A novel fully automated MRI-based deep-learning method for classification of IDH mutation status in brain gliomas

Chandan Ganesh Bangalore Yogananda, Bhavya R. Shah, Maryam Vejdani-Jahromi, Sahil S. Nalawade, Gowtham K. Murugesan, Frank F. Yu, Marco C. Pinho, Benjamin C. Wagner, Bruce Mickey, Toral R. Patel, Baowei Fei, Ananth J. Madhuranthakam, Joseph A. Maldjian

Research output: Contribution to journalArticlepeer-review

92 Scopus citations


Background: Isocitrate dehydrogenase (IDH) mutation status has emerged as an important prognostic marker in gliomas. Currently, reliable IDH mutation determination requires invasive surgical procedures. The purpose of this study was to develop a highly accurate, MRI-based, voxelwise deep-learning IDH classification network using T2-weighted (T2w) MR images and compare its performance to a multicontrast network. Methods: Multiparametric brain MRI data and corresponding genomic information were obtained for 214 subjects (94 IDH-mutated, 120 IDH wild-type) from The Cancer Imaging Archive and The Cancer Genome Atlas. Two separate networks were developed, including a T2w image-only network (T2-net) and a multicontrast (T2w, fluid attenuated inversion recovery, and T1 postcontrast) network (TS-net) to perform IDH classification and simultaneous single label tumor segmentation. The networks were trained using 3D Dense-UNets. Three-fold cross-validation was performed to generalize the networks' performance. Receiver operating characteristic analysis was also performed. Dice scores were computed to determine tumor segmentation accuracy. Results: T2-net demonstrated a mean cross-validation accuracy of 97.14% ± 0.04 in predicting IDH mutation status, with a sensitivity of 0.97 ± 0.03, specificity of 0.98 ± 0.01, and an area under the curve (AUC) of 0.98 ± 0.01. TS-net achieved a mean cross-validation accuracy of 97.12% ± 0.09, with a sensitivity of 0.98 ± 0.02, specificity of 0.97 ± 0.001, and an AUC of 0.99 ± 0.01. The mean whole tumor segmentation Dice scores were 0.85 ± 0.009 for T2-net and 0.89 ± 0.006 for TS-net. Conclusion: We demonstrate high IDH classification accuracy using only T2-weighted MR images. This represents an important milestone toward clinical translation.

Original languageEnglish (US)
Pages (from-to)402-411
Number of pages10
Issue number3
StatePublished - Mar 5 2020


  • CNN
  • IDH
  • MRI
  • deep learning
  • glioma

ASJC Scopus subject areas

  • Oncology
  • Clinical Neurology
  • Cancer Research


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