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Title: Single-nucleotide polymorphism data support the general unrelatedness of the males in the agricultural health study.
Authors: Jack JR,  Motsinger-Reif AA,  Koutros S,  Alavanja MC,  Beane Freeman LE,  Hoppin JA
Journal: Cancer Epidemiol Biomarkers Prev
Date: 2014 Oct
Branches: OEEB
PubMed ID: 25047895
PMC ID: not available
Abstract: 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.