title: QTLRel: an R package for genome-wide association studies in which relatedness is a concern.
abstract: BACKGROUND
  Existing software for quantitative trait mapping is either not able to model polygenic variation or does not allow incorporation of more than one genetic variance component. Improperly modeling the genetic relatedness among subjects can result in excessive false positives. We have developed an R package, QTLRel, to enable more flexible modeling of genetic relatedness as well as covariates and non-genetic variance components.
  
  
  RESULTS
  We have successfully used the package to analyze many datasets, including F₃₄ body weight data that contains 688 individuals genotyped at 3105 SNP markers and identified 11 QTL. It took 295 seconds to estimate variance components and 70 seconds to perform the genome scan on an Linux machine equipped with a 2.40GHz Intel(R) Core(TM)2 Quad CPU.
  
  
  CONCLUSIONS
  QTLRel provides a toolkit for genome-wide association studies that is capable of calculating genetic incidence matrices from pedigrees, estimating variance components, performing genome scans, incorporating interactive covariates and genetic and non-genetic variance components, as well as other functionalities such as multiple-QTL mapping and genome-wide epistasis.
authors.affiliation: Department of Human Genetics, The University of Chicago, IL 60637, USA.
authors.forename: Riyan
authors.initials: R
authors.lastname: Cheng
authors.forename: Mark
authors.initials: M
authors.lastname: Abney
authors.forename: Abraham A
authors.initials: AA
authors.lastname: Palmer
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Skol
mesh_terms: D014644:Genetic Variation; D055106:Genome-Wide Association Study; D006801:Humans; D015233:Models, Statistical; D010375:Pedigree; D040641:Quantitative Trait Loci; D012984:Software