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@ARTICLE{Stichel:166489,
      author       = {D. Stichel$^*$ and D. Schrimpf$^*$ and P. Sievers$^*$ and
                      A. Reinhardt$^*$ and A. K. Suwala$^*$ and M. Sill$^*$ and D.
                      E. Reuss$^*$ and A. Korshunov$^*$ and B. M. Casalini$^*$ and
                      A. C. Sommerkamp$^*$ and J. Ecker$^*$ and F. Selt$^*$ and D.
                      Sturm$^*$ and A. Gnekow and A. Koch and M. Simon and P.
                      Hernáiz Driever and U. Schüller and D. Capper$^*$ and C.
                      M. van Tilburg$^*$ and O. Witt$^*$ and T. Milde$^*$ and S.
                      M. Pfister$^*$ and D. T. W. Jones$^*$ and A. von
                      Deimling$^*$ and F. Sahm$^*$ and A. Wefers$^*$},
      title        = {{A}ccurate calling of {KIAA}1549-{BRAF} fusions from {DNA}
                      of human brain tumours using methylation array-based copy
                      number and gene panel sequencing data.},
      journal      = {Neuropathology $\&$ applied neurobiology},
      volume       = {47},
      number       = {3},
      issn         = {1365-2990},
      address      = {Oxford [u.a.]},
      publisher    = {Wiley-Blackwell},
      reportid     = {DKFZ-2020-02932},
      pages        = {406-414},
      year         = {2021},
      note         = {#EA:B300#LA:B300#2021 Apr;47(3):406-414},
      abstract     = {KIAA1549-BRAF fusions occur in certain brain tumours and
                      provide druggable targets due to a constitutive activation
                      of the MAP-kinase pathway. We introduce workflows for
                      calling the KIAA1549-BRAF fusion from DNA
                      methylation-array-derived copy number as well as DNA panel
                      sequencing data.Copy number profiles were analysed by
                      automated screening and visual verification of a tandem
                      duplication on chromosome 7q34, indicative of the
                      KIAA1549-BRAF fusion. Pilocytic astrocytomas of the ICGC
                      cohort with known fusion status were used for validation.
                      KIAA1549-BRAF fusions were called from DNA panel sequencing
                      data using the fusion callers Manta, Arriba with modified
                      filtering criteria and deFuse. We screened DNA methylation
                      and panel sequencing data of 7790 specimens from brain
                      tumour and sarcoma entities.We identified the fusion in 337
                      brain tumours with both DNA methylation and panel sequencing
                      data. Among these, we detected the fusion from copy number
                      data in $84\%$ and from DNA panel sequencing data in more
                      than $90\%$ using Arriba with modified filters. While in
                      $74\%$ the KIAA1549-BRAF fusion was detected from both
                      methylation-array-derived copy number and panel sequencing
                      data, in $9\%$ it was detected from copy number data only
                      and in $16\%$ from panel data only. The fusion was almost
                      exclusively found in pilocytic astrocytomas, diffuse
                      leptomeningeal glioneuronal tumours and high-grade
                      astrocytomas with piloid features.The KIAA1549-BRAF fusion
                      can be reliably detected from either DNA methylation array
                      or DNA panel data. The use of both methods is recommended
                      for the most sensitive detection of this diagnostically and
                      therapeutically important marker.},
      keywords     = {KIAA1549-BRAF (Other) / Arriba (Other) / DNA methylation
                      (Other) / DNA panel sequencing (Other) / gene fusion (Other)
                      / pilocytic astrocytoma (Other)},
      cin          = {B300 / B062 / HD01 / B360 / B310 / BE01},
      ddc          = {610},
      cid          = {I:(DE-He78)B300-20160331 / I:(DE-He78)B062-20160331 /
                      I:(DE-He78)HD01-20160331 / I:(DE-He78)B360-20160331 /
                      I:(DE-He78)B310-20160331 / I:(DE-He78)BE01-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:33336421},
      doi          = {10.1111/nan.12683},
      url          = {https://inrepo02.dkfz.de/record/166489},
}