Proceedings of SPIE
Medical Imaging 2020: Biomedical Applications in Molecular, Structural, and Functional Imaging, 18-20 February 2020, Houston, Texas, U.S.A.
An updated classification of diffuse lower-grade gliomas is established in the 2016 World Health Organization Classification of Tumors of the Central Nervous System based on their molecular mutations such as TP53 mutation. This study investigates machine learning methods for TP53 mutation status prediction and classification using radiomics and genomics features, respectively. Radiomics features represent patients' age and imaging features that are extracted from conventional MRI. Genomics feature is represented by patients’ gene expression using RNA sequencing. This study uses a total of 105 LGG patients, where the patient dataset is divided into a training set (80 patients) and testing set (25 patients). Three TP53 mutation prediction models are constructed based on the source of the training features; TP53-radiomics model, TP53-genomics model, and TP53-radiogenomics model, respectively. Radiomics feature selection is performed using recursive feature selection method. For genomics data, EdgeR method is utilized to select the differentially expressed genes between the mutated TP53 versus the non-mutated TP53 cases in the training set. The training classification model is constructed using Random Forest and cross-validated using repeated 10-fold cross validation. Finally, the predictive performance of the three models is assessed using the testing set. The three models, TP53-Radiomics, TP53-RadioGenomics, and TP53-Genomics, achieve a predictive accuracy of 0.84±0.04, 0.92±0.04, and 0.89±0.07, respectively. These results show promise of non-invasive MRI radiomics features and fusion of radiomics with genomics features for prediction of TP53.
Original Publication Citation
Shboul, Z., & Iftekharuddin, K. (2020). Efficacy of radiomics and genomics in predicting TP53 mutations in diffuse lower grade glioma. In Krol, A. and Gimi, B.S. (Eds.), Medical Imaging 2020: Biomedical Applications in Molecular, Structural and Functional Imaging, Houston, Texas, U.S.A. 113170Y (1-7). SPIE. https://doi.org/10.1117/12.2550764
Shboul, Zeina A. and Iftekharuddin, Khan, "Efficacy of Radiomics and Genomics in Predicting TP53 Mutations in Diffuse Lower Grade Glioma" (2020). Electrical & Computer Engineering Faculty Publications. 284.