Combining radiomics and deep convolutional neural network features from preoperative MRI for predicting clinically relevant genetic biomarkers in glioblastoma

Abstract Background Glioblastoma is the most common primary brain malignancy, yet treatment options are limited, and prognosis remains guarded. Individualized tumor genetic assessment has become important for accurate prognosis and for guiding emerging targeted therapies. However, challenges remain for widespread tumor genetic testing due to costs and the need for tissue sampling. The aim of this study is to evaluate a novel artificial intelligence method for predicting clinically relevant genetic biomarkers from preoperative brain MRI in patients with glioblastoma. Methods We retrospectively analyzed preoperative MRI data from 400 patients with glioblastoma, IDH-wildtype or WHO grade 4 astrocytoma, IDH mutant who underwent resection and genetic testing. Nine genetic biomarkers were assessed: hotspot mutations of IDH1 or TERT promoter, pathogenic mutations of TP53, PTEN, ATRX, or CDKN2A/B, MGMT promoter methylation, EGFR amplification, and combined aneuploidy of chromosomes 7 and 10. Models were developed to predict biomarker status from MRI data using radiomics features, convolutional neural network (CNN) features, and a combination of both. Results Combined model performance was good for IDH1 and TERT promoter hotspot mutations, pathogenic mutations of ATRX and CDKN2A/B, and combined aneuploidy of chromosomes 7 and 10, with receiver operating characteristic area under the curve (ROC AUC) 0.85 and was fair for all other tested biomarkers with ROC AUC 0.7. Combined model performance was statistically superior to individual radiomics and CNN feature models for prediction chromosome 7 and 10 aneuploidy, MGMT promoter methylation, and PTEN mutation. Conclusions Combining radiomics and CNN features from preoperative MRI yields improved noninvasive genetic biomarker prediction performance in patients with WHO grade 4 diffuse astrocytic gliomas.