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@ARTICLE{Klever:285056,
      author       = {M.-K. Klever and E. Sträng and S. Hetzel and J. Jungnitsch
                      and A. Dolnik and R. Schöpflin and J.-F. Schrezenmeier and
                      F. Schick and O. Blau and J. Westermann and F. G. Rücker
                      and Z. Xia and K. Döhner and H. Schrezenmeier and M.
                      Spielmann and A. Meissner and U. S. Melo and S. Mundlos and
                      L. Bullinger$^*$},
      title        = {{AML} with complex karyotype: extreme genomic complexity
                      revealed by combined long-read sequencing and {H}i-{C}
                      technology.},
      journal      = {Blood advances},
      volume       = {7},
      number       = {21},
      issn         = {2473-9529},
      address      = {Washington, DC},
      publisher    = {American Society of Hematology},
      reportid     = {DKFZ-2023-02199},
      pages        = {6520 - 6531},
      year         = {2023},
      abstract     = {Acute myeloid leukemia with complex karyotype (CK-AML) is
                      associated with poor prognosis, which is only in part
                      explained by underlying TP53 mutations. Especially in the
                      presence of complex chromosomal rearrangements, such as
                      chromothripsis, the outcome of CK-AML is dismal. However,
                      this degree of complexity of genomic rearrangements
                      contributes to the leukemogenic phenotype and treatment
                      resistance of CK-AML remains largely unknown. Applying an
                      integrative workflow for the detection of structural
                      variants (SVs) based on Oxford Nanopore (ONT) genomic DNA
                      long-read sequencing (gDNA-LRS) and high-throughput
                      chromosome confirmation capture (Hi-C) in a well-defined
                      cohort of CK-AML identified regions with an extreme density
                      of SVs. These rearrangements consisted to a large degree of
                      focal amplifications enriched in the proximity of
                      mammalian-wide interspersed repeat elements, which often
                      result in oncogenic fusion transcripts, such as USP7::MVD,
                      or the deregulation of oncogenic driver genes as confirmed
                      by RNA-seq and ONT direct complementary DNA sequencing. We
                      termed this novel phenomenon chromocataclysm. Thus, our
                      integrative SV detection workflow combing gDNA-LRS and Hi-C
                      enables to unravel complex genomic rearrangements at a very
                      high resolution in regions hard to analyze by conventional
                      sequencing technology, thereby providing an important tool
                      to identify novel important drivers underlying cancer with
                      complex karyotypic changes.},
      keywords     = {Humans / Leukemia, Myeloid, Acute: diagnosis / Leukemia,
                      Myeloid, Acute: genetics / Leukemia, Myeloid, Acute: therapy
                      / Abnormal Karyotype / Chromosome Aberrations / Mutation /
                      Genomics / Ubiquitin-Specific Peptidase 7: genetics / USP7
                      protein, human (NLM Chemicals) / Ubiquitin-Specific
                      Peptidase 7 (NLM Chemicals)},
      cin          = {BE01},
      ddc          = {610},
      cid          = {I:(DE-He78)BE01-20160331},
      pnm          = {899 - ohne Topic (POF4-899)},
      pid          = {G:(DE-HGF)POF4-899},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:37582288},
      doi          = {10.1182/bloodadvances.2023010887},
      url          = {https://inrepo02.dkfz.de/record/285056},
}