Heterogeneity in terms of tumor characteristics, prognosis, and survival among cancer patients has been a persistent problem for many decades. Currently, prognosis and outcome predictions are made based on clinical factors and/or by incorporating molecular profiling data. However, inaccurate prognosis and prediction may result by using only clinical or molecular information directly. One of the main shortcomings of past studies is the failure to incorporate prior biological information into the

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... predictive model, given strong evidence of pathway-based genetic nature of cancer, i.e. the potential for oncogenes to be grouped into pathways based on biological functions such as cell survival, proliferation and metastatic dissemination. To address this problem, we propose a two-stage procedure to incorporate pathway information into the prognostic modeling using large-scale gene expression data. In the first stage, we fit all predictors within each pathway using penalized Cox model (Lasso, Ridge and Elastic Net) and Bayesian hierarchical Cox model. In the second stage, we combine the cross-validated prognostic scores of all pathways obtained in the first stage as new predictors to build an integrated prognostic model for prediction. We apply the proposed method to analyze breast cancer data from The Cancer Genome Atlas (TCGA), predicting overall survival using clinical data and gene expression profiling. The data includes ~20000 genes mapped into 109 pathways for 505 patients. The results show that the proposed approach not only improves survival prediction compared with the alternative analysis that ignores the pathway information, but also identifies significant biological pathways.