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@ARTICLE{Brandes:277759,
      author       = {D. Brandes and L. Yasin and K. Nebral and J. Ebler and D.
                      Schinnerl and D. Picard and A. K. Bergmann and J. Alam and
                      S. Köhrer and O. A. Haas and A. Attarbaschi and T.
                      Marschall and M. Stanulla and A. Borkhardt$^*$ and T.
                      Brozou$^*$ and U. Fischer$^*$ and R. Wagener$^*$},
      title        = {{O}ptical {G}enome {M}apping {I}dentifies {N}ovel
                      {R}ecurrent {S}tructural {A}lterations in {C}hildhood
                      {ETV}6::{RUNX}1+ and {H}igh {H}yperdiploid {A}cute
                      {L}ymphoblastic {L}eukemia.},
      journal      = {HemaSphere},
      volume       = {7},
      number       = {8},
      issn         = {2572-9241},
      address      = {[Philadelphia, Pennsylvania]},
      publisher    = {Wolters Kluwer Health},
      reportid     = {DKFZ-2023-01476},
      pages        = {e925},
      year         = {2023},
      abstract     = {The mutational landscape of B-cell precursor acute
                      lymphoblastic leukemia (BCP-ALL), the most common pediatric
                      cancer, is not fully described partially because commonly
                      applied short-read next generation sequencing has a limited
                      ability to identify structural variations. By combining
                      comprehensive analysis of structural variants (SVs),
                      single-nucleotide variants (SNVs), and small
                      insertions-deletions, new subtype-defining and therapeutic
                      targets may be detected. We analyzed the landscape of
                      somatic alterations in 60 pediatric patients diagnosed with
                      the most common BCP-ALL subtypes, ETV6::RUNX1+ and classical
                      hyperdiploid (HD), using conventional cytogenetics, single
                      nucleotide polymorphism (SNP) array, whole exome sequencing
                      (WES), and the novel optical genome mapping (OGM) technique.
                      Ninety-five percent of SVs detected by cytogenetics and
                      SNP-array were verified by OGM. OGM detected an additional
                      677 SVs not identified using the conventional methods,
                      including (subclonal) IKZF1 deletions. Based on OGM,
                      ETV6::RUNX1+ BCP-ALL harbored 2.7 times more SVs than HD
                      BCP-ALL, mainly focal deletions. Besides SVs in known
                      leukemia development genes (ETV6, PAX5, BTG1, CDKN2A), we
                      identified 19 novel recurrently altered regions (in n ≥ 3)
                      including 9p21.3 (FOCAD/HACD4), 8p11.21 (IKBKB), 1p34.3
                      (ZMYM1), 4q24 (MANBA), 8p23.1 (MSRA), and 10p14 (SFMBT2), as
                      well as ETV6::RUNX1+ subtype-specific SVs (12p13.1 (GPRC5A),
                      12q24.21 (MED13L), 18q11.2 (MIB1), 20q11.22 (NCOA6)). We
                      detected 3 novel fusion genes (SFMBT2::DGKD, PDS5B::STAG2,
                      and TDRD5::LPCAT2), for which the sequence and expression
                      were validated by long-read and whole transcriptome
                      sequencing, respectively. OGM and WES identified double hits
                      of SVs and SNVs (ETV6, BTG1, STAG2, MANBA, TBL1XR1, NSD2) in
                      the same patient demonstrating the power of the combined
                      approach to define the landscape of genomic alterations in
                      BCP-ALL.},
      cin          = {ED01},
      ddc          = {610},
      cid          = {I:(DE-He78)ED01-20160331},
      pnm          = {899 - ohne Topic (POF4-899)},
      pid          = {G:(DE-HGF)POF4-899},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:37469802},
      pmc          = {pmc:PMC10353714},
      doi          = {10.1097/HS9.0000000000000925},
      url          = {https://inrepo02.dkfz.de/record/277759},
}