Bayes factors for detection of quantitative trait loci

Genetics, Selection, Evolution : GSE
L VaronaM Pérez-Enciso

Abstract

A fundamental issue in quantitative trait locus (QTL) mapping is to determine the plausibility of the presence of a QTL at a given genome location. Bayesian analysis offers an attractive way of testing alternative models (here, QTL vs. no-QTL) via the Bayes factor. There have been several numerical approaches to computing the Bayes factor, mostly based on Markov Chain Monte Carlo (MCMC), but these strategies are subject to numerical or stability problems. We propose a simple and stable approach to calculating the Bayes factor between nested models. The procedure is based on a reparameterization of a variance component model in terms of intra-class correlation. The Bayes factor can then be easily calculated from the output of a MCMC scheme by averaging conditional densities at the null intra-class correlation. We studied the performance of the method using simulation. We applied this approach to QTL analysis in an outbred population. We also compared it with the Likelihood Ratio Test and we analyzed its stability. Simulation results were very similar to the simulated parameters. The posterior probability of the QTL model increases as the QTL effect does. The location of the QTL was also correctly obtained. The use of meta-analys...Continue Reading

Citations

Feb 1, 2008·Animal : an International Journal of Animal Bioscience·J CasellasM C Rodríguez
Jan 18, 2006·Bioinformatics·M Pérez-Enciso
Oct 8, 2009·Genetics, Selection, Evolution : GSE·Yoshitaka NagamineChris S Haley
Mar 1, 2012·Genetics·Joaquim CasellasJuan F Medrano
Sep 13, 2006·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·J Casellas, J Piedrafita
Oct 2, 2014·Genetics·Joaquim CasellasMarcel Amills
Apr 27, 2010·Journal of Animal Science·J CasellasR Quintanilla
Dec 22, 2009·Journal of Animal Science·J CasellasJ Piedrafita
Nov 24, 2012·Animal : an International Journal of Animal Bioscience·J CasellasJ L Noguera
Sep 16, 2008·Journal of Animal Science·J CasellasL Varona
Aug 20, 2015·Genetics, Selection, Evolution : GSE·Raphael B CostaLucia G Albuquerque
Jan 12, 2010·Journal of Dairy Science·J P SánchezL F de la Fuente
Jan 16, 2010·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Luis Varona
Sep 29, 2011·Journal of Animal Science·A CecchinatoG Bittante
Aug 16, 2019·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Thaise Pinto de MeloRoberto Carvalheiro
Jun 5, 2002·Trends in Genetics : TIG·Mikko J Sillanpää, Jukka Corander

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