Demonstrating stratification in a European American population

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

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)868-872
Number of pages5
JournalNature genetics
Issue number8
StatePublished - Aug 1 2005
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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