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@ARTICLE{Whalley:163954,
      author       = {J. P. Whalley and I. Buchhalter$^*$ and E. Rheinbay and K.
                      M. Raine and M. D. Stobbe and K. Kleinheinz$^*$ and J.
                      Werner and S. Beltran and M. Gut and D. Hübschmann$^*$ and
                      B. Hutter$^*$ and D. Livitz and M. D. Perry and M. Rosenberg
                      and G. Saksena and J.-R. Trotta and R. Eils and D. S.
                      Gerhard and P. J. Campbell and M. Schlesner$^*$ and I. G.
                      Gut},
      title        = {{F}ramework for quality assessment of whole genome cancer
                      sequences.},
      journal      = {Nature Communications},
      volume       = {11},
      number       = {1},
      issn         = {2041-1723},
      address      = {[London]},
      publisher    = {Nature Publishing Group UK},
      reportid     = {DKFZ-2020-02167},
      pages        = {5040},
      year         = {2020},
      abstract     = {Bringing together cancer genomes from different projects
                      increases power and allows the investigation of pan-cancer,
                      molecular mechanisms. However, working with whole genomes
                      sequenced over several years in different sequencing centres
                      requires a framework to compare the quality of these
                      sequences. We used the Pan-Cancer Analysis of Whole Genomes
                      cohort as a test case to construct such a framework. This
                      cohort contains whole cancer genomes of 2832 donors from 18
                      sequencing centres. We developed a non-redundant set of five
                      quality control (QC) measurements to establish a star rating
                      system. These QC measures reflect known differences in
                      sequencing protocol and provide a guide to downstream
                      analyses and allow for exclusion of samples of poor quality.
                      We have found that this is an effective framework of quality
                      measures. The implementation of the framework is available
                      at:
                      $https://dockstore.org/containers/quay.io/jwerner_dkfz/pancanqc:1.2.2$
                      .},
      cin          = {B080 / W610 / G200 / B330 / B240},
      ddc          = {500},
      cid          = {I:(DE-He78)B080-20160331 / I:(DE-He78)W610-20160331 /
                      I:(DE-He78)G200-20160331 / I:(DE-He78)B330-20160331 /
                      I:(DE-He78)B240-20160331},
      pnm          = {312 - Functional and structural genomics (POF3-312)},
      pid          = {G:(DE-HGF)POF3-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:33028839},
      doi          = {10.1038/s41467-020-18688-y},
      url          = {https://inrepo02.dkfz.de/record/163954},
}