Rapid comprehensive molecular profiling of CNS tumors

Watch on demand to hear Areeba Patel (German Cancer Research Center) discuss rapid, comprehensive molecular profiling of CNS tumors using methylation-based nanopore sequencing, showcasing its potential for clinical implementation.

Abstract: Integrating molecular data is pivotal in CNS tumour diagnostics, yet conventional assays are constrained by technical complexity, cost, and long turnaround times. We developed Rapid-CNS2, an adaptive-sampling based nanopore sequencing workflow, and clinically validated it in a multicentre study of 301 archival and prospective cases, including 18 sequenced intraoperatively. The optimised pipeline delivers real-time methylation classification and genome-wide copy-number profiling within a 30-minute intraoperative window, and completes molecular profiling within 24 hours, reporting mutations, copy-number variants, gene fusions, and MGMT promoter status. Across the study, misleading results were rare (<2%), supporting reliability for routine and intraoperative use.  To expand access to methylation-based diagnosis, we developed MNP-Flex, a platform-agnostic classifier covering 184 CNS tumour classes compatible with the latest version of the Heidelberg classifier. In validation across a global cohort of >78,000 frozen and FFPE samples spanning five technologies, MNP-Flex achieved 99.6% accuracy at the methylation-family level and 99.2% at the class level using clinically actionable thresholds.  Together, these results demonstrate rapid end-to-end turnaround (minutes for intraoperative calls;24 hours for full profiling), high analytical performance with very low rates of misleading outputs, and broad technical compatibility, enabling scalable deployment across centres. This clinically validated workflow provides timely, comprehensive molecular characterisation to underpin evidence-based decision-making in CNS tumour care.

This talk was originally presented at AMP 2025, Boston.