Cox proportional hazards survival regression in haplotype-based association analysis using the Stochastic-EM algorithm.
It is now widely recognized that haplotype information inferred from genotypes can be of great interest to better characterize the role of a candidate gene in the etiology of a complex trait in the context of association studies. Several works have recently advocated the simultaneous estimation of haplotype frequencies and haplotype effects in order to get a better efficiency in parameter estimation. Most of the available models can deal with a binary or a quantitative phenotype, but none has yet discussed the application of haplotype-based association analysis to a survival outcome. We describe how the recently proposed Stochastic-EM (SEM) algorithm can be applied to estimate haplotype effects in censored data analysis using a standard Cox proportional hazards formulation. This model has been implemented in the THESIAS software freely available at http://www.genecanvas.org.
Tregouet
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INSERM U525, 75634 Paris, France. david.tregouet@chups.jussieu.fr
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D000465:Algorithms; D006239:Haplotypes; D006801:Humans; D016016:Proportional Hazards Models; D012044:Regression Analysis; D016019:Survival Analysis