Single-nucleotide polymorphism data support the general unrelatedness of the males in the agricultural health study

Cancer Epidemiol Biomarkers Prev. 2014 Oct;23(10):2192-5. doi: 10.1158/1055-9965.EPI-14-0276. Epub 2014 Jul 21.


Background: Farming is often a family and multigenerational business. Relatedness among farmers could bias gene-environment interaction analysis. To evaluate the potential relatedness of farmers, we used data from a nested case-control study of prostate cancer conducted in the Agricultural Health Study (AHS), a prospective study of farmers in Iowa and North Carolina.

Methods: We analyzed the genetic data for 25,009 SNPs (single-nucleotide polymorphisms) from 2,220 White participants to test for cryptic relatedness among these farmers. We used two software packages: (i) PLINK, to calculate inbreeding coefficients and identity-by-descent (IBD) statistics and (ii) EIGENSOFT, to perform a principal component analysis on the genetic data.

Results: Inbreeding coefficients estimates and IBD statistics show that the subjects are overwhelmingly unrelated, with little potential for cryptic relatedness in these data.

Conclusions: Our analysis rejects the hypothesis that individuals in the case-control study exhibit cryptic relatedness.

Impact: These findings are important for all subsequent analyses of gene-environment interactions in the AHS.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural

MeSH terms

  • Agriculture*
  • Case-Control Studies*
  • Cohort Studies
  • Consanguinity*
  • Gene-Environment Interaction*
  • Humans
  • Male
  • Occupational Exposure
  • Polymorphism, Single Nucleotide
  • Principal Component Analysis
  • Research Design