Genetics, Vol. 164, 1129-1138, July 2003, Copyright © 2003

Stochastic Search Variable Selection for Identifying Multiple Quantitative Trait Loci

Nengjun Yia,b, Varghese Georgea,b, and David B. Allisona,b,c
a Department of Biostatistics, University of Alabama, Birmingham, Alabama 35294-0022
b Section on Statistical Genetics, University of Alabama, Birmingham, Alabama 35294-0022
c Clinical Nutrition Research Center, University of Alabama, Birmingham, Alabama 35294-0022

Corresponding author: Nengjun Yi, Ryals Public Health Bldg., 1665 University Blvd., University of Alabama, Birmingham, AL 35294-0022., nyi{at}ms.soph.uab.edu (E-mail)

Communicating editor: J. B. WALSH

In this article, we utilize stochastic search variable selection methodology to develop a Bayesian method for identifying multiple quantitative trait loci (QTL) for complex traits in experimental designs. The proposed procedure entails embedding multiple regression in a hierarchical normal mixture model, where latent indicators for all markers are used to identify the multiple markers. The markers with significant effects can be identified as those with higher posterior probability included in the model. A simple and easy-to-use Gibbs sampler is employed to generate samples from the joint posterior distribution of all unknowns including the latent indicators, genetic effects for all markers, and other model parameters. The proposed method was evaluated using simulated data and illustrated using a real data set. The results demonstrate that the proposed method works well under typical situations of most QTL studies in terms of number of markers and marker density.




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