@article{8767425,
  abstract     = {{We assess the performance of mRNA capture sequencing to identify fusion transcripts in FFPE tissue of different sarcoma types, followed by RT-qPCR confirmation. To validate our workflow, six positive control tumors with a specific chromosomal rearrangement were analyzed using the TruSight RNA Pan-Cancer Panel. Fusion transcript calling by FusionCatcher confirmed these aberrations and enabled the identification of both fusion gene partners and breakpoints. Next, whole-transcriptome TruSeq RNA Exome sequencing was applied to 17 fusion gene-negative alveolar rhabdomyosarcoma (ARMS) or undifferentiated round cell sarcoma (URCS) tumors, for whom fluorescence in situ hybridization (FISH) did not identify the classical pathognomonic rearrangements. For six patients, a pathognomonic fusion transcript was readily detected, i.e., PAX3-FOXO1 in two ARMS patients, and EWSR1-FLI1, EWSR1-ERG, or EWSR1-NFATC2 in four URCS patients. For the 11 remaining patients, 11 newly identified fusion transcripts were confirmed by RT-qPCR, including COPS3-TOM1L2, NCOA1-DTNB, WWTR1-LINC01986, PLAA-MOB3B, AP1B1-CHEK2, and BRD4-LEUTX fusion transcripts in ARMS patients. Additionally, recurrently detected secondary fusion transcripts in patients diagnosed with EWSR1-NFATC2-positive sarcoma were confirmed (COPS4-TBC1D9, PICALM-SYTL2, SMG6-VPS53, and UBE2F-ALS2). In conclusion, this study shows that mRNA capture sequencing enhances the detection rate of pathognomonic fusions and enables the identification of novel and secondary fusion transcripts in sarcomas.}},
  articleno    = {{11007}},
  author       = {{Decock, Anneleen and Creytens, David and Lefever, Steve and Van der Meulen, Joni and Anckaert, Jasper and De Ganck, Ariane and Deleu, Jill and De Wilde, Bram and Fierro, Carolina and Kuersten, Scott and Luypaert, Manuel and Rottiers, Isabelle and Schroth, Gary and Steyaert, Sandra and Vanderheyden, Katrien and Vanden Eynde, Eveline and Verniers, Kimberly and Verreth, Joke and Van Dorpe, Jo and Vandesompele, Jo}},
  issn         = {{1422-0067}},
  journal      = {{INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}},
  keywords     = {{undifferentiated round cell sarcoma,mRNA capture sequencing,RT-qPCR,formalin-fixed paraffin-embedded (FFPE) tissue,fusion gene,fusion transcript,sarcoma}},
  language     = {{eng}},
  number       = {{19}},
  pages        = {{19}},
  title        = {{mRNA capture sequencing and RT-qPCR for the detection of pathognomonic, novel, and secondary fusion transcripts in FFPE tissue : a sarcoma showcase}},
  url          = {{http://doi.org/10.3390/ijms231911007}},
  volume       = {{23}},
  year         = {{2022}},
}

Altmetric

View in Altmetric

Web of Science

Times cited: