MGMT Promoter Methylation Prediction in Glioblastoma Using 3D CNNs with Advanced MRI Sequences

Tran Nguyen Tuan Minh, Quang Hien Kha, Viet Huan Le, Matthew Chin Heng Chua, Nguyen Quoc Khanh Le
Proceedings of The 9th International Conference on Medical Imaging with Deep Learning, PMLR 315:3885-3898, 2026.

Abstract

Accurate determination of O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status is essential for therapeutic planning in glioblastoma (GBM). Although molecular assays remain the reference standard, they are costly, invasive, and not always feasible in routine practice. This has motivated the development of non-invasive MRI-based deep learning approaches, particularly those leveraging advanced physiological imaging sequences. In this study, we investigated whether arterial spin labeling (ASL) and apparent diffusion coefficient (ADC) imaging provide complementary information for predicting MGMT methylation status in IDH-wildtype GBM. We analyzed 351 patients from the UCSF Preoperative Diffuse Glioma MRI dataset and trained 3D convolutional neural network models based on a ResNet-10 architecture using ASL, ADC, diffusion-weighted imaging (DWI), and conventional T2-FLAIR sequences. Among single-sequence models, ASL achieved the highest performance (accuracy of 0.76, precision of 0.75, and F1 score of 0.73). A dual-sequence model combining ASL and ADC further improved prediction, yielding an AUC of 0.83, significantly outperforming both the ASL-only model and the T2-FLAIR model (AUC 0.6524; DeLong test, $p<0.05$). These results demonstrate that integrating perfusion- and diffusion-based MRI captures complementary physiological characteristics relevant to MGMT methylation, offering a more accurate and fully non-invasive alternative for biomarker assessment. Incorporating advanced MRI sequences into deep learning pipelines may support more informed treatment planning and improve clinical decision-making for patients with GBM.

Cite this Paper

BibTeX
@InProceedings{pmlr-v315-minh26a, title = {MGMT Promoter Methylation Prediction in Glioblastoma Using 3D CNNs with Advanced MRI Sequences}, author = {Minh, Tran Nguyen Tuan and Kha, Quang Hien and Le, Viet Huan and Chua, Matthew Chin Heng and Le, Nguyen Quoc Khanh}, booktitle = {Proceedings of The 9th International Conference on Medical Imaging with Deep Learning}, pages = {3885--3898}, year = {2026}, editor = {Huo, Yuankai and Gao, Mingchen and Kuo, Chang-Fu and Jin, Yueming and Deng, Ruining}, volume = {315}, series = {Proceedings of Machine Learning Research}, month = {08--10 Jul}, publisher = {PMLR}, pdf = {https://raw.githubusercontent.com/mlresearch/v315/main/assets/minh26a/minh26a.pdf}, url = {https://proceedings.mlr.press/v315/minh26a.html}, abstract = {Accurate determination of O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status is essential for therapeutic planning in glioblastoma (GBM). Although molecular assays remain the reference standard, they are costly, invasive, and not always feasible in routine practice. This has motivated the development of non-invasive MRI-based deep learning approaches, particularly those leveraging advanced physiological imaging sequences. In this study, we investigated whether arterial spin labeling (ASL) and apparent diffusion coefficient (ADC) imaging provide complementary information for predicting MGMT methylation status in IDH-wildtype GBM. We analyzed 351 patients from the UCSF Preoperative Diffuse Glioma MRI dataset and trained 3D convolutional neural network models based on a ResNet-10 architecture using ASL, ADC, diffusion-weighted imaging (DWI), and conventional T2-FLAIR sequences. Among single-sequence models, ASL achieved the highest performance (accuracy of 0.76, precision of 0.75, and F1 score of 0.73). A dual-sequence model combining ASL and ADC further improved prediction, yielding an AUC of 0.83, significantly outperforming both the ASL-only model and the T2-FLAIR model (AUC 0.6524; DeLong test, $p<0.05$). These results demonstrate that integrating perfusion- and diffusion-based MRI captures complementary physiological characteristics relevant to MGMT methylation, offering a more accurate and fully non-invasive alternative for biomarker assessment. Incorporating advanced MRI sequences into deep learning pipelines may support more informed treatment planning and improve clinical decision-making for patients with GBM.} }
Endnote
%0 Conference Paper %T MGMT Promoter Methylation Prediction in Glioblastoma Using 3D CNNs with Advanced MRI Sequences %A Tran Nguyen Tuan Minh %A Quang Hien Kha %A Viet Huan Le %A Matthew Chin Heng Chua %A Nguyen Quoc Khanh Le %B Proceedings of The 9th International Conference on Medical Imaging with Deep Learning %C Proceedings of Machine Learning Research %D 2026 %E Yuankai Huo %E Mingchen Gao %E Chang-Fu Kuo %E Yueming Jin %E Ruining Deng %F pmlr-v315-minh26a %I PMLR %P 3885--3898 %U https://proceedings.mlr.press/v315/minh26a.html %V 315 %X Accurate determination of O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status is essential for therapeutic planning in glioblastoma (GBM). Although molecular assays remain the reference standard, they are costly, invasive, and not always feasible in routine practice. This has motivated the development of non-invasive MRI-based deep learning approaches, particularly those leveraging advanced physiological imaging sequences. In this study, we investigated whether arterial spin labeling (ASL) and apparent diffusion coefficient (ADC) imaging provide complementary information for predicting MGMT methylation status in IDH-wildtype GBM. We analyzed 351 patients from the UCSF Preoperative Diffuse Glioma MRI dataset and trained 3D convolutional neural network models based on a ResNet-10 architecture using ASL, ADC, diffusion-weighted imaging (DWI), and conventional T2-FLAIR sequences. Among single-sequence models, ASL achieved the highest performance (accuracy of 0.76, precision of 0.75, and F1 score of 0.73). A dual-sequence model combining ASL and ADC further improved prediction, yielding an AUC of 0.83, significantly outperforming both the ASL-only model and the T2-FLAIR model (AUC 0.6524; DeLong test, $p<0.05$). These results demonstrate that integrating perfusion- and diffusion-based MRI captures complementary physiological characteristics relevant to MGMT methylation, offering a more accurate and fully non-invasive alternative for biomarker assessment. Incorporating advanced MRI sequences into deep learning pipelines may support more informed treatment planning and improve clinical decision-making for patients with GBM.
APA
Minh, T.N.T., Kha, Q.H., Le, V.H., Chua, M.C.H. & Le, N.Q.K.. (2026). MGMT Promoter Methylation Prediction in Glioblastoma Using 3D CNNs with Advanced MRI Sequences. Proceedings of The 9th International Conference on Medical Imaging with Deep Learning, in Proceedings of Machine Learning Research 315:3885-3898 Available from https://proceedings.mlr.press/v315/minh26a.html.

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