On the Generalized Poisson Regression Mixture Model for Mapping Quantitative Trait Loci with Count Data

Statistical methods for mapping quantitative trait loci (QTL) have been extensively studied. While most existing methods assume normal distribution of the phenotype, the normality assumption could be easily violated when phenotypes are measured in counts. One natural choice to deal with count trait is to apply the classical Poisson regression model. However, conditional on covariates, the Poisson assumption of mean-variance equality may not be valid when data are potentially under- or over-dispersed. In this article, we propose an interval-mapping approach for phenotypes measured in counts. We model the effects of QTL through generalized Poisson regression model and develop efficient likelihood-based inference procedures. This approach, implemented with the EM algorithm, allows for a genome-wide scan for the existence of QTL throughout the entire genome. The performance of the proposed method is evaluated through extensive simulation studies along with comparisons with existing approaches such as the Poisson regression and the generalized estimating equation approach. An application to a rice tiller number dataset is given. Our approach provides a standard procedure for mapping QTL involved in the genetic control of complex traits measured in counts.

Key Words: EM algorithm, Generalized Poisson regression, Maximum likelihood, Mixture model, Quantitative trait loci

This article has been cited by other articles:

				C.-X. Ma, Q. Yu, A. Berg, D. Drost, E. Novaes, G. Fu, J. S. Yap, A. Tan, M. Kirst, Y. Cui, et al. A Statistical Model for Testing the Pleiotropic Control of Phenotypic Plasticity for a Count Trait Genetics, May 1, 2008; 179(1): 627 - 636. [Abstract] [Full Text] [PDF]

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