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

Neuro Oncol. 2020 Mar 5;22(3):402-411. doi: 10.1093/neuonc/noz199.


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.

Keywords: CNN; IDH; MRI; deep learning; glioma.

Publication types

  • Research Support, N.I.H., Extramural
  • Retracted Publication

MeSH terms

  • Brain Neoplasms / diagnostic imaging*
  • Brain Neoplasms / genetics*
  • Deep Learning*
  • Female
  • Glioma / diagnostic imaging*
  • Glioma / genetics*
  • Humans
  • Isocitrate Dehydrogenase / genetics*
  • Magnetic Resonance Imaging*
  • Male
  • Middle Aged
  • Sensitivity and Specificity


  • Isocitrate Dehydrogenase