Prospective, multicentre validation of a platform for rapid molecular profiling of central nervous system tumours


The Oxford Nanopore-based workflow, Rapid-CNS2, together with MNP-Flex classified central nervous system tumours in under 30 minutes. The method detected key variants previously missed by short-read methods, and up to 94.6% of results matched standard diagnostic tests, highlighting the potential for this Oxford Nanopore-based approach to accelerate personalised cancer care in the future.

Key points:

  • Patel et al. combined Rapid-CNS2 (an adaptive sampling-based Oxford Nanopore sequencing workflow) with the methylation classifier MNP-Flex

  • Methylation classification and copy number profiles were reported within a 30-minute intraoperative window, and comprehensive molecular profiling followed within 24 hours

  • Rapid-CNS2 achieved concordance with current diagnostic tools in 285/301 cases (94.6%)

  • Oxford Nanopore sequencing detected clinically relevant mutations, fusions, and structural variants, including alterations missed by short-read methods

Watch Areeba Patel discuss this research at NCM 2021

'The fact that the capital expense for the smallest device allowing for Rapid-CNS2 is of the magnitude of one-fiftieth of the minimal required set-up for conventional methylation testing will likely facilitate swift proliferation of [Oxford Nanopore] technology'

Areeba Patel et al.

Sample type: human CNS tumour samples

Kit: Ligation Sequencing Kit, Ultra-Long DNA Sequencing Kit

Authors: 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 TW Jones, Matthew Loose, Matthias Schlesner, Martin Sill, Felix Sahm