Efficient Bayesian approach for multilocus association mapping including gene-gene interactions

BMC Bioinformatics

Methodology Article

Pekka Marttinen¹  Jukka Corander² 

[1] Department of Biomedical Engineering and Computational Science, Helsinki University of Technology, FI-02015, Finland;Department of Mathematics and Statistics, University of Helsinki, FI-00014, Finland;Department of Mathematics, Åbo Akademi University, FI-20500, Finland;

关键词: Receiver Operating Characteristic Curve;    Minor Allele Frequency;    Marginal Likelihood;    Markov Chain Monte Carlo Algorithm;    Bayesian Model Average;   

DOI  :  10.1186/1471-2105-11-443

 received in 2009-10-08, accepted in 2010-09-02,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundSince the introduction of large-scale genotyping methods that can be utilized in genome-wide association (GWA) studies for deciphering complex diseases, statistical genetics has been posed with a tremendous challenge of how to most appropriately analyze such data. A plethora of advanced model-based methods for genetic mapping of traits has been available for more than 10 years in animal and plant breeding. However, most such methods are computationally intractable in the context of genome-wide studies. Therefore, it is hardly surprising that GWA analyses have in practice been dominated by simple statistical tests concerned with a single marker locus at a time, while the more advanced approaches have appeared only relatively recently in the biomedical and statistical literature.ResultsWe introduce a novel Bayesian modeling framework for association mapping which enables the detection of multiple loci and their interactions that influence a dichotomous phenotype of interest. The method is shown to perform well in a simulation study when compared to widely used standard alternatives and its computational complexity is typically considerably smaller than that of a maximum likelihood based approach. We also discuss in detail the sensitivity of the Bayesian inferences with respect to the choice of prior distributions in the GWA context.ConclusionsOur results show that the Bayesian model averaging approach which explicitly considers gene-gene interactions may improve the detection of disease associated genetic markers in two respects: first, by providing better estimates of the locations of the causal loci; second, by reducing the number of false positives. The benefits are most apparent when the interacting genes exhibit no main effects. However, our findings also illustrate that such an approach is somewhat sensitive to the prior distribution assigned on the model structure.

【 授权许可】

CC BY   
© Marttinen and Corander; licensee BioMed Central Ltd. 2010