ArticleThoracic cancer2020
Copy number variation in plasma as a tool for lung cancer prediction using Extreme Gradient Boosting (XGBoost) classifier.
Article in Thoracic cancer, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed.
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- Whole Exome Sequencing of Thymoma Patients Exhibiting Exceptional Responses to Pemetrexed Monotherapy.Cancers · 2023Article
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- Multi-Process Remora Enhanced Hyperparameters of Convolutional Neural Network for Lung Cancer Prediction.Biomedicines · 2023Article
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9 authors.
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Abstract
backgroundThe main cause of cancer death is lung cancer (LC) which usually presents at an advanced stage, but its early detection would increase the benefits of treatment. Blood is particularly favored in clinical research given the possibility of using it for relatively noninvasive analyses. Copy number variation (CNV) is a common genetic change in tumor genomes, and many studies have indicated that CNV-derived cell-free DNA (cfDNA) from plasma could be feasible as a biomarker for cancer diagnosis.
methodsIn this study, we determined the possibility of using chromosomal arm-level CNV from cfDNA as a biomarker for lung cancer diagnosis in a small cohort of 40 patients and 41 healthy controls. Arm-level CNV distributions were analyzed based on z score, and the machine-learning algorithm Extreme Gradient Boosting (XGBoost) was applied for cancer prediction.
resultsThe results showed that amplifications tended to emerge on chromosomes 3q, 8q, 12p, and 7q. Deletions were frequently detected on chromosomes 22q, 3p, 5q, 16q, 10q, and 15q. Upon applying a trained XGBoost classifier, specificity and sensitivity of 100% were finally achieved in the test group (12 patients and 13 healthy controls). In addition, five-fold cross-validation proved the stability of the model. Finally, our results suggested that the integration of four arm-level CNVs and the concentration of cfDNA into the trained XGBoost classifier provides a potential method for detecting lung cancer.
conclusionOur results suggested that the integration of four arm-level CNVs and the concentration from of cfDNA integrated withinto the trained XGBoost classifier could become provides a potentially method for detecting lung cancer detection. KEY POINTS: Significant findings of the study: Healthy individuals have different arm-level CNV profiles from cancer patients. Amplifications tend to emerge on chromosome 3q, 8q, 12p, 7q and deletions tend to emerge on chromosome 22q, 3p, 5q, 16q, 10q, 15q. WHAT THIS STUDY ADDS: CfDNA concentration, arm 10q, 3q, 8q, 3p, and 22q are key features for prediction. Trained XGBoost classifier is a potential method for lung cancer detection.
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