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Demonstrating stratification in a European American population

Campbell, Catarina D, Ogburn, Elizabeth L, Lunetta, Kathryn L, Lyon, Helen N, Freedman, Matthew L, Groop, Leif C, Altshuler, David, Ardlie, Kristin G, Hirschhorn, Joel N·2005·Nature Genetics

DOI 10.1038/ng1607

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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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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: Campbell, Catarina D
Ogburn, Elizabeth L
Lunetta, Kathryn L
Freedman, Matthew L
Groop, Leif C
Altshuler, David
Ardlie, Kristin G
Hirschhorn, Joel N
Venue: Nature Genetics
Publisher: Springer Science and Business Media LLC
Published: 2005-07-24
Volume: 37
Issue: 8
Pages: 868-872
ISSN: 1061-4036 (ISSN-L)
1546-1718
DOI: 10.1038/ng1607
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
Social Sciences › Anthropology › 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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Demonstrating stratification in a European American population

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