title: Single-nucleotide polymorphism data support the general unrelatedness of the males in the agricultural health study.
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.
  
  
  CONCLUSIONS
  These findings are important for all subsequent analyses of gene-environment interactions in the AHS.
authors.affiliation: Department of Statistics, Bioinformatics Research Center, Center for Human Health and the Environment, Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina. jrjack@ncsu.edu.
authors.forename: John R
authors.initials: JR
authors.lastname: Jack
authors.affiliation: Department of Statistics, Bioinformatics Research Center, Center for Human Health and the Environment, Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina.
authors.forename: Alison A
authors.initials: AA
authors.lastname: Motsinger-Reif
authors.affiliation: Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, NIH, Bethesda, Maryland.
authors.forename: Stella
authors.initials: S
authors.lastname: Koutros
authors.affiliation: Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, NIH, Bethesda, Maryland.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Alavanja
authors.affiliation: Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, NIH, Bethesda, Maryland.
authors.forename: Laura E
authors.initials: LE
authors.lastname: Beane Freeman
authors.affiliation: Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina.
authors.forename: Jane A
authors.initials: JA
authors.lastname: Hoppin
mesh_terms: D000383:Agriculture; D016022:Case-Control Studies; D015331:Cohort Studies; D003241:Consanguinity; D059647:Gene-Environment Interaction; D006801:Humans; D008297:Male; D016273:Occupational Exposure; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D012107:Research Design