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Erschienen in: Acta Neuropathologica 6/2016

15.12.2015 | Original Paper

Next-generation sequencing in routine brain tumor diagnostics enables an integrated diagnosis and identifies actionable targets

verfasst von: Felix Sahm, Daniel Schrimpf, David T. W. Jones, Jochen Meyer, Annekathrin Kratz, David Reuss, David Capper, Christian Koelsche, Andrey Korshunov, Benedikt Wiestler, Ivo Buchhalter, Till Milde, Florian Selt, Dominik Sturm, Marcel Kool, Manuela Hummel, Melanie Bewerunge-Hudler, Christian Mawrin, Ulrich Schüller, Christine Jungk, Antje Wick, Olaf Witt, Michael Platten, Christel Herold-Mende, Andreas Unterberg, Stefan M. Pfister, Wolfgang Wick, Andreas von Deimling

Erschienen in: Acta Neuropathologica | Ausgabe 6/2016

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Abstract

With the number of prognostic and predictive genetic markers in neuro-oncology steadily growing, the need for comprehensive molecular analysis of neuropathology samples has vastly increased. We therefore developed a customized enrichment/hybrid-capture-based next-generation sequencing (NGS) gene panel comprising the entire coding and selected intronic and promoter regions of 130 genes recurrently altered in brain tumors, allowing for the detection of single nucleotide variations, fusions, and copy number aberrations. Optimization of probe design, library generation and sequencing conditions on 150 samples resulted in a 5-workday routine workflow from the formalin-fixed paraffin-embedded sample to neuropathological report. This protocol was applied to 79 retrospective cases with established molecular aberrations for validation and 71 prospective cases for discovery of potential therapeutic targets. Concordance of NGS compared to established, single biomarker methods was 98.0 %, with discrepancies resulting from one case where a TERT promoter mutation was not called by NGS and three ATRX mutations not being detected by Sanger sequencing. Importantly, in samples with low tumor cell content, NGS was able to identify mutant alleles that were not detectable by traditional methods. Information derived from NGS data identified potential targets for experimental therapy in 37/47 (79 %) glioblastomas, 9/10 (90 %) pilocytic astrocytomas, and 5/14 (36 %) medulloblastomas in the prospective target discovery cohort. In conclusion, we present the settings for high-throughput, adaptive next-generation sequencing in routine neuropathology diagnostics. Such an approach will likely become highly valuable in the near future for treatment decision making, as more therapeutic targets emerge and genetic information enters the classification of brain tumors.
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Metadaten
Titel
Next-generation sequencing in routine brain tumor diagnostics enables an integrated diagnosis and identifies actionable targets
verfasst von
Felix Sahm
Daniel Schrimpf
David T. W. Jones
Jochen Meyer
Annekathrin Kratz
David Reuss
David Capper
Christian Koelsche
Andrey Korshunov
Benedikt Wiestler
Ivo Buchhalter
Till Milde
Florian Selt
Dominik Sturm
Marcel Kool
Manuela Hummel
Melanie Bewerunge-Hudler
Christian Mawrin
Ulrich Schüller
Christine Jungk
Antje Wick
Olaf Witt
Michael Platten
Christel Herold-Mende
Andreas Unterberg
Stefan M. Pfister
Wolfgang Wick
Andreas von Deimling
Publikationsdatum
15.12.2015
Verlag
Springer Berlin Heidelberg
Erschienen in
Acta Neuropathologica / Ausgabe 6/2016
Print ISSN: 0001-6322
Elektronische ISSN: 1432-0533
DOI
https://doi.org/10.1007/s00401-015-1519-8

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