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Algorithms 2009, 2(2), 667-691; doi:10.3390/a2020667

A Bayesian Algorithm for Functional Mapping of Dynamic Complex Traits

1, 2
1, 3, 4,*
1 Department of Statistics, University of Florida, Gainesville, FL 32611, USA 2 Genome Institute of Singapore, 60 Biopolis Street 02-01 Genome, Singapore 3 Department of Public Health Sciences, Pennsylvania State College of Medicine, Hershey, PA 17033, USA 4 Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA
* Author to whom correspondence should be addressed.
Received: 8 January 2009 / Revised: 6 March 2009 / Accepted: 24 March 2009 / Published: 21 April 2009
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
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Functional mapping of dynamic traits measured in a longitudinal study was originally derived within the maximum likelihood (ML) context and implemented with the EM algorithm. Although ML-based functional mapping possesses many favorable statistical properties in parameter estimation, it may be computationally intractable for analyzing longitudinal data with high dimensions and high measurement errors. In this article, we derive a general functional mapping framework for quantitative trait locus mapping of dynamic traits within the Bayesian paradigm. Markov chain Monte Carlo techniques were implemented for functional mapping to estimate biologically and statistically sensible parameters that model the structures of time-dependent genetic effects and covariance matrix. The Bayesian approach is useful to handle difficulties in constructing confidence intervals as well as the identifiability problem, enhancing the statistical inference of functional mapping. We have undertaken simulation studies to investigate the statistical behavior of Bayesian-based functional mapping and used a real example with F2 mice to validate the utilization and usefulness of the model.
Keywords: Bayesian; functional mapping; MCMC; Quantitative trait loci Bayesian; functional mapping; MCMC; Quantitative trait loci
This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Liu, T.; Wu, R. A Bayesian Algorithm for Functional Mapping of Dynamic Complex Traits. Algorithms 2009, 2, 667-691.

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