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@ARTICLE{Reuss:285695,
      author       = {D. E. Reuss$^*$ and D. Schrimpf$^*$ and D. Stichel$^*$ and
                      A. Ebrahimi and C. Dampier and K. Aldape and M. Snuderl and
                      D. Capper$^*$ and M. Sill$^*$ and D. T. W. Jones$^*$ and S.
                      M. Pfister$^*$ and F. Sahm$^*$ and A. von Deimling$^*$},
      title        = {{R}eference on copy number variations in pleomorphic
                      xanthoastrocytoma: {I}mplications for diagnostic approach.},
      journal      = {Free Neuropathology},
      volume       = {4},
      issn         = {2699-4445},
      address      = {Muenster},
      publisher    = {Prof. Dr. Werner Paulus, University of Muenster, Institute
                      of Neuropathology},
      reportid     = {DKFZ-2023-02510},
      pages        = {4-19},
      year         = {2023},
      note         = {#EA:B300#LA:B300#},
      abstract     = {Pleomorphic xanthoastrocytoma (PXA) poses a diagnostic
                      challenge. The present study relies on methylation-based
                      predictions and focuses on copy number variations (CNV) in
                      PXA. We identified 551 tumors from patients having received
                      the histologic diagnosis or differential diagnosis
                      pleomorphic xanthoastrocytoma (PXA) uploaded to the web page
                      www.molecularneuropathology.org. Of these 551 tumors, 165
                      received the prediction 'methylation class (anaplastic)
                      pleomorphic xanthoastrocytoma' with a calibrated score >=0.9
                      by the brain tumor classifier version v12.8 and, therefore,
                      were defined the PXA reference set designated mcPXAref. In
                      addition to these 165 mcPXAref, 767 other tumors received
                      the prediction mcPXA with a calibrated score >=0.9 but
                      without a histological PXA diagnosis. The total number of
                      individual tumors predicted by histology and/or by methylome
                      based classification as PXA, mcPXA or both was 1318, and
                      these were designated the study cohort. The selection of a
                      control cohort was guided by methylation-based predictions
                      recurrently observed for the other 386/551 tumors diagnosed
                      as histologic PXA. 131/386 received predictions for another
                      entity besides PXA with a score >=0.9. Control tumors
                      corresponding to the 11 most common other predictions were
                      selected, adding up to 1100 reference cases. CNV profiles
                      were calculated from all methylation datasets of the study
                      and control cohorts. Special attention was given to the 7/10
                      signature, gene amplifications and homozygous deletion of
                      CDKN2A/B. Comparison of CNV in the subsets of the study
                      cohort and the control cohort were used to establish
                      relations independent of histological diagnoses. Tumors in
                      mcPXA were highly homogenous in regard to CNV alterations,
                      irrespective of the histological diagnoses. The 7/10
                      signature commonly present in glioblastoma, IDH-wildtype,
                      was present in $15-20\%$ of mcPXA, whereas amplification of
                      oncogenes (likewise common in glioblastoma) was very rare in
                      mcPXA $(<1\%).$ In contrast, the histology-based PXA group
                      exhibited high variance in regard to methylation classes as
                      well as to CNVs. Our data add to the notion, that
                      histologically defined PXA likely only represent a subset of
                      the biological disease.},
      keywords     = {7/10 signature (Other) / Amplification (Other) / CDKN2A/B
                      (Other) / CNV (Other) / Classification (Other) / Copy Number
                      Variations (Other) / EGFR (Other) / Homozygous deletion
                      (Other) / Methylation (Other) / PXA (Other) / Pleomorphic
                      Xanthoastrocytoma (Other)},
      cin          = {B300 / HD01 / BE01 / B062 / B360},
      ddc          = {610},
      cid          = {I:(DE-He78)B300-20160331 / I:(DE-He78)HD01-20160331 /
                      I:(DE-He78)BE01-20160331 / I:(DE-He78)B062-20160331 /
                      I:(DE-He78)B360-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:38026572},
      pmc          = {pmc:PMC10646999},
      doi          = {10.17879/FREENEUROPATHOLOGY-2023-5156},
      url          = {https://inrepo02.dkfz.de/record/285695},
}