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@ARTICLE{Rausch:275428,
      author       = {T. Rausch and R. Snajder$^*$ and A. Leger and M.
                      Simovic$^*$ and M. Giurgiu and L. Villacorta and A. G.
                      Henssen$^*$ and S. Fröhling$^*$ and O. Stegle$^*$ and E.
                      Birney and M. J. Bonder$^*$ and A. Ernst$^*$ and J.
                      Korbel$^*$},
      title        = {{L}ong-read sequencing of diagnosis and post-therapy
                      medulloblastoma reveals complex rearrangement patterns and
                      epigenetic signatures},
      journal      = {Cell genomics},
      volume       = {3},
      number       = {4},
      issn         = {2666-979X},
      address      = {Amsterdam},
      publisher    = {Elsevier},
      reportid     = {DKFZ-2023-00751},
      pages        = {100281},
      year         = {2023},
      note         = {#EA:B260#LA:B420#LA:B480#},
      abstract     = {Cancer genomes harbor a broad spectrum of structural
                      variants (SVs) driving tumorigenesis, a relevant subset of
                      which escape discovery using short-read sequencing. We
                      employed Oxford Nanopore Technologies (ONT) long-read
                      sequencing in a paired diagnostic and post-therapy
                      medulloblastoma to unravel the haplotype-resolved somatic
                      genetic and epigenetic landscape. We assembled complex
                      rearrangements, including a 1.55-Mbp chromothripsis event,
                      and we uncover a complex SV pattern termed templated
                      insertion (TI) thread, characterized by short (mostly <1 kb)
                      insertions showing prevalent self-concatenation into highly
                      amplified structures of up to 50 kbp in size. TI threads
                      occur in $3\%$ of cancers, with a prevalence up to $74\%$ in
                      liposarcoma, and frequent colocalization with
                      chromothripsis. We also perform long-read-based methylome
                      profiling and discover allele-specific methylation (ASM)
                      effects, complex rearrangements exhibiting differential
                      methylation, and differential promoter methylation in
                      cancer-driver genes. Our study shows the advantage of
                      long-read sequencing in the discovery and characterization
                      of complex somatic rearrangements.},
      cin          = {B260 / B420 / HD01 / B340 / B480 / BE01},
      ddc          = {610},
      cid          = {I:(DE-He78)B260-20160331 / I:(DE-He78)B420-20160331 /
                      I:(DE-He78)HD01-20160331 / I:(DE-He78)B340-20160331 /
                      I:(DE-He78)B480-20160331 / 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:37082141},
      doi          = {10.1016/j.xgen.2023.100281},
      url          = {https://inrepo02.dkfz.de/record/275428},
}