medRxivGenetic & Genomic MedicinePreprint
Towards accesible brain-tumor classification at the point of care Nanopore methylation sequencing from Formalin Fixed Paraffin Embedded (FFPE) pathology samples
Galina Feinberg‐GorenshteiniD, Assaf Grunwald, Carlo VermeuleniD, Nurit Gal Mark, Lena Shinderman Maman, Keren Shihrur, Michal Hameiri-GrossmaniD, Orly Michaeli, Suzanna Fichman, Abraham Natan, Tali SiegaliD, Shlomit Yust‐KatziD, Hanna Weiss, Adva Levy‐BardaiD, Osnat KoneniD, Amir Kershenovich, Jeroen de RidderiD, Helen ToledanoiD, Yehudit BirgeriD, Shai IzraeliiD, Yuval EbensteiniD
Abstract
Oxford Nanopore Technology (ONT) based methylation sequencing is increasingly recognized for its rapid and accurate classification of brain tumors. A process that is crucial for optimal patient treatment. However, widespread clinical utility is currently limited by the need for fresh-frozen biopsies and not the standard-of-care formalin-fixed, paraffin-embedded (FFPE) samples. Our study explores the impact of FFPE on DNA methylation and presents a developed and validated protocol for ONT-based FFPE tumor classification. We present a practical solution for precise brain tumor diagnoses in routine clinical settings and facilitating timely treatment decisions at the point of care and without interfering with operating room standards.
- Citations
- 1
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing
Efrat Katsman, Shari Orlanski, … Benjamin P. Berman·Genome biologyPeer-reviewed·Jul 15, 2022
- Single molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing
Billy T. Lau, Alison Figueroa Almeda, … Hanlee P. Ji·Genome MedicinePeer-reviewed·May 3, 2023
- Ultra-fast deep-learned pediatric CNS tumor classification during surgery
Carlo Vermeulen, Marc Pagès-Gallego, … Jeroen de Ridder·NaturePeer-reviewed·Oct 11, 2023
- Nanopore-based cell-free DNA fragmentation and methylation profiles from the cerebral spinal fluid of patients with lung cancer brain metastases
Tianqi Chen, Xiangqi Bai, … Hanlee P. Ji·bioRxiv·Jul 28, 2025
- Epigenetic Profiling for the Molecular Classification of Metastatic Brain Tumors
J. I. J. Orozco, T. A. Knijnenburg, … D. M. Marzese·bioRxiv·Feb 22, 2018
- Assessing methylation detection for primary human tissue using Nanopore sequencing
Rylee M. Genner, Stuart Akeson, … Miten Jain·bioRxiv·Feb 29, 2024