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@ARTICLE{Bailey:165904,
      author       = {Bailey, Matthew H and others},
      collaboration = {M. W. Group and P. n. s. m. c. m. w. group and P.
                      Consortium},
      title        = {{R}etrospective evaluation of whole exome and genome
                      mutation calls in 746 cancer samples.},
      journal      = {Nature Communications},
      volume       = {11},
      number       = {1},
      issn         = {2041-1723},
      address      = {[London]},
      publisher    = {Nature Publishing Group UK},
      reportid     = {DKFZ-2020-02461},
      pages        = {4748},
      year         = {2020},
      abstract     = {The Cancer Genome Atlas (TCGA) and International Cancer
                      Genome Consortium (ICGC) curated consensus somatic mutation
                      calls using whole exome sequencing (WES) and whole genome
                      sequencing (WGS), respectively. Here, as part of the
                      ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG)
                      Consortium, which aggregated whole genome sequencing data
                      from 2,658 cancers across 38 tumour types, we compare WES
                      and WGS side-by-side from 746 TCGA samples, finding that
                      $~80\%$ of mutations overlap in covered exonic regions. We
                      estimate that low variant allele fraction (VAF < $15\%)$ and
                      clonal heterogeneity contribute up to $68\%$ of private WGS
                      mutations and $71\%$ of private WES mutations. We observe
                      that $~30\%$ of private WGS mutations trace to mutations
                      identified by a single variant caller in WES consensus
                      efforts. WGS captures both $~50\%$ more variation in exonic
                      regions and un-observed mutations in loci with variable
                      GC-content. Together, our analysis highlights technological
                      divergences between two reproducible somatic variant
                      detection efforts.},
      keywords     = {Base Composition / DNA, Intergenic / Databases, Genetic /
                      Exome: genetics / Exons / Genome, Human: genetics / Humans /
                      Mutation / Neoplasms: genetics / Retrospective Studies /
                      Whole Exome Sequencing / Whole Genome Sequencing / DNA,
                      Intergenic (NLM Chemicals)},
      cin          = {B080 / HD01 / B240 / B370 / B330 / B060 / B062 / B360 /
                      B087 / B340 / W190 / B063 / BE01 / B066 / W610 / B260 /
                      B300},
      ddc          = {500},
      cid          = {I:(DE-He78)B080-20160331 / I:(DE-He78)HD01-20160331 /
                      I:(DE-He78)B240-20160331 / I:(DE-He78)B370-20160331 /
                      I:(DE-He78)B330-20160331 / I:(DE-He78)B060-20160331 /
                      I:(DE-He78)B062-20160331 / I:(DE-He78)B360-20160331 /
                      I:(DE-He78)B087-20160331 / I:(DE-He78)B340-20160331 /
                      I:(DE-He78)W190-20160331 / I:(DE-He78)B063-20160331 /
                      I:(DE-He78)BE01-20160331 / I:(DE-He78)B066-20160331 /
                      I:(DE-He78)W610-20160331 / I:(DE-He78)B260-20160331 /
                      I:(DE-He78)B300-20160331},
      pnm          = {312 - Functional and structural genomics (POF3-312)},
      pid          = {G:(DE-HGF)POF3-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:32958763},
      pmc          = {pmc:PMC7505971},
      doi          = {10.1038/s41467-020-18151-y},
      url          = {https://inrepo02.dkfz.de/record/165904},
}