1. SNPs and blood inflammatory marker featured machine learning for predicting the efficacy of fluorouracil-based chemotherapy in colorectal cancer.
- Author
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Li J, Zhang W, Chen L, Mao X, Wang X, Liu J, Huang Y, Qi H, Chen L, Shi H, Chen B, Zhong M, Li Q, and Wang T
- Subjects
- Humans, Male, Female, Middle Aged, Aged, Biomarkers, Tumor blood, Biomarkers, Tumor genetics, Prognosis, Adult, Colorectal Neoplasms drug therapy, Colorectal Neoplasms genetics, Colorectal Neoplasms blood, Fluorouracil therapeutic use, Polymorphism, Single Nucleotide, Machine Learning
- Abstract
Fluorouracil-based chemotherapy responses in colorectal cancer (CRC) patients vary widely, highlighting the role of pharmacogenomics in developing better predictive models. We analyzed 379 CRC patients receiving fluorouracil-based chemotherapy, collecting data on fluorouracil metabolism-related SNPs (TYMS, MTHFR, DPYD, RRM1), blood inflammatory markers, and clinical status. Six machine learning models-K-nearest neighbors, support vector machine, gradient boosting decision trees (GBDT), eXtreme Gradient Boosting (XGBoost), LightGBM, and random forest-were compared against multivariate logistic regression and a deep learning model (i.e., multilayer perceptron, MLP). Feature importance analysis highlighted seven predictors: histological grade, N and M staging, monocyte count, platelet-to-lymphocyte ratio, MTHFR rs1801131, and RRM1 rs11030918. In a five-fold cross-validation, XGBoost and GBDT exhibited superior performance, with Area Under Curve (AUC) of 0.88 ± 0.02. XGBoost excelled in identifying favorable prognosis (recall = 0.939). GBDT demonstrated balance in recognizing both categories, with a recall for favorable prognosis of 0.908 and a precision for unfavorable prognosis of 0.863. MLP had a similar AUC (0.87) with high precision for favorable prognosis (recall = 0.946). In external validation, XGBoost model achieved an accuracy of 0.79. An online prognostic tool based on XGBoost was developed, integrating metabolism-related SNPs and inflammatory markers, enhancing CRC treatment precision and supporting tailored chemotherapy., Competing Interests: Data Availability The data that support the findings of this study are openly available in Github at https://github.com/xxxxljyf/SNPs-and-Blood-Inflammatory-Marker-Featured-Machine-Learning-Models-in-CRC., (© 2024. The Author(s).)
- Published
- 2024
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