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@ARTICLE{Weischenfeldt:119229,
      author       = {J. Weischenfeldt and T. D. Dubash$^*$ and A. P. Drainas and
                      B. R. Mardin and Y. Chen and A. M. Stütz and S. M. Waszak
                      and G. Bosco and A. R. Halvorsen and B. Raeder and T.
                      Efthymiopoulos and S. Erkek$^*$ and C. Siegl$^*$ and H.
                      Brenner$^*$ and O. T. Brustugun and S. Dieter$^*$ and P. A.
                      Northcott and I. Petersen and S. Pfister$^*$ and M.
                      Schneider and S. K. Solberg and E. Thunissen and W. Weichert
                      and T. Zichner and R. Thomas and M. Peifer and A. Helland
                      and C. Ball$^*$ and M. Jechlinger and R. Sotillo$^*$ and H.
                      Glimm$^*$ and J. O. Korbel},
      title        = {{P}an-cancer analysis of somatic copy-number alterations
                      implicates {IRS}4 and {IGF}2 in enhancer hijacking.},
      journal      = {Nature genetics},
      volume       = {49},
      number       = {1},
      issn         = {1546-1718},
      address      = {New York, NY},
      publisher    = {Nature America},
      reportid     = {DKFZ-2017-00019},
      pages        = {65 - 74},
      year         = {2017},
      abstract     = {Extensive prior research focused on somatic copy-number
                      alterations (SCNAs) affecting cancer genes, yet the extent
                      to which recurrent SCNAs exert their influence through
                      rearrangement of cis-regulatory elements (CREs) remains
                      unclear. Here we present a framework for inferring
                      cancer-related gene overexpression resulting from CRE
                      reorganization (e.g., enhancer hijacking) by integrating
                      SCNAs, gene expression data and information on topologically
                      associating domains (TADs). Analysis of 7,416 cancer genomes
                      uncovered several pan-cancer candidate genes, including
                      IRS4, SMARCA1 and TERT. We demonstrate that IRS4
                      overexpression in lung cancer is associated with recurrent
                      deletions in cis, and we present evidence supporting a
                      tumor-promoting role. We additionally pursued
                      cancer-type-specific analyses and uncovered IGF2 as a target
                      for enhancer hijacking in colorectal cancer. Recurrent
                      tandem duplications intersecting with a TAD boundary mediate
                      de novo formation of a 3D contact domain comprising IGF2 and
                      a lineage-specific super-enhancer, resulting in high-level
                      gene activation. Our framework enables systematic inference
                      of CRE rearrangements mediating dysregulation in cancer.},
      cin          = {C070 / G110 / B062 / B220 / G100 / L101 / L701},
      ddc          = {570},
      cid          = {I:(DE-He78)C070-20160331 / I:(DE-He78)G110-20160331 /
                      I:(DE-He78)B062-20160331 / I:(DE-He78)B220-20160331 /
                      I:(DE-He78)G100-20160331 / I:(DE-He78)L101-20160331 /
                      I:(DE-He78)L701-20160331},
      pnm          = {312 - Functional and structural genomics (POF3-312)},
      pid          = {G:(DE-HGF)POF3-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:27869826},
      doi          = {10.1038/ng.3722},
      url          = {https://inrepo02.dkfz.de/record/119229},
}