A Unified Markov Chain Monte Carlo Framework for Mapping Multiple Quantitative Trait Loci.pdfVIP

Copyright ? 2004 by the Genetics Society of America DOI: 10.1534/genetics.104.026286 A Uni?ed Markov Chain Monte Carlo Framework for Mapping Multiple Quantitative Trait Loci Nengjun Yi1 Section on Statistical Genetics, Department of Biostatistics, University of Alabama, Birmingham, Alabama 35294-0022 Manuscript received January 6, 2004 Accepted for publication February 25, 2004 ABSTRACT In this article, a uni?ed Markov chain Monte Carlo MCMC framework is proposed to identify multiple quantitative trait loci QTL for complex traits in experimental designs, based on a composite space representation of the problem that has ?xed dimension. The proposed uni?ed approach includes the existing Bayesian QTL mapping methods using reversible jump MCMC algorithm as special cases. We also show that a variety of Bayesian variable selection methods using Gibbs sampling can be applied to the composite model space for mapping multiple QTL. The uni?ed framework not only results in some new algorithms, but also gives useful insight into some of the important factors governing the performance of Gibbs sampling and reversible jump for mapping multiple QTL. Finally, we develop strategies to improve the performance of MCMC algorithms. ANY complex traits are controlled by multiple eral and widely applicable technique Green 1995, M genetic [quantitative trait loci QTL ] and envi- 2003 . It appears to be suited for implementing model ronmental factors. Mapping QTL is the process of esti- selection procedures across a wide range of possible mating the number of QTL, their genomic positions, genetic architectures. However, this ?exible method has and genetic effects conditional on the observed pheno- been deemed somewhat “dif?cult” to understand, cum- typic data and marker data. This is essentially a problem bersome to conduct, and dif?cult to tune. It also has of model selection e.g., Broman and Speed 2002; Sil- bee