title: A decision rule for quantitative trait locus detection under the extended Bayesian LASSO model.
abstract: Bayesian shrinkage analysis is arguably the state-of-the-art technique for large-scale multiple quantitative trait locus (QTL) mapping. However, when the shrinkage model does not involve indicator variables for marker inclusion, QTL detection remains heavily dependent on significance thresholds derived from phenotype permutation under the null hypothesis of no phenotype-to-genotype association. This approach is computationally intensive and more importantly, the hypothetical data generation at the heart of the permutation-based method violates the Bayesian philosophy. Here we propose a fully Bayesian decision rule for QTL detection under the recently introduced extended Bayesian LASSO for QTL mapping. Our new decision rule is free of any hypothetical data generation and relies on the well-established Bayes factors for evaluating the evidence for QTL presence at any locus. Simulation results demonstrate the remarkable performance of our decision rule. An application to real-world data is considered as well.
authors.affiliation: Department of Mathematics and Statistics, University of Helsinki, FIN-00014 Helsinki, Finland.
authors.forename: Crispin M
authors.initials: CM
authors.lastname: Mutshinda
authors.forename: Mikko J
authors.initials: MJ
authors.lastname: Sillanpää
mesh_terms: D001499:Bayes Theorem; D002874:Chromosome Mapping / Q000379:methods; D003198:Computer Simulation; D056726:Genetic Association Studies; D005819:Genetic Markers; D001467:Hordeum / Q000235:genetics; D008957:Models, Genetic; D010641:Phenotype; D040641:Quantitative Trait Loci
chemical_list: D005819:Genetic Markers