Radiogenomics in Clear Cell Renal Cell Carcinoma: Machine Learning-Based High-Dimensional Quantitative CT Texture Analysis in Predicting PBRM1 Mutation Status

OBJECTIVE. The purpose of this study is to evaluate the potential value of machine learning (ML)-based high-dimensional quantitative CT texture analysis in predicting the mutation status of the gene encoding the protein polybromo-1 (PBRM1) in patients with clear cell renal cell carcinoma (RCC). MATERIALS AND METHODS. In this retrospective study, 45 patients with clear cell RCC (29 without the PBRM1 mutation and 16 with the PBRM1 mutation) were identified in The Cancer Genome Atlas-Kidney Renal Clear Cell Carcinoma database. To create stable ML models and balanced classes, the data were augmented to a total of 161 labeled segmentations (87 without the PBRM1 mutation and 74 with the PBRM1 mutation) by obtaining three to five different samples per patient. Texture features were extracted from corticomedullary phase contrast-enhanced CT images with the use of an open-source software package for the extraction of radiomic data from medical images. Reproducibility analysis (intraclass correlation) was performed by two radiologists. Attribute selection and model optimization were done using a wrapper-based classifier-specific algorithm with nested cross-validation. ML classifiers were an artificial neural network (ANN) algorithm and a random forest (RF) algorithm. The models were validated using 10-fold cross-validation. The reference standard was the PBRM1 mutation status. The main performance metric was the AUC value. RESULTS. Of 828 extracted texture features, 759 had excellent reproducibility. Using 10 selected features, the ANN algorithm correctly classified 88.2% (142 of 161) of the clear cell RCCs in terms of PBRM1 mutation status (AUC value, 0.925). Using five selected features, the RF algorithm correctly classified 95.0% (153 of 161) of the clear cell RCCs (AUC value, 0.987). Overall, the RF algorithm performed better than the ANN algorithm (z score = -2.677; p = 0.007). CONCLUSION. ML-based high-dimensional quantitative CT texture analysis might be a feasible and potential method for predicting PBRM1 mutation status in patients with clear cell RCC.