Integration of Cancer Genomics Data for Tree‐based Dimensionality Reduction and Cancer Outcome Prediction

Abstract Accurate outcome prediction is crucial for precision medicine and personalized treatment of cancer. Researchers have found that multi‐dimensional cancer omics studies outperform each data type (mRNA, microRNA, methylation or somatic copy number alteration) study in human disease research. Existing methods leveraging multiple level of molecular data often suffer from various limitations, e. g ., heterogeneity, poor robustness or loss of generality. To overcome these limitations, we presented the tree‐based dimensionality reduction approach for the identification of smooth tree graph and developed accurate predictive model for clinical outcome prediction. We demonstrated that 1) Discriminative Dimensionality Reduction via learning a Tree (DDRTree) achieved reduced dimension space tree with statistical significance; 2) Tree based support vector machine (SVM) classifier improved prediction performance of cancer recurrence as compared to t ‐test based SVM classifier; 3) Tree based SVM classifier was robust with regard to the different number of multi‐markers; 4) Combining multiple omics data improved prediction performance of cancer recurrence as compared to a single‐omics data; and 5) Tree based SVM classifier achieved similar or better prediction performance when compared to the features from state‐of‐the‐art feature selection methods. Our results demonstrated great potential of the tree‐based dimensionality reduction approach based clinical outcome prediction.