A risk prediction model of gene signatures in ovarian cancer through bagging of GA-XGBoost models

Journal of Advanced Research

Tzu-Pin Lu¹  Eric Y. Chuang²  Chun-Liang Tao³  Yi-Wen Hsiao³ 

[1] Graduate Institute of Biomedical Electronics and Bioinformatics, Department of Electrical Engineering, National Taiwan University, Taiwan;Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan;Department of Public Health, Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan;

关键词: Ovarian cancer;    Risk prediction;    Gene expression;    Machine learning;    GA-XGBoost;    Bagging algorithm;   

DOI  :  

来源: DOAJ

【 摘 要 】

Introduction: Ovarian cancer (OC) is one of the most frequent gynecologic cancers among women, and high-accuracy risk prediction techniques are essential to effectively select the best intervention strategies and clinical management for OC patients at different risk levels. Current risk prediction models used in OC have low sensitivity, and few of them are able to identify OC patients at high risk of mortality, which would both optimize the treatment of high-risk patients and prevent unnecessary medical intervention in those at low risk. Objectives: To this end, we have developed a bagging-based algorithm with GA-XGBoost models that predicts the risk of death from OC using gene expression profiles. Methods: Four gene expression datasets from public sources were used as training (n = 1) or validation (n = 3) sets. The performance of our proposed algorithm was compared with fine-tuning and other existing methods. Moreover, the biological function of selected genetic features was further interpreted, and the response to a panel of approved drugs was predicted for different risk levels. Results: The proposed algorithm showed good sensitivity (74–100%) in the validation sets, compared with two simple models whose sensitivity only reached 47% and 60%. The prognostic gene signature used in this study was highly connected to AKT, a key component of the PI3K/AKT/mTOR signaling pathway, which influences the tumorigenesis, proliferation, and progression of OC. Conclusion: These findings demonstrated an improvement in the sensitivity of risk classification of OC patients with our risk prediction models compared with other methods. Ongoing effort is needed to validate the outcomes of this approach for precise clinical treatment.

【 授权许可】

Unknown