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
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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.
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