. Stratification may lead to false positive associations, although this issue remains controversial. Empirical studies have found little evidence of stratification in European-derived populations, but potentially significant levels of stratification could not be ruled out. We studied a European American panel discordant for height, a heritable trait that varies widely across Europe. Genotyping 178 SNPs and applying standard analytical methods yielded no evidence of stratification. But a SNP in the gene LCT that varies widely in frequency across Europe was strongly associated with height (P < 10(-6)). This apparent association was largely or completely due to stratification; rematching individuals on the basis of European ancestry greatly reduced the apparent association, and no association was observed in Polish or Scandinavian individuals. The failure of standard methods to detect this stratification indicates that new methods may be required.
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The false positive association between the LCT locus and skin pigmentation mirrors the false positive association found between the LCT locus and height.
“This false positive association between the LCT locus and skin pigmentation mirrors the false positive association found between the LCT locus and height [31], [32].”
From Genome-Wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations (2012) · cites this paper as [31]
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- Authors
- Campbell, C. D., Ogburn, E. L., Lunetta, K. L., Lyon, H. N., Freedman, M. L., Groop, L. C., Altshuler, D., Ardlie, K. G., & Hirschhorn, J. N.
- Affiliations
- Boston Children's Hospital (US)
- Boston University (US)
- Broad Institute (US)
- Lund University (SE)
- Corresponding author
- Hirschhorn, Joel N
- ORCID
- Venue
- Nature Genetics
- Published
- 2005-07-24
- Volume
- 37
- Issue
- 8
- Pages
- 868-872
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W2047923046
- Cited by
- 444
- References
- 31
- Citations by year
- 2026: 1 · 2025: 5 · 2024: 4 · 2023: 5 · 2022: 7 · 2021: 16 · 2020: 13 · 2019: 11 · 2018: 20 · 2017: 18 · 2016: 16 · 2015: 17 · 2014: 18 · 2013: 23 · 2012: 24
- FWCI
- 26.96
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Lund University Publications (Lund University) (submittedVersion)
- 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 › Race, Genetics, and Society
- Keywords
- population stratification, European Americans, height, LCT gene, lactase persistence, false positive association, case-control association, SNP genotyping, European ancestry
- MeSH terms
- Genetics, Population, Genotype, Humans, Polymorphism, Single Nucleotide, White People
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