International Journal of COPD (Nov 2024)
Screening the Best Risk Model and Susceptibility SNPs for Chronic Obstructive Pulmonary Disease (COPD) Based on Machine Learning Algorithms
Abstract
Zehua Yang,* Yamei Zheng,* Lei Zhang, Jie Zhao, Wenya Xu, Haihong Wu, Tian Xie, Yipeng Ding Department of Respiratory and Critical Care Medicine, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, 570311, People’s Republic of China*These authors contributed equally to this workCorrespondence: Yipeng Ding; Tian Xie, Department of Respiratory and Critical Care Medicine, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, 19 Xiuhua Road, Xiuying District, Haikou, Hainan, 570311, People’s Republic of China, Tel +86-18976335858, Email [email protected]; [email protected] and Purpose: Chronic obstructive pulmonary disease (COPD) is a common and progressive disease that is influenced by both genetic and environmental factors, and genetic factors are important determinants of COPD. This study focuses on screening the best predictive models for assessing COPD-associated SNPs and then using the best models to predict potential risk factors for COPD.Methods: Healthy subjects (n=290) and COPD patients (n=233) were included in this study, the Agena MassARRAY platform was applied to genotype the subjects for SNPs. The selected sample loci were first screened by logistic regression analysis, based on which the key SNPs were further screened by LASSO regression, RFE algorithm and Random Forest algorithm, and the ROC curves were plotted to assess the discriminative performance of the models to screen the best prediction model. Finally, the best prediction model was used for the prediction of risk factors for COPD.Results: One-way logistic regression analysis screened 44 candidate SNPs from 146 SNPs, on the basis of which 44 SNPs were screened or feature ranked using LASSO model, RFE-Caret, RFE-Lda, RFE-lr, RFE-nb, RFE-rf, RFE-treebag algorithms and random forest model, respectively, and obtained ROC curve values of 0.809, 0.769, 0.798, 0.743, 0.686, 0.766, 0.743, 0.719, respectively, so we selected the lasso model as the best model, and then constructed a column-line graph model for the 25 SNPs screened in it, and found that rs12479210 might be the potential risk factors for COPD.Conclusion: The LASSO model is the best predictive model for COPD and rs12479210 may be a potential risk locus for COPD.Keywords: COPD, LASSO, machine learning, predictive model, SNP
