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@ARTICLE{Tretter:277913,
      author       = {C. Tretter$^*$ and N. de Andrade Krätzig and M. Pecoraro
                      and S. Lange and P. Seifert and C. von Frankenberg and J.
                      Untch and G. Zuleger and M. Wilhelm and D. P. Zolg and F. S.
                      Dreyer and E. Bräunlein and T. Engleitner and S. Uhrig and
                      M. Boxberg$^*$ and K. Steiger$^*$ and J. Slotta-Huspenina
                      and S. Ochsenreither$^*$ and N. von Bubnoff$^*$ and S.
                      Bauer$^*$ and M. Börries$^*$ and P. J. Jost$^*$ and K.
                      Schenck$^*$ and I. Dresing$^*$ and F. Bassermann$^*$ and H.
                      Friess and D. Reim and K. Grützmann$^*$ and K. Pfütze$^*$
                      and B. Klink$^*$ and E. Schröck$^*$ and B. Haller and B.
                      Kuster$^*$ and M. Mann and W. Weichert$^*$ and S.
                      Fröhling$^*$ and R. Rad$^*$ and M. Hiltensperger$^*$ and A.
                      Krackhardt$^*$},
      title        = {{P}roteogenomic analysis reveals {RNA} as a source for
                      tumor-agnostic neoantigen identification.},
      journal      = {Nature Communications},
      volume       = {14},
      number       = {1},
      issn         = {2041-1723},
      address      = {[London]},
      publisher    = {Nature Publishing Group UK},
      reportid     = {DKFZ-2023-01572},
      pages        = {4632},
      year         = {2023},
      abstract     = {Systemic pan-tumor analyses may reveal the significance of
                      common features implicated in cancer immunogenicity and
                      patient survival. Here, we provide a comprehensive
                      multi-omics data set for 32 patients across 25 tumor types
                      for proteogenomic-based discovery of neoantigens. By using
                      an optimized computational approach, we discover a large
                      number of tumor-specific and tumor-associated antigens. To
                      create a pipeline for the identification of neoantigens in
                      our cohort, we combine DNA and RNA sequencing with MS-based
                      immunopeptidomics of tumor specimens, followed by the
                      assessment of their immunogenicity and an in-depth
                      validation process. We detect a broad variety of
                      non-canonical HLA-binding peptides in the majority of
                      patients demonstrating partially immunogenicity. Our
                      validation process allows for the selection of 32 potential
                      neoantigen candidates. The majority of neoantigen candidates
                      originates from variants identified in the RNA data set,
                      illustrating the relevance of RNA as a still understudied
                      source of cancer antigens. This study underlines the
                      importance of RNA-centered variant detection for the
                      identification of shared biomarkers and potentially relevant
                      neoantigen candidates.},
      cin          = {MU01 / HD01 / B340 / BE01 / FR01 / ED01 / DD01},
      ddc          = {500},
      cid          = {I:(DE-He78)MU01-20160331 / I:(DE-He78)HD01-20160331 /
                      I:(DE-He78)B340-20160331 / I:(DE-He78)BE01-20160331 /
                      I:(DE-He78)FR01-20160331 / I:(DE-He78)ED01-20160331 /
                      I:(DE-He78)DD01-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:37532709},
      doi          = {10.1038/s41467-023-39570-7},
      url          = {https://inrepo02.dkfz.de/record/277913},
}