Braendl, Bjoern and Steiger, Mara and Kubelt, Carolin and Rohrandt, Christian and Zhu, Zhihan and Evers, Maximilian and Wang, Gaojianyong and Schuldt, Bernhard and Afflerbach, Ann-Kristin and Wong, Derek and Lum, Amy and Halldorsson, Skarphedinn and Djirackor, Luna and Leske, Henning and Magadeeva, Svetlana and Smicius, Romualdas and Quedenau, Claudia and Schmidt, Nils Ole and Schueller, Ulrich and Vik-Mo, Einar O. and Proescholdt, Martin and Riemenschneider, Markus J. and Zadeh, Gelareh and Ammerpohl, Ole and Yip, Stephen and Synowitz, Michael and van Boemmel, Alena and Kretzmer, Helene and Mueller, Franz-Josef (2025) Rapid brain tumor classification from sparse epigenomic data. NATURE MEDICINE, 31 (3). pp. 840-848. ISSN 1078-8956, 1546-170X
Full text not available from this repository. (Request a copy)Abstract
Although the intraoperative molecular diagnosis of the approximately 100 known brain tumor entities described to date has been a goal of neuropathology for the past decade, achieving this within a clinically relevant timeframe of under 1 h after biopsy collection remains elusive. Advances in third-generation sequencing have brought this goal closer, but established machine learning techniques rely on computationally intensive methods, making them impractical for live diagnostic workflows in clinical applications. Here we present MethyLYZR, a naive Bayesian framework enabling fully tractable, live classification of cancer epigenomes. For evaluation, we used nanopore sequencing to classify over 200 brain tumor samples, including 10 sequenced in a clinical setting next to the operating room, achieving highly accurate results within 15 min of sequencing. MethyLYZR can be run in parallel with an ongoing nanopore experiment with negligible computational overhead. Therefore, the only limiting factors for even faster time to results are DNA extraction time and the nanopore sequencer's maximum parallel throughput. Although more evidence from prospective studies is needed, our study suggests the potential applicability of MethyLYZR for live molecular classification of nervous system malignancies using nanopore sequencing not only for the neurosurgical intraoperative use case but also for other oncologic indications and the classification of tumors from cell-free DNA in liquid biopsies.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | CENTRAL-NERVOUS-SYSTEM; Q-PROBES ANALYSIS; DIAGNOSIS; ERRORS; |
| Subjects: | 600 Technology > 610 Medical sciences Medicine |
| Divisions: | Medicine > Lehrstuhl für Neurochirurgie Medicine > Abteilung für Neuropathologie Medicine > Zentren des Universitätsklinikums Regensburg > Zentrum für Hirntumore (ZHT) |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 19 May 2026 05:14 |
| Last Modified: | 19 May 2026 05:14 |
| URI: | https://pred.uni-regensburg.de/id/eprint/67491 |
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