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RNA-based detection of gene fusions in formalin-fixed and paraffin-embedded solid cancer samples

Oncogenic gene fusions are important drivers in many cancer types, including carcinomas, with diagnostic and therapeutic implications. Hence, sensitive and rapid methods for parallel profiling in formalin-fixed and paraffin-embedded (FFPE) specimens are needed. In this study we analyzed gene fusions...

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Main Authors: Kirchner, Martina (Author) , Neumann, Olaf (Author) , Volckmar, Anna-Lena (Author) , Stögbauer, Fabian (Author) , Allgäuer, Michael (Author) , Kazdal, Daniel (Author) , Budczies, Jan (Author) , Rempel, Eugen (Author) , Brandt, Regine (Author) , Talla, Suranand Babu (Author) , Winterfeld, Moritz von (Author) , Leichsenring, Jonas (Author) , Bochtler, Tilmann (Author) , Krämer, Alwin (Author) , Springfeld, Christoph (Author) , Schirmacher, Peter (Author) , Penzel, Roland (Author) , Endris, Volker (Author) , Stenzinger, Albrecht (Author)
Format: Article (Journal)
Language:English
Published: 5 September 2019
In: Cancers
Year: 2019, Volume: 11, Issue: 9
ISSN:2072-6694
DOI:10.3390/cancers11091309
Online Access:Verlag, kostenfrei, Volltext: https://doi.org/10.3390/cancers11091309
Verlag, kostenfrei, Volltext: https://www.mdpi.com/2072-6694/11/9/1309
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Author Notes:Martina Kirchner, Olaf Neumann, Anna-Lena Volckmar, Fabian Stögbauer, Michael Allgäuer, Daniel Kazdal, Jan Budczies, Eugen Rempel, Regine Brandt, Suranand Babu Talla, Moritz von Winterfeld, Jonas Leichsenring, Tilmann Bochtler, Alwin Krämer, Christoph Springfeld, Peter Schirmacher, Roland Penzel, Volker Endris and Albrecht Stenzinger
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Summary:Oncogenic gene fusions are important drivers in many cancer types, including carcinomas, with diagnostic and therapeutic implications. Hence, sensitive and rapid methods for parallel profiling in formalin-fixed and paraffin-embedded (FFPE) specimens are needed. In this study we analyzed gene fusions in a cohort of 517 cases where standard treatment options were exhausted. To this end the Archer® DX Solid tumor panel (AMP; 285 cases) and the Oncomine Comprehensive Assay v3 (OCA; 232 cases) were employed. Findings were validated by Sanger sequencing, fluorescence in situ hybridization (FISH) or immunohistochemistry. Both assays demonstrated minimal dropout rates (AMP: 2.4%; n = 7/292, OCA: 2.1%; n = 5/237) with turnaround times of 6 - 9 working days (median, OCA and AMP, respectively). Hands-on-time for library preparation was 6 h (AMP) and 2 h (OCA). We detected n = 40 fusion-positive cases (7.7%) with TMPRSS2::ERG in prostate cancer being most prevalent (n = 9/40; 22.5%), followed by other gene fusions identified in cancers of unknown primary (n = 6/40; 15.0%), adenoid cystic carcinoma (n = 7/40; 17.5%), and pancreatic cancer (n = 7/40; 17.5%). Our results demonstrate that targeted RNA-sequencing of FFPE samples is feasible, and a well-suited approach for the detection of gene fusions in a routine clinical setting.
Item Description:Gesehen am 15.10.2019
Physical Description:Online Resource
ISSN:2072-6694
DOI:10.3390/cancers11091309

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