Open Access

Areeba Patel, Kirsten Göbel, Sebastian Ille, Felix Hinz, Natalie Schoebe, Henri Bogumil, Jochen Meyer, Michelle Brehm, Helin Kardo, Daniel Schrimpf, Artem Lomakin, Michael Ritter, Pauline Göller, Paul Kerbs, Lisa Pfeifer, Stefan Hamelmann, Christina Blume, Franziska M. Ippen, Natalie Berghaus, Philipp Euskirchen, Leonille Schweizer, Claus Hultschig, Nadine Van Roy, Jo Van Dorpe, Joni Van der Meulen, Siebe Loontiens, Franceska Dedeurwaerdere, Henning Leske, Skarphéðinn Halldórsson, Graeme Fox, Simon Deacon, Inswasti Cahyani, Nadine Holmes, Satrio Wibowo, Rory Munro, Dan Martin, Abid Sharif, Mark Housley, Robert Goldspring, Sebastian Brandner, Somak Roy, Jürgen Hench, Stephan Frank, Andreas Unterberg, Violaine Goidts, Natalie Jäger, Simon Paine, Stuart Smith, Christel Herold-Mende, Wolfgang Wick, Stefan M. Pfister, Einar O. Vik-Mo, Andreas von Deimling, Sandro Krieg, David T. W. Jones, Matthew Loose, Matthias Schlesner, Martin Sill, Felix Sahm

• Molecular data integration plays a central role in central nervous system (CNS) tumor diagnostics but currently used assays pose limitations due to technical complexity, equipment and reagent costs, as well as lengthy turnaround times. We previously reported the development of Rapid-CNS2, an adaptive-sampling-based nanopore sequencing workflow. Here we comprehensively validated and further developed Rapid-CNS2 for intraoperative use. It now offers real-time methylation classification and DNA copy number information within a 30-min intraoperative window, followed by comprehensive molecular profiling within 24 h, covering the complete spectrum of diagnostically and therapeutically relevant information for the respective entity. We validated Rapid-CNS2 in a multicenter setting on 301 archival and prospective samples including 18 samples sequenced intraoperatively. To broaden the utility of methylation-based CNS tumor classification, we developed MNP-Flex, a platform-agnostic methylationMolecular data integration plays a central role in central nervous system (CNS) tumor diagnostics but currently used assays pose limitations due to technical complexity, equipment and reagent costs, as well as lengthy turnaround times. We previously reported the development of Rapid-CNS2, an adaptive-sampling-based nanopore sequencing workflow. Here we comprehensively validated and further developed Rapid-CNS2 for intraoperative use. It now offers real-time methylation classification and DNA copy number information within a 30-min intraoperative window, followed by comprehensive molecular profiling within 24 h, covering the complete spectrum of diagnostically and therapeutically relevant information for the respective entity. We validated Rapid-CNS2 in a multicenter setting on 301 archival and prospective samples including 18 samples sequenced intraoperatively. To broaden the utility of methylation-based CNS tumor classification, we developed MNP-Flex, a platform-agnostic methylation classifier encompassing 184 classes. MNP-Flex achieved 99.6% accuracy for methylation families and 99.2% accuracy for methylation classes with clinically applicable thresholds across a global validation cohort of more than 78,000 frozen and formalin-fixed paraffin-embedded samples spanning five different technologies. Integration of these tools has the potential to advance CNS tumor diagnostics by providing broad access to rapid, actionable molecular insights crucial for personalized treatment strategies.…