% IMPORTANT: The following is UTF-8 encoded.  This means that in the presence
% of non-ASCII characters, it will not work with BibTeX 0.99 or older.
% Instead, you should use an up-to-date BibTeX implementation like “bibtex8” or
% “biber”.

@ARTICLE{Alioto:126033,
      author       = {T. S. Alioto and I. Buchhalter$^*$ and S. Derdak and B.
                      Hutter$^*$ and M. D. Eldridge and E. Hovig and L. E. Heisler
                      and T. A. Beck and J. T. Simpson and L. Tonon and A.-S.
                      Sertier and A.-M. Patch and N. Jäger$^*$ and P. Ginsbach
                      and R. Drews$^*$ and N. Paramasivam$^*$ and R. Kabbe$^*$ and
                      S. Chotewutmontri$^*$ and N. Diessl$^*$ and C. Previti$^*$
                      and S. Schmidt$^*$ and B. Brors$^*$ and L. Feuerbach$^*$ and
                      M. Heinold$^*$ and S. Gröbner$^*$ and A. Korshunov$^*$ and
                      P. S. Tarpey and A. P. Butler and J. Hinton and D. Jones and
                      A. Menzies and K. Raine and R. Shepherd and L. Stebbings and
                      J. W. Teague and P. Ribeca and F. C. Giner and S. Beltran
                      and E. Raineri and M. Dabad and S. C. Heath and M. Gut and
                      R. E. Denroche and N. J. Harding and T. N. Yamaguchi and A.
                      Fujimoto and H. Nakagawa and V. Quesada and R. Valdés-Mas
                      and S. Nakken and D. Vodák and L. Bower and A. G. Lynch and
                      C. L. Anderson and N. Waddell and J. V. Pearson and S. M.
                      Grimmond and M. Peto and P. Spellman and M. He and C.
                      Kandoth and S. Lee and J. Zhang and L. Létourneau and S. Ma
                      and S. Seth and D. Torrents and L. Xi and D. A. Wheeler and
                      C. López-Otín and E. Campo and P. J. Campbell and P. C.
                      Boutros and X. S. Puente and D. S. Gerhard and S.
                      Pfister$^*$ and J. D. McPherson and T. J. Hudson and M.
                      Schlesner$^*$ and P. Lichter$^*$ and R. Eils$^*$ and D.
                      Jones$^*$ and I. G. Gut},
      title        = {{A} comprehensive assessment of somatic mutation detection
                      in cancer using whole-genome sequencing.},
      journal      = {Nature Communications},
      volume       = {6},
      issn         = {2041-1723},
      address      = {London},
      publisher    = {Nature Publishing Group},
      reportid     = {DKFZ-2017-02148},
      pages        = {10001},
      year         = {2015},
      abstract     = {As whole-genome sequencing for cancer genome analysis
                      becomes a clinical tool, a full understanding of the
                      variables affecting sequencing analysis output is required.
                      Here using tumour-normal sample pairs from two different
                      types of cancer, chronic lymphocytic leukaemia and
                      medulloblastoma, we conduct a benchmarking exercise within
                      the context of the International Cancer Genome Consortium.
                      We compare sequencing methods, analysis pipelines and
                      validation methods. We show that using PCR-free methods and
                      increasing sequencing depth to ∼ 100 × shows benefits, as
                      long as the tumour:control coverage ratio remains balanced.
                      We observe widely varying mutation call rates and low
                      concordance among analysis pipelines, reflecting the
                      artefact-prone nature of the raw data and lack of standards
                      for dealing with the artefacts. However, we show that, using
                      the benchmark mutation set we have created, many issues are
                      in fact easy to remedy and have an immediate positive impact
                      on mutation detection accuracy.},
      cin          = {B060 / B062 / B080 / G200 / W190 / G380},
      ddc          = {500},
      cid          = {I:(DE-He78)B060-20160331 / I:(DE-He78)B062-20160331 /
                      I:(DE-He78)B080-20160331 / I:(DE-He78)G200-20160331 /
                      I:(DE-He78)W190-20160331 / I:(DE-He78)G380-20160331},
      pnm          = {312 - Functional and structural genomics (POF3-312)},
      pid          = {G:(DE-HGF)POF3-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:26647970},
      pmc          = {pmc:PMC4682041},
      doi          = {10.1038/ncomms10001},
      url          = {https://inrepo02.dkfz.de/record/126033},
}