Association of Toll-Like Receptor 9 Gene Polymorphisms With Remission in Patients With Rheumatoid Arthritis Receiving Tumor Necrosis Factor Alpha Inhibitors and Development of Machine Learning Models

Studies that investigate the association between toll-like receptor (TLR)-4 or TLR9 gene polymorphisms and remission from the disease in RA patients taking tumor necrosis factor alpha (TNF-α) inhibitors have yet to be conducted. In this context, this study was designed to investigate the effects of polymorphisms in TLR4 and TLR9 on response to TNF-α inhibitor and develop various machine learning approaches to predict remission. A total of six single nucleotide polymorphisms (SNPs) were investigated. Logistic regression analysis was used to investigate the association between genetic polymorphisms and response to treatment. Various machine learning methods were utilized for prediction of remission. After adjusting for covariates, the rate of remission of T-allele carriers of TLR9 rs352139 was about 5 times that of the CC-genotype carriers (95% confidence interval (CI) 1.325–19.231, p = 0.018). Among machine learning algorithms, multivariate logistic regression and elastic net showed the best prediction with the AUROC value of 0.71 (95% CI 0.597 - 0.823 for both models). This study showed an association between a TLR9 polymorphism (rs352139) and treatment response in RA patients receiving TNF-α inhibitors. Moreover, this study developed various machine learning methods for prediction, among which the elastic net provided the best model for remission prediction.