Accurate Prediction of Cancer Prognosis by Exploiting Patient-Specific Cancer Driver Genes

Abstract

Accurate prediction of the prognoses of cancer patients and identification of prognostic biomarkers are both important for the improved treatment of cancer patients, in addition to enhanced anticancer drugs. Many previous bioinformatic studies have been carried out to achieve this goal; however, there remains room for improvement in terms of accuracy. In this study, we demonstrated that patient-specific cancer driver genes could be used to predict cancer prognoses more accurately. To identify patient-specific cancer driver genes, we first generated patient-specific gene networks before using modified PageRank to generate feature vectors that represented the impacts genes had on the patient-specific gene network. Subsequently, the feature vectors of the good and poor prognosis groups were used to train the deep feedforward network. For the 11 cancer types in the TCGA data, the proposed method showed a significantly better prediction performance than the existing state-of-the-art methods for three cancer types (BRCA, CESC and PAAD), better performance for five cancer types (COAD, ESCA, HNSC, KIRC and STAD), and a similar or slightly worse performance for the remaining three cancer types (BLCA, LIHC and LUAD). Furthermore, the case study for the identified breast cancer and cervical squamous cell carcinoma prognostic genes and their subnetworks included several pathways associated with the progression of breast cancer and cervical squamous cell carcinoma. These results suggested that heterogeneous cancer driver information may be associated with cancer prognosis.