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@ARTICLE{Cmero:180877,
      author       = {M. Cmero and K. Yuan and C. S. Ong and J. Schröder and E.
                      PCAWG and G. Heterogeneity Working and N. M. Corcoran and T.
                      Papenfuss and C. M. Hovens and F. Markowetz and G. Macintyre
                      and PCAWGConsortium},
      title        = {{I}nferring structural variant cancer cell fraction.},
      journal      = {Nature Communications},
      volume       = {11},
      number       = {1},
      issn         = {2041-1723},
      address      = {[London]},
      publisher    = {Nature Publishing Group UK},
      reportid     = {DKFZ-2022-01626},
      pages        = {730},
      year         = {2020},
      note         = {siehe Correction: DKFZ Autoren affiliiert im PCAWG
                      Consortium:https://inrepo02.dkfz.de/record/212436 /
                      https://doi.org/10.1038/s41467-022-32338-5},
      abstract     = {We present SVclone, a computational method for inferring
                      the cancer cell fraction of structural variant (SV)
                      breakpoints from whole-genome sequencing data. SVclone
                      accurately determines the variant allele frequencies of both
                      SV breakends, then simultaneously estimates the cancer cell
                      fraction and SV copy number. We assess performance using in
                      silico mixtures of real samples, at known proportions,
                      created from two clonal metastases from the same patient. We
                      find that SVclone's performance is comparable to
                      single-nucleotide variant-based methods, despite having an
                      order of magnitude fewer data points. As part of the
                      Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium,
                      which aggregated whole-genome sequencing data from 2658
                      cancers across 38 tumour types, we use SVclone to reveal a
                      subset of liver, ovarian and pancreatic cancers with
                      subclonally enriched copy-number neutral rearrangements that
                      show decreased overall survival. SVclone enables improved
                      characterisation of SV intra-tumour heterogeneity.},
      keywords     = {Algorithms / Computational Biology: methods / Computer
                      Simulation / DNA Copy Number Variations / Female / Gene
                      Frequency / Genome, Human / Humans / Liver Neoplasms:
                      genetics / Liver Neoplasms: pathology / Male / Neoplasms:
                      genetics / Neoplasms: pathology / Ovarian Neoplasms:
                      genetics / Ovarian Neoplasms: pathology / Pancreatic
                      Neoplasms: genetics / Pancreatic Neoplasms: pathology /
                      Prostatic Neoplasms: genetics / Prostatic Neoplasms:
                      pathology / Sensitivity and Specificity / Whole Genome
                      Sequencing},
      cin          = {B080 / B240 / B370 / B330 / HD01 / B060 / B360 / BE01 /
                      B062 / B066 / B063 / W190 / W610 / B260},
      ddc          = {500},
      cid          = {I:(DE-He78)B080-20160331 / I:(DE-He78)B240-20160331 /
                      I:(DE-He78)B370-20160331 / I:(DE-He78)B330-20160331 /
                      I:(DE-He78)HD01-20160331 / I:(DE-He78)B060-20160331 /
                      I:(DE-He78)B360-20160331 / I:(DE-He78)BE01-20160331 /
                      I:(DE-He78)B062-20160331 / I:(DE-He78)B066-20160331 /
                      I:(DE-He78)B063-20160331 / I:(DE-He78)W190-20160331 /
                      I:(DE-He78)W610-20160331 / I:(DE-He78)B260-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:32024845},
      pmc          = {pmc:PMC7002525},
      doi          = {10.1038/s41467-020-14351-8},
      url          = {https://inrepo02.dkfz.de/record/180877},
}