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@ARTICLE{Thomas:168504,
      author       = {C. Thomas and K. Oehl-Huber and S. Bens and P. Soschinski
                      and A. Koch and K. Nemes and F. Oyen and U. Kordes and M.
                      Kool$^*$ and M. C. Frühwald and M. Hasselblatt and R.
                      Siebert},
      title        = {{T}ransposable element insertion as a mechanism of
                      {SMARCB}1 inactivation in atypical teratoid/rhabdoid tumor.},
      journal      = {Genes, chromosomes $\&$ cancer},
      volume       = {60},
      number       = {8},
      issn         = {1098-2264},
      address      = {New York, NY},
      publisher    = {Wiley-Liss},
      reportid     = {DKFZ-2021-00936},
      pages        = {586-590},
      year         = {2021},
      note         = {2021 Aug;60(8):586-590},
      abstract     = {Atypical teratoid/rhabdoid tumor (AT/RT) is a malignant
                      brain tumor predominantly occurring in infants. Biallelic
                      SMARCB1 mutations causing loss of nuclear SMARCB1/INI1
                      protein expression represent the characteristic genetic
                      lesion. Pathogenic SMARCB1 mutations comprise single
                      nucleotide variants, small insertions/deletions, large
                      deletions, which may be also present in the germline
                      (rhabdoid tumor predisposition syndrome 1), as well as
                      somatic copy-number neutral loss of heterozygosity (LOH). In
                      some SMARCB1-deficient AT/RT underlying biallelic mutations
                      cannot be identified. Here we report the case of a
                      24-months-old girl diagnosed with a large brain tumor. The
                      malignant rhabdoid tumor showed loss of nuclear SMARCB1/INI1
                      protein expression and the diagnosis of AT/RT was confirmed
                      by DNA methylation profiling. While FISH, MLPA, Sanger
                      sequencing and DNA methylation data-based imbalance analysis
                      did not disclose alterations affecting SMARCB1, OncoScan
                      array analysis revealed a 28.29 Mb sized region of
                      copy-number neutral LOH on chromosome 22q involving the
                      SMARCB1 locus. Targeted next-generation sequencing did also
                      not detect a single nucleotide variant but instead revealed
                      insertion of an AluY element into exon 2 of SMARCB1.
                      Specific PCR-based Sanger sequencing verified the Alu
                      insertion (SMARCB1 $c.199_200$ Alu ins) resulting in a
                      frame-shift truncation not present in the patient's
                      germline. In conclusion, transposable element insertion
                      represents a hitherto not widely recognized mechanism of
                      SMARCB1 disruption in AT/RT, which might not be detected by
                      several widely applied conventional diagnostics assays. This
                      finding has particular clinical implications, if rhabdoid
                      predisposition syndrome 1 is suspected, but germline SMARCB1
                      alterations cannot be identified. This article is protected
                      by copyright. All rights reserved.},
      keywords     = {Alu element (Other) / SMARCB1 (Other) / transposable
                      element insertion (Other) / typical teratoid/rhabdoid tumor
                      (Other)},
      cin          = {B062 / HD01},
      ddc          = {610},
      cid          = {I:(DE-He78)B062-20160331 / I:(DE-He78)HD01-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:33896072},
      doi          = {10.1002/gcc.22954},
      url          = {https://inrepo02.dkfz.de/record/168504},
}