Predicting overall survival of patients with hepatocellular carcinoma using a three-category method based on DNA methylation and machine learning.

Journal: Journal of cellular and molecular medicine
Published Date: Feb 19, 2019

Abstract

Hepatocellular carcinoma (HCC) is closely associated with abnormal DNA methylation. In this study, we analyzed 450K methylation chip data from 377 HCC samples and 50 adjacent normal samples in the TCGA database. We screened 47,099 differentially methylated sites using Cox regression as well as SVM-RFE and FW-SVM algorithms, and constructed a model using three risk categories to predict the overall survival based on 134 methylation sites. The model showed a 10-fold cross-validation score of 0.95 and satisfactory predictive power, and correctly classified 26 of 33 samples in testing set obtained by stratified sampling from high, intermediate and low risk groups.

Authors

  • Rui-Zhao Dong
    Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
  • Xuan Yang
    Dongfang College, Zhejiang University of Finance & Economics, Haining 314408, Zhejiang, China. yx_321@zufe.edu.cn.
  • Xin-Yu Zhang
    Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
  • Ping-Ting Gao
    Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
  • Ai-Wu Ke
    Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
  • Hui-Chuan Sun
    Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
  • Jian Zhou
    CTIQ, Canon Medical Research USA, Inc., Vernon Hills, 60061, USA.
  • Jia Fan
    Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
  • Jia-Bin Cai
    Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
  • Guo-Ming Shi
    Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.

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