Survival prediction using gene expression data: A review and comparison
Computational Statistics & Data Analysis
Inference of an oscillating model for the yeast cell cycle
Discrete Applied Mathematics
Bayesian inference of gene regulatory networks using gene expression time series data
BIRD'07 Proceedings of the 1st international conference on Bioinformatics research and development
BIRD'07 Proceedings of the 1st international conference on Bioinformatics research and development
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Motivation: DNA microarrays allow the simultaneous measurement of thousands of gene expression levels in any given patient sample. Gene expression data have been shown to correlate with survival in several cancers, however, analysis of the data is difficult, since typically at most a few hundred patients are available, resulting in severely underdetermined regression or classification models. Several approaches exist to classify patients in different risk classes, however, relatively little has been done with respect to the prediction of actual survival times. We introduce CASPAR, a novel method to predict true survival times for the individual patient based on microarray measurements. CASPAR is based on a multivariate Cox regression model that is embedded in a Bayesian framework. A hierarchical prior distribution on the regression parameters is specifically designed to deal with high dimensionality (large number of genes) and low sample size settings, that are typical for microarray measurements. This enables CASPAR to automatically select small, most informative subsets of genes for prediction. Results: Validity of the method is demonstrated on two publicly available datasets on diffuse large B-cell lymphoma (DLBCL) and on adenocarcinoma of the lung. The method successfully identifies long and short survivors, with high sensitivity and specificity. We compare our method with two alternative methods from the literature, demonstrating superior results of our approach. In addition, we show that CASPAR can further refine predictions made using clinical scoring systems such as the International Prognostic Index (IPI) for DLBCL and clinical staging for lung cancer, thus providing an additional tool for the clinician. An analysis of the genes identified confirms previously published results, and furthermore, new candidate genes correlated with survival are identified. Availability: The software is available upon request from the authors. Contact: kaderali@zpr.uni-koeln.de Supplementary information: http://www.zaik.uni-koeln.de/bioinformatik/caspar.html