Single-Nucleotide Polymorphism Data Support the General Unrelatedness of the Males in the Agricultural Health Study

J. R. Jack, A. A. Motsinger-Reif, S. Koutros, M. C. Alavanja, L. E. Beane Freeman, J. A. Hoppin
2014 Cancer Epidemiology, Biomarkers and Prevention  
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
more » ... tedness 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.
doi:10.1158/1055-9965.epi-14-0276 pmid:25047895 fatcat:utiwkq3d7zbrrk3yd4a3vukjxi