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@ARTICLE{Stichel:144235,
      author       = {D. Stichel$^*$ and D. Schrimpf$^*$ and B. Casalini$^*$ and
                      J. Meyer$^*$ and A. K. Wefers$^*$ and P. Sievers$^*$ and A.
                      Korshunov$^*$ and C. Koelsche$^*$ and D. E. Reuss$^*$ and A.
                      Reinhardt$^*$ and A. Ebrahimi$^*$ and F.
                      Fernández-Klett$^*$ and T. Kessler$^*$ and D. Sturm$^*$ and
                      J. Ecker$^*$ and T. Milde$^*$ and C. Herold-Mende and O.
                      Witt$^*$ and S. M. Pfister$^*$ and W. Wick$^*$ and D. T. W.
                      Jones$^*$ and A. von Deimling$^*$ and F. Sahm$^*$},
      title        = {{R}outine {RNA} sequencing of formalin-fixed
                      paraffin-embedded specimens in neuropathology diagnostics
                      identifies diagnostically and therapeutically relevant gene
                      fusions.},
      journal      = {Acta neuropathologica},
      volume       = {138},
      number       = {5},
      issn         = {1432-0533},
      address      = {Heidelberg},
      publisher    = {Springer},
      reportid     = {DKFZ-2019-01755},
      pages        = {827-835},
      year         = {2019},
      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.},
      cin          = {B300 / B320 / B062 / B310 / B360},
      ddc          = {610},
      cid          = {I:(DE-He78)B300-20160331 / I:(DE-He78)B320-20160331 /
                      I:(DE-He78)B062-20160331 / I:(DE-He78)B310-20160331 /
                      I:(DE-He78)B360-20160331},
      pnm          = {312 - Functional and structural genomics (POF3-312)},
      pid          = {G:(DE-HGF)POF3-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:31278449},
      doi          = {10.1007/s00401-019-02039-3},
      url          = {https://inrepo02.dkfz.de/record/144235},
}