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@ARTICLE{Legrand:286226,
      author       = {C. Legrand$^*$ and R. Andriantsoa$^*$ and P. Lichter$^*$
                      and G. Raddatz$^*$ and F. Lyko$^*$},
      title        = {{T}ime-resolved, integrated analysis of clonally evolving
                      genomes.},
      journal      = {PLoS Genetics},
      volume       = {19},
      number       = {12},
      issn         = {1553-7390},
      address      = {San Francisco, Calif.},
      publisher    = {Public Library of Science},
      reportid     = {DKFZ-2023-02724},
      pages        = {e1011085 -},
      year         = {2023},
      note         = {DKFZ-ZMBH Alliance / #EA:A130#LA:A130#},
      abstract     = {Clonal genome evolution is a key feature of asexually
                      reproducing species and human cancer development. While many
                      studies have described the landscapes of clonal genome
                      evolution in cancer, few determine the underlying
                      evolutionary parameters from molecular data, and even fewer
                      integrate theory with data. We derived theoretical results
                      linking mutation rate, time, expansion dynamics, and
                      biological/clinical parameters. Subsequently, we inferred
                      time-resolved estimates of evolutionary parameters from
                      mutation accumulation, mutational signatures and selection.
                      We then applied this framework to predict the time of
                      speciation of the marbled crayfish, an enigmatic, globally
                      invasive parthenogenetic freshwater crayfish. The results
                      predict that speciation occurred between 1986 and 1990,
                      which is consistent with biological records. We also used
                      our framework to analyze whole-genome sequencing datasets
                      from primary and relapsed glioblastoma, an aggressive brain
                      tumor. The results identified evolutionary subgroups and
                      showed that tumor cell survival could be inferred from
                      genomic data that was generated during the resection of the
                      primary tumor. In conclusion, our framework allowed a
                      time-resolved, integrated analysis of key parameters in
                      clonally evolving genomes, and provided novel insights into
                      the evolutionary age of marbled crayfish and the progression
                      of glioblastoma.},
      cin          = {A130 / B060 / HD01},
      ddc          = {610},
      cid          = {I:(DE-He78)A130-20160331 / I:(DE-He78)B060-20160331 /
                      I:(DE-He78)HD01-20160331},
      pnm          = {311 - Zellbiologie und Tumorbiologie (POF4-311)},
      pid          = {G:(DE-HGF)POF4-311},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:38096267},
      doi          = {10.1371/journal.pgen.1011085},
      url          = {https://inrepo02.dkfz.de/record/286226},
}