title: An Efficient Genome-Wide Multilocus Epistasis Search.
abstract: There has been a continuing interest in approaches that analyze pairwise locus-by-locus (epistasis) interactions using multilocus association models in genome-wide data sets. In this paper, we suggest an approach that uses sure independence screening to first lower the dimension of the problem by considering the marginal importance of each interaction term within the huge loop. Subsequent multilocus association steps are executed using an extended Bayesian least absolute shrinkage and selection operator (LASSO) model and fast generalized expectation-maximization estimation algorithms. The potential of this approach is illustrated and compared with PLINK software using data examples where phenotypes have been simulated conditionally on marker data from the Quantitative Trait Loci Mapping and Marker Assisted Selection (QTLMAS) Workshop 2008 and real pig data sets.
authors.affiliation: Department of Biology and Biocenter Oulu, University of Oulu, Oulu FIN-90014, Finland.
authors.forename: Hanni P
authors.initials: HP
authors.lastname: Kärkkäinen
authors.affiliation: Department of Biology and Biocenter Oulu, University of Oulu, Oulu FIN-90014, Finland Department of Mathematical Sciences, University of Oulu, Oulu FIN-90014, Finland.
authors.forename: Zitong
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Biology and Biocenter Oulu, University of Oulu, Oulu FIN-90014, Finland Department of Mathematical Sciences, University of Oulu, Oulu FIN-90014, Finland mjs@rolf.helsinki.fi.
authors.forename: Mikko J
authors.initials: MJ
authors.lastname: Sillanpää
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D004843:Epistasis, Genetic; D016678:Genome; D008957:Models, Genetic; D040641:Quantitative Trait Loci; D012984:Software; D013552:Swine / Q000235:genetics*
keywords: epistasis; extended Bayesian LASSO; genome-wide data; multilocus association model; sure independence screening