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. 2025 Jun 21;27(5):1313-1324.
doi: 10.1093/neuonc/noae279.

Nanopore sequencing as a cutting-edge technology for medulloblastoma classification

Mathilde Filser  1   2 , Jacob Torrejon  3   1 , Kevin Merchadou  4 , Christelle Dufour  5 , Elodie Girard  6   1 , Christine Bourneix  1   2 , Elisa Lemaître  1   2 , Tarek Gharsalli  3   1 , Riwan Brillet  6   1 , Jennifer Wong  1   2 , David Gentien  7 , Audrey Rapinat  7 , Nicolas Servant  6   1 , Alexandre Vasiljevic  8   9 , Anne Isabelle Bertozzi  10 , Sandra Raimbault  11 , Arnault Tauziede Espariat  12 , Benoit Lhermitte  13 , Cécile Faure-Conter  14 , Céline Icher  15 , Claire Berger  16 , Claude Alain Maurage  17 , Damien Bodet  18 , David Meyronet  19   20 , Emmanuelle Uro-Coste  21 , Emilie De Carli  22 , Fabien Forest  23 , Gilles Palenzuela  24 , Guillaume Chotard  25 , Guillaume Gauchotte  26   27 , Helene Sudour  28 , Ludovic Mansuy  29   30 , Marianna Deparis  31 , Matthias Tallegas  32 , Maxime Faisant  33 , Natacha Entz-Werle  34   35 , Pascale Varlet  12 , Pierre Leblond  36   37   14 , Sophie Michalak-Provost  38 , Stéphanie Proust Houdemont  39 , Valérie Rigau  40   41 , François Doz  42   43 , Olivier Delattre  44   43   2 , Franck Bourdeaut  42   44   43 , Olivier Ayrault  3   1 , Julien Masliah-Planchon  44   1   2
Affiliations

Nanopore sequencing as a cutting-edge technology for medulloblastoma classification

Mathilde Filser et al. Neuro Oncol. .

Abstract

Background: Medulloblastoma (MB) is one of the most prevalent embryonal malignant brain tumors. Current classification organizes these tumors into 4 molecular subgroups (WNT, SHH, Group 3, and Group 4 MB). Recently, a comprehensive classification has been established, identifying numerous subtypes, some of which exhibit a poor prognosis. It is critical to establish effective subtyping methods for accurate diagnosis and patient's management that strikes a delicate balance between improving outcomes and minimizing the risk of comorbidities.

Methods: We evaluated the ability of Nanopore sequencing to provide clinically relevant methylation and copy number profiles of MB. Nanopore sequencing was applied to an EPIC cohort of 44 frozen MB, benchmarked against the gold standard EPIC array, and further evaluated on an integrated diagnosis cohort of 116 MB.

Results: Most MB of both cohorts (42/44; 95.5% and 106/116; 91.4%, respectively) were accurately subgrouped by Nanopore sequencing. Employing Flongle flow cells for 18 MB allowed a more rapid and cost-effective analysis, with 94.4% (17/18) being correctly classified. Nanopore sequencing enabled us to accurately subtype 28/30 (93.3%) MB.

Conclusion: This study, conducted on the largest cohort of MB analyzed with Nanopore sequencing to date, establishes the proof of concept that this modern and innovative technology is well-suited for MB classification. Nanopore sequencing demonstrates a robust capacity for precise subtyping of MB, a critical advancement that holds significant potential for enhancing patient stratification in future clinical trials. Its ability to deliver quick and cost-effective results firmly establishes it as a game-changer in the field of MB classification.

Keywords: Nanopore sequencing; brain tumors; medulloblastoma subgrouping; methylation.

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