Copy number variation in plasma as a tool for lung cancer prediction using Extreme Gradient Boosting (XGBoost) classifier
Open accessAbstract
BACKGROUND: The 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. METHODS: In 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. RESULTS: The 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. CONCLUSION: Our 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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- Authors
- Yu, D., Liu, Z., Su, C., Han, Y., Duan, X., Zhang, R., Liu, X., Yang, Y., & Xu, S.
- Affiliations
- Capital Medical University (CN)
- Ping An (China) (CN)
- Beijing Gencode Diagnostics Laboratory Beijing China
- Corresponding author
- Yu, Daping
- Venue
- Thoracic Cancer
- Publisher
- Wiley
- Published
- 2019-11-06
- Volume
- 11
- Issue
- 1
- Pages
- 95-102
- ISSN
- 1759-7706 (ISSN-L)
- 1759-7714
- PMC
- PMC6938748
- OpenAlex
- W2989341121
- Cited by
- 80
- References
- 38
- Citations by year
- 2026: 2 · 2025: 8 · 2024: 18 · 2023: 20 · 2022: 17 · 2021: 11 · 2020: 4
- FWCI
- 2.53
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Thoracic Cancer (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- Beijing Jiaotong University
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Lung Cancer Diagnosis and Treatment
- Keywords
- lung cancer, copy number variation, cell-free DNA, plasma biomarkers, liquid biopsy, XGBoost classifier, cancer prediction, early cancer detection, cfDNA concentration, chromosomal amplification, chromosomal deletion
- MeSH terms
- Circulating Tumor DNA, Adult, Aged, Aged, 80 and over, Female, Follow-Up Studies, Humans, Lung Neoplasms, Male, Middle Aged, Prognosis, Biomarkers, Tumor, Cohort Studies, Case-Control Studies, Young Adult, DNA Copy Number Variations
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