Kirchner, Martina, Glade, Julia, Lehmann, Ulrich, Merkelbach-Bruse, Sabine, Hummel, Michael, Lehmann, Annika, Trautmann, Marcel ORCID: 0000-0002-5842-1196, Kumbrink, Jorg, Jung, Andreas, Dietmaier, Wolfgang, Endris, Volker, Kazdal, Daniel ORCID: 0000-0001-8187-3281, Ploeger, Carolin, Evert, Matthias, Horst, David, Kreipe, Hans, Kirchner, Thomas, Wardelmann, Eva, Buettner, Reinhard, Weichert, Wilko, Dietel, Manfred, Schirmacher, Peter, Stenzinger, Albrecht and Pfarr, Nicole (2020). NTRK testing: First results of the QuiP-EQA scheme and a comprehensive map of NTRK fusion variants and their diagnostic coverage by targeted RNA-based NGS assays. Gene Chromosomes Cancer, 59 (8). S. 445 - 454. HOBOKEN: WILEY. ISSN 1098-2264

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Abstract

Gene fusions involving the three neurotrophic tyrosine receptor kinase genes NTRK1, NTRK2, or NTRK3 were identified as oncogenic drivers in many cancer types. Two small molecule inhibitors have been tested in clinical trials recently and require the detection of a NTRK fusion gene prior to therapeutic application. Fluorescence in situ hybridization (FISH) and targeted next-generation sequencing (tNGS) assays are commonly used for diagnostic profiling of gene fusions. In the presented study we applied an external quality assessment (EQA) scheme in order to investigate the suitability of FISH and RNA-/DNA-based tNGS for detection of NTRK fusions in a multinational and multicentric ring trial. In total 27 participants registered for this study. Nine institutions took part in the FISH-based and 18 in the NGS-based round robin test, the latter additionally subdivided into low-input and high-input NGS methods (regarding nucleic acid input). Regardless of the testing method applied, all participants received tumor sections of 10 formalin-fixed and paraffin-embedded (FFPE) tissue blocks for in situ hybridization or RNA/DNA extraction, and the results were submitted via an online questionnaire. For FISH testing, eight of nine (88.8%) participants, and for NGS-based testing 15 of 18 (83.3%) participants accomplished the round robin test successfully. The overall high success rate demonstrates that FISH- and tNGS-based NTRK testing can be well established in a routine diagnostic setting. Complementing this dataset, we provide an updated in silico analysis on the coverage of more than 150 NTRK fusion variants by several commercially available RNA-based tNGS panels.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Kirchner, MartinaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Glade, JuliaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lehmann, UlrichUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Merkelbach-Bruse, SabineUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hummel, MichaelUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lehmann, AnnikaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Trautmann, MarcelUNSPECIFIEDorcid.org/0000-0002-5842-1196UNSPECIFIED
Kumbrink, JorgUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Jung, AndreasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Dietmaier, WolfgangUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Endris, VolkerUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kazdal, DanielUNSPECIFIEDorcid.org/0000-0001-8187-3281UNSPECIFIED
Ploeger, CarolinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Evert, MatthiasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Horst, DavidUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kreipe, HansUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kirchner, ThomasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wardelmann, EvaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Buettner, ReinhardUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Weichert, WilkoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Dietel, ManfredUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Schirmacher, PeterUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Stenzinger, AlbrechtUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Pfarr, NicoleUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-334149
DOI: 10.1002/gcc.22853
Journal or Publication Title: Gene Chromosomes Cancer
Volume: 59
Number: 8
Page Range: S. 445 - 454
Date: 2020
Publisher: WILEY
Place of Publication: HOBOKEN
ISSN: 1098-2264
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
SOLID TUMORS; LAROTRECTINIB; ONCOGENEMultiple languages
Oncology; Genetics & HeredityMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/33414

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