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Bioinformatics 2007 23(13):i569-i576; doi:10.1093/bioinformatics/btm164
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Semiparametric functional mapping of quantitative trait loci governing long-term HIV dynamics

Song Wu , Jie Yang and Rongling Wu *

Department of Statistics, University of Florida, Gainesville, FL 32611, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Functional mapping has proven to be powerful for characterizing quantitative trait loci (QTL) that control complex dynamic traits. More recently, functional mapping has been extended to identify the host QTL responsible for HIV dynamics by incorporating a parametric bi-exponential function for earlier stages of viral load trajectories. However, existing functional mapping cannot be used to map long-term HIV dynamics because no mathematical functions are available for later stages of HIV dynamic changes.

Results: We derived a statistical model for functional mapping of dynamic QTL through characterizing HIV load trajectories during a long-term period semiparametrically. The new model was constructed within the maximum likelihood framework and implemented with the EM-simplex algorithm. It allows for the test of differences in the genetic control of short- and long-term HIV dynamics and the characterization of the effects of viral-host genome interaction. Extensive simulation studies have been performed to test the statistical behavior of this model. The new model will provide an important tool for genetic and genomic studies of human complex diseases like HIV/AIDS and their pathological progression.

Availability: Available on request from the corresponding author.

Contact: rwu{at}stat.ufl.edu


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