A Fully Automated Deep-Learning Model for Predicting the Molecular Subtypes of Posterior Fossa Ependymomas Using T2-Weighted Images

• Published in: Clinical cancer research 2024-01, Vol.30 (1), p.150-158
• Main Authors: Cheng, Dan, Zhuo, Zhizheng, Du, Jiang, Weng, Jinyuan, Zhang, Chengzhou, Duan, Yunyun, Sun, Ting, Wu, Minghao, Guo, Min, Hua, Tiantian, Jin, Ying, Peng, Boyang, Li, Zhaohui, Zhu, Mingwang, Imami, Maliha, Bettegowda, Chetan, Sair, Haris, Bai, Harrison X, Barkhof, Frederik, Liu, Xing, Liu, Yaou
• Format: Article
• Language: English
• Subjects: Area Under Curve; Clinical Decision-Making; Deep Learning; Ependymoma - diagnostic imaging; Ependymoma - genetics; Humans; Magnetic Resonance Imaging; Phenylphosphonothioic Acid, 2-Ethyl 2-(4-Nitrophenyl) Ester; Retrospective Studies
• ISSN: 1078-0432; 1557-3265
• DOI: 10.1158/1078-0432.CCR-23-1461

We aimed to develop and validate a deep learning (DL) model to automatically segment posterior fossa ependymoma (PF-EPN) and predict its molecular subtypes [Group A (PFA) and Group B (PFB)] from preoperative MR images. We retrospectively identified 227 PF-EPNs (development and internal test sets) with available preoperative T2-weighted (T2w) MR images and molecular status to develop and test a 3D nnU-Net (referred to as T2-nnU-Net) for tumor segmentation and molecular subtype prediction. The network was externally tested using an external independent set [n = 40; subset-1 (n = 31) and subset-2 (n =9)] and prospectively enrolled cases [prospective validation set (n = 27)]. The Dice similarity coefficient was used to evaluate the segmentation performance. Receiver operating characteristic analysis for molecular subtype prediction was performed. For tumor segmentation, the T2-nnU-Net achieved a Dice score of 0.94 ± 0.02 in the internal test set. For molecular subtype prediction, the T2-nnU-Net achieved an AUC of 0.93 and accuracy of 0.89 in the internal test set, an AUC of 0.99 and accuracy of 0.93 in the external test set. In the prospective validation set, the model achieved an AUC of 0.93 and an accuracy of 0.89. The predictive performance of T2-nnU-Net was superior or comparable to that of demographic and multiple radiologic features (AUCs ranging from 0.87 to 0.95). A fully automated DL model was developed and validated to accurately segment PF-EPNs and predict molecular subtypes using only T2w MR images, which could help in clinical decision-making.