The use of a next-generation sequencing-derived machine-learning risk-prediction model (OncoCast-MPM) for malignant pleural mesothelioma: a retrospective study. Issue 9 (September 2021)

• Record Type: Journal Article
• Authors: Zauderer, Marjorie G; Martin, Axel; Egger, Jacklynn; Rizvi, Hira; Offin, Michael; Rimner, Andreas; Adusumilli, Prasad S; Rusch, Valerie W; Kris, Mark G; Sauter, Jennifer L; Ladanyi, Marc; Shen, Ronglai
• Is Part Of: Lancet. Volume 3:Issue 9(2021)
• Page Start: e565
• Page End: e576
• Publication Date: 2021-09
• Subjects: Medical care -- Data processing -- Periodicals; Medical care -- Information technology -- Periodicals; Medical informatics -- Periodicals; 610.285
• DOI: 10.1016/S2589-7500(21)00104-7
• Languages: English
• ISSNs: 2589-7500

Abstract

Summary: Background: Current risk stratification for patients with malignant pleural mesothelioma based on disease stage and histology is inadequate. For some individuals with early-stage epithelioid tumours, a good prognosis by current guidelines can progress rapidly; for others with advanced sarcomatoid cancers, a poor prognosis can progress slowly. Therefore, we aimed to develop and validate a machine-learning tool—known as OncoCast-MPM—that could create a model for patient prognosis. Methods: We did a retrospective study looking at malignant pleural mesothelioma tumours using next-generation sequencing from the Memorial Sloan Kettering Cancer Center-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT). We collected clinical, pathological, and routine next-generation sequencing data from consecutive patients with malignant pleural mesothelioma treated at the Memorial Sloan Kettering Cancer Center (New York, NY, USA), as well as the MSK-IMPACT data. Together, these data comprised the MSK-IMPACT cohort. Using OncoCast-MPM, an open-source, web-accessible, machine-learning risk-prediction model, we integrated available data to create risk scores that stratified patients into low-risk and high-risk groups. Risk stratification of the MSK-IMPACT cohort was then validated using publicly available malignant pleural mesothelioma data from The Cancer Genome Atlas (ie, the TCGA cohort). Findings: Between Feb 15, 2014, and Jan 28, 2019, we collected MSK-IMPACT data from the tumour tissue of 194 patients in the MSK-IMPACT cohort. The median overall survival was higher in the low-risk group than in the high-risk group as determined by OncoCast-MPM (30·8 months [95% CI 22·7–36·2] vs 13·9 months [10·7–18·0]; hazard ratio [HR] 3·0 [95% CI 2·0–4·5]; p<0·0001). No single factor or gene alteration drove risk differentiation. OncoCast-MPM was validated against the TCGA cohort, which consisted of 74 patients. The median overall survival was higher in the low-risk group than in the high-risk group (23·6 months [95% CI 15·1–28·4] vs 13·6 months [9·8–17·9]; HR 2·3 [95% CI 1·3–3·8]; p=0·0019). Although stage-based risk stratification was unable to differentiate survival among risk groups at 3 years in the MSK-IMPACT cohort (31% for early-stage disease vs 30% for advanced-stage disease; p=0·90), the OncoCast-MPM-derived 3-year survival was significantly higher in the low-risk group than in the high-risk group (40% vs 7%; p=0·0052). Interpretation: OncoCast-MPM generated accurate, individual patient-level risk assessment scores. After prospective validation with the TCGA cohort, OncoCast-MPM might offer new opportunities for enhanced risk stratification of patients with malignant pleural mesothelioma in clinical trials and drug development. Funding: US National Institutes of Health/National Cancer Institute.