Deep Radiogenomics of Lower-Grade Gliomas: Convolutional Neural Networks Predict Tumor Genomic Subtypes Using MR Images.
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ABSTRACT: Purpose
To employ deep learning to predict genomic subtypes of lower-grade glioma (LLG) tumors based on their appearance at MRI.Materials and methods
Imaging data from The Cancer Imaging Archive and genomic data from The Cancer Genome Atlas from 110 patients from five institutions with lower-grade gliomas (World Health Organization grade II and III) were used in this study. A convolutional neural network was trained to predict tumor genomic subtype based on the MRI of the tumor. Two different deep learning approaches were tested: training from random initialization and transfer learning. Deep learning models were pretrained on glioblastoma MRI, instead of natural images, to determine if performance was improved for the detection of LGGs. The models were evaluated using area under the receiver operating characteristic curve (AUC) with cross-validation. Imaging data and annotations used in this study are publicly available.Results
The best performing model was based on transfer learning from glioblastoma MRI. It achieved AUC of 0.730 (95% confidence interval [CI]: 0.605, 0.844) for discriminating cluster-of-clusters 2 from others. For the same task, a network trained from scratch achieved an AUC of 0.680 (95% CI: 0.538, 0.811), whereas a model pretrained on natural images achieved an AUC of 0.640 (95% CI: 0.521, 0.763).Conclusion
These findings show the potential of utilizing deep learning to identify relationships between cancer imaging and cancer genomics in LGGs. However, more accurate models are needed to justify clinical use of such tools, which might be obtained using substantially larger training datasets.Supplemental material is available for this article.© RSNA, 2020.
SUBMITTER: Buda M
PROVIDER: S-EPMC8017403 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Purpose: Isocitrate dehydrogenase (IDH) mutations in glioma patients confer longer survival and may guide treatment decision making. We aimed to predict the IDH status of gliomas from MR imaging by applying a residual convolutional neural network to preoperative radiographic data.Experimental Design: Preoperative imaging was acquired for 201 patients from the Hospital of University of Pennsylvania (HUP), 157 patients from Brigham and Women's Hospital (BWH), and 138 patients from The Cancer Imaging Archive (TCIA) and divided into training, validation, and testing sets. We trained a residual convolutional neural network for each MR sequence (FLAIR, T2, T1 precontrast, and T1 postcontrast) and built a predictive model from the outputs. To increase the size of the training set and prevent overfitting, we augmented the training set images by introducing random rotations, translations, flips, shearing, and zooming.Results: With our neural network model, we achieved IDH prediction accuracies of 82.8% (AUC = 0.90), 83.0% (AUC = 0.93), and 85.7% (AUC = 0.94) within training, validation, and testing sets, respectively. When age at diagnosis was incorporated into the model, the training, validation, and testing accuracies increased to 87.3% (AUC = 0.93), 87.6% (AUC = 0.95), and 89.1% (AUC = 0.95), respectively.Conclusions: We developed a deep learning technique to noninvasively predict IDH genotype in grade II-IV glioma using conventional MR imaging using a multi-institutional data set. Clin Cancer Res; 24(5); 1073-81. ©2017 AACR.
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