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Acta Neuropathologica

, Volume 131, Issue 6, pp 903–910 | Cite as

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

  • 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
Original Paper

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.

Keywords

Medulloblastoma Pilocytic Astrocytoma FFPE Tissue Copy Number Aberration Diffuse Glioma 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

This study was supported by the German Cancer Aid (110670) and by a PostDoc fellowship of the Medical Faculty Heidelberg to FS. We also thank the DKFZ-Heidelberg Center for Personalized Oncology (DKFZ-HIPO) for funding through HIPO_036 and HIPO_057.

Supplementary material

401_2015_1519_MOESM1_ESM.docx (1.9 mb)
Supplementary material 1 (DOCX 1920 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Felix Sahm
    • 1
    • 2
  • Daniel Schrimpf
    • 1
    • 2
  • David T. W. Jones
    • 3
  • Jochen Meyer
    • 2
  • Annekathrin Kratz
    • 1
    • 2
  • David Reuss
    • 1
    • 2
  • David Capper
    • 1
    • 2
  • Christian Koelsche
    • 1
    • 2
  • Andrey Korshunov
    • 1
    • 2
  • Benedikt Wiestler
    • 4
    • 5
  • Ivo Buchhalter
    • 6
    • 7
  • Till Milde
    • 8
    • 9
  • Florian Selt
    • 8
    • 9
  • Dominik Sturm
    • 3
    • 8
  • Marcel Kool
    • 3
  • Manuela Hummel
    • 10
  • Melanie Bewerunge-Hudler
    • 11
  • Christian Mawrin
    • 12
  • Ulrich Schüller
    • 13
  • Christine Jungk
    • 14
  • Antje Wick
    • 4
    • 5
  • Olaf Witt
    • 8
    • 9
  • Michael Platten
    • 4
    • 15
  • Christel Herold-Mende
    • 14
  • Andreas Unterberg
    • 14
  • Stefan M. Pfister
    • 3
    • 8
  • Wolfgang Wick
    • 4
    • 5
  • Andreas von Deimling
    • 1
    • 2
  1. 1.Department of Neuropathology, Institute of PathologyRuprecht-Karls-University HeidelbergHeidelbergGermany
  2. 2.Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
  3. 3.Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
  4. 4.Neurology ClinicHeidelberg University HospitalHeidelbergGermany
  5. 5.Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
  6. 6.Division of Theoretical BioinformaticsGerman Cancer Research Center (DKFZ)HeidelbergGermany
  7. 7.Division of Applied BioinformaticsGerman Cancer Research Center (DKFZ)HeidelbergGermany
  8. 8.Department of Pediatric Oncology, Haematology and ImmunologyHeidelberg University Hospital, and National Center for Tumor Diseases (NCT)HeidelbergGermany
  9. 9.Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ)German Consortium for Translational Cancer Research (DKTK)HeidelbergGermany
  10. 10.Division of BiostatisticsGerman Cancer Research Center (DKFZ)HeidelbergGermany
  11. 11.Genomics and Proteomics Core FacilityGerman Cancer Research Center (DKFZ)HeidelbergGermany
  12. 12.Department of NeuropathologyOtto von Guericke University MagdeburgMagdeburgGermany
  13. 13.Center of NeuropathologyLudwig-Maximilians-UniversityMunichGermany
  14. 14.Department of NeurosurgeryHeidelberg University HospitalHeidelbergGermany
  15. 15.Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Consortium for Translational Cancer Research (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany

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