A machine learning model for periodontitis based on integrative gene expression analysis: validation in an independent patient cohort.

purposeTo develop a gene expression-based prediction model for periodontitis by identifying a compact set of predictive genes and to validate the model using an independent cohort of patient samples analyzed by reverse transcription quantitative polymerase chain reaction (RT-qPCR).

methodsUsing a total of 9 Gene Expression Omnibus (GEO) series, we first performed feature selection through differential expression analysis and SHapley Additive exPlanations (SHAP) values in 2 GEO series (GSE10334 and GSE16134). The remaining datasets were then integrated to construct an extended multi-cohort dataset (680 samples: 193 healthy and 487 with periodontitis) for model development using the XGBoost classifier. An exhaustive search with nested cross-validation (CV) was conducted to identify the optimal gene subset. Model performance was estimated using repeated 10-fold CV and summarized by the area under the receiver operating characteristic curve (AUC) with corresponding standard deviations. Gene-level interpretation was performed using SHAP rankings and univariate analyses. Validation was conducted in a newly collected RT-qPCR patient cohort (n=20; 10 healthy individuals and 10 patients with periodontitis) derived from gingival tissue samples, using z-score-transformed ΔCt values without model retraining.

resultsThe optimal 4-gene model (tissue inhibitor of metalloproteinases-4 [

conclusionsThe compact 4-gene XGBoost model provides reproducible and interpretable prediction of periodontitis across GEO datasets and demonstrates moderate performance in a newly collected RT-qPCR patient cohort, suggesting preliminary cross-platform feasibility. However, the wide confidence intervals underscore the need for larger prospective cohorts to confirm its clinical utility.