Originally published as Genetics Published Articles Ahead of Print on March 2, 2009.

Genetics, Vol. 182, 337-342, May 2009, Copyright © 2009
doi:10.1534/genetics.108.099028

Multiple-Interval Mapping for Quantitative Trait Loci With a Spike in the Trait Distribution

Wenyun Li^* and Zehua Chen^,1

^* School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People's Republic of China 510275 and Department of Statistics and Applied Probability, National University of Singapore, Singapore 117546

¹ Corresponding author: Department of Statistics and Applied Probability, National University of Singapore, 3 Science Dr. 2, Singapore 117546.
E-mail: stachenz{at}nus.edu.sg

For phenotypic distributions where many individuals share a common value—such as survival time following a pathogenic infection—a spike occurs at that common value. This spike affects quantitative trait loci (QTL) mapping methodologies and causes standard approaches to perform suboptimally. In this article, we develop a multiple-interval mapping (MIM) procedure based on mixture generalized linear models (GLIMs). An extended Bayesian information criterion (EBIC) is used for model selection. To demonstrate its utility, this new approach is compared to single-QTL models that appropriately handle the phenotypic distribution. The method is applied to data from Listeria infection as well as data from simulation studies. Compared to the single-QTL model, the findings demonstrate that the MIM procedure greatly improves the efficiency in terms of positive selection rate and false discovery rate. The method developed has been implemented using functions in R and is freely available to download and use.

International Access Link

Online ISSN: 1943-2361  Print ISSN: 0016-6731
Copyright 2009 by the Genetics Society of America
phone: 412-268-1812   fax: 412-268-1813   email: genetics-gsa{at}andrew.cmu.edu