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Acta Neuropathologica

, Volume 138, Issue 5, pp 827–835 | Cite as

Routine RNA sequencing of formalin-fixed paraffin-embedded specimens in neuropathology diagnostics identifies diagnostically and therapeutically relevant gene fusions

  • Damian Stichel
  • Daniel Schrimpf
  • Belén Casalini
  • Jochen Meyer
  • Annika K. Wefers
  • Philipp Sievers
  • Andrey Korshunov
  • Christian Koelsche
  • David E. Reuss
  • Annekathrin Reinhardt
  • Azadeh Ebrahimi
  • Francisco Fernández-Klett
  • Tobias Kessler
  • Dominik Sturm
  • Jonas Ecker
  • Till Milde
  • Christel Herold-Mende
  • Olaf Witt
  • Stefan M. Pfister
  • Wolfgang Wick
  • David T. W. Jones
  • Andreas von DeimlingEmail author
  • Felix SahmEmail author
Original Paper

Abstract

Molecular markers have become pivotal in brain tumor diagnostics. Mutational analyses by targeted next-generation sequencing of DNA and array-based DNA methylation assessment with copy number analyses are increasingly being used in routine diagnostics. However, the broad variety of gene fusions occurring in brain tumors is marginally covered by these technologies and often only assessed by targeted assays. Here, we assessed the feasibility and clinical value of investigating gene fusions in formalin-fixed paraffin-embedded (FFPE) tumor tissues by next-generation mRNA sequencing in a routine diagnostic setting. After establishment and optimization of a workflow applicable in a routine setting, prospective diagnostic application in a neuropathology department for 26 months yielded relevant fusions in 66 out of 101 (65%) analyzed cases. In 43 (43%) cases, the fusions were of decisive diagnostic relevance and in 40 (40%) cases the fusion genes rendered a druggable target. A major strength of this approach was its ability to detect fusions beyond the canonical alterations for a given entity, and the unbiased search for any fusion event in cases with uncertain diagnosis and, thus, uncertain spectrum of expected fusions. This included both rare variants of established fusions which had evaded prior targeted analyses as well as the detection of previously unreported fusion events. While the impact of fusion detection on diagnostics is highly relevant, it is especially the detection of “druggable” fusions which will most likely provide direct benefit to the patients. The wider application of this approach for unbiased fusion identification therefore promises to be a major advance in identifying alterations with immediate impact on patient care.

Keywords

RNA sequencing Gene fusions Molecular diagnostics Molecular classification Targeted treatment 

Notes

Acknowledgements

We thank Hai Yen Nguyen, Laura Dörner, and Lisa Kreinbihl for skillful technical assistance. This study was supported by the Else Kröner-Fresenius Stiftung (EKFS, 2017_EKES.24) and the Pediatric Low Grade Astrocytoma Fund (PLGA Fund) at the Pediatric Brain Tumor Foundation (PBTF).

Supplementary material

401_2019_2039_MOESM1_ESM.docx (266 kb)
Supplementary material 1 (DOCX 284 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Damian Stichel
    • 1
    • 2
  • Daniel Schrimpf
    • 1
    • 2
  • Belén Casalini
    • 1
    • 2
  • Jochen Meyer
    • 1
    • 2
  • Annika K. Wefers
    • 1
    • 2
    • 3
  • Philipp Sievers
    • 1
    • 2
  • Andrey Korshunov
    • 1
    • 2
    • 3
  • Christian Koelsche
    • 1
    • 2
    • 10
  • David E. Reuss
    • 1
    • 2
  • Annekathrin Reinhardt
    • 1
    • 2
  • Azadeh Ebrahimi
    • 1
    • 2
  • Francisco Fernández-Klett
    • 1
    • 2
  • Tobias Kessler
    • 4
    • 5
  • Dominik Sturm
    • 3
    • 6
    • 7
  • Jonas Ecker
    • 3
    • 7
    • 9
  • Till Milde
    • 3
    • 7
    • 9
  • Christel Herold-Mende
    • 11
  • Olaf Witt
    • 3
    • 7
    • 9
  • Stefan M. Pfister
    • 3
    • 6
    • 7
  • Wolfgang Wick
    • 4
    • 5
  • David T. W. Jones
    • 3
    • 8
  • Andreas von Deimling
    • 1
    • 2
    Email author
  • Felix Sahm
    • 1
    • 2
    • 3
    Email author
  1. 1.Department of Neuropathology, Institute of PathologyUniversity Hospital HeidelbergHeidelbergGermany
  2. 2.Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
  3. 3.Hopp Children’s Cancer Center (KiTZ)HeidelbergGermany
  4. 4.Department of Neurology and Neurooncology Program, National Center for Tumor DiseasesHeidelberg University HospitalHeidelbergGermany
  5. 5.Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
  6. 6.Division of Pediatric Neurooncology, German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
  7. 7.Department of Pediatric Oncology, Hematology, Immunology and PulmonologyUniversity Hospital HeidelbergHeidelbergGermany
  8. 8.Pediatric Glioma Research Group, German Consortium for Translational Cancer Research (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
  9. 9.CCU Pediatric Oncology, German Cancer Research Center (DKFZ)German Cancer Consortium (DKTK)HeidelbergGermany
  10. 10.Department of General Pathology, Institute of PathologyHeidelberg University HospitalHeidelbergGermany
  11. 11.Division of Experimental NeurosurgeryUniversity Hospital HeidelbergHeidelbergGermany

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