PMID- 32319699 OWN - NLM STAT- MEDLINE DCOM- 20210706 LR - 20210706 IS - 1098-2264 (Electronic) IS - 1045-2257 (Linking) VI - 59 IP - 8 DP - 2020 Aug TI - 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. PG - 445-453 LID - 10.1002/gcc.22853 [doi] AB - 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. CI - (c) 2020 Wiley Periodicals, Inc. FAU - Kirchner, Martina AU - Kirchner M AD - Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany. FAU - Glade, Julia AU - Glade J AD - Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany. FAU - Lehmann, Ulrich AU - Lehmann U AD - Institute of Pathology, University Hospital Hannover, Hannover, Germany. FAU - Merkelbach-Bruse, Sabine AU - Merkelbach-Bruse S AD - Institute of Pathology, University Hospital Cologne, Cologne, Germany. FAU - Hummel, Michael AU - Hummel M AD - Institute of Pathology, Charite University Hospital, Berlin, Germany. FAU - Lehmann, Annika AU - Lehmann A AD - Institute of Pathology, Charite University Hospital, Berlin, Germany. FAU - Trautmann, Marcel AU - Trautmann M AUID- ORCID: 0000-0002-5842-1196 AD - Institute of Pathology, University Hospital Munster, Munster, Germany. FAU - Kumbrink, Jorg AU - Kumbrink J AD - Institute of Pathology, Ludwig Maximilian University (LMU), Munich, Germany. FAU - Jung, Andreas AU - Jung A AD - Institute of Pathology, Ludwig Maximilian University (LMU), Munich, Germany. FAU - Dietmaier, Wolfgang AU - Dietmaier W AD - Institute of Pathology, University Hospital Regensburg, Regensburg, Germany. FAU - Endris, Volker AU - Endris V AD - Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany. FAU - Kazdal, Daniel AU - Kazdal D AD - Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany. FAU - Ploeger, Carolin AU - Ploeger C AD - Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany. FAU - Evert, Matthias AU - Evert M AD - Institute of Pathology, University Hospital Regensburg, Regensburg, Germany. FAU - Horst, David AU - Horst D AD - Institute of Pathology, Charite University Hospital, Berlin, Germany. FAU - Kreipe, Hans AU - Kreipe H AD - Institute of Pathology, University Hospital Hannover, Hannover, Germany. FAU - Kirchner, Thomas AU - Kirchner T AD - Institute of Pathology, Ludwig Maximilian University (LMU), Munich, Germany. FAU - Wardelmann, Eva AU - Wardelmann E AD - Institute of Pathology, University Hospital Munster, Munster, Germany. FAU - Buttner, Reinhard AU - Buttner R AD - Institute of Pathology, University Hospital Cologne, Cologne, Germany. FAU - Weichert, Wilko AU - Weichert W AD - Institute of Pathology, Technical University Munich (TUM), Munich, Germany. FAU - Dietel, Manfred AU - Dietel M AD - Institute of Pathology, Charite University Hospital, Berlin, Germany. AD - Quality Assurance Initiative in Pathology (QuiP), Berlin, Germany. FAU - Schirmacher, Peter AU - Schirmacher P AD - Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany. FAU - Stenzinger, Albrecht AU - Stenzinger A AUID- ORCID: 0000-0003-1001-103X AD - Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany. FAU - Pfarr, Nicole AU - Pfarr N AUID- ORCID: 0000-0002-5977-5375 AD - Institute of Pathology, Technical University Munich (TUM), Munich, Germany. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200509 PL - United States TA - Genes Chromosomes Cancer JT - Genes, chromosomes & cancer JID - 9007329 RN - 0 (Biomarkers, Tumor) RN - 0 (Oncogene Proteins, Fusion) RN - EC 2.7.10.1 (Receptor Tyrosine Kinase-like Orphan Receptors) SB - IM MH - Biomarkers, Tumor/*genetics MH - Genetic Testing/*methods/standards MH - Humans MH - In Situ Hybridization, Fluorescence/methods MH - Neoplasms/diagnosis/*genetics MH - Oncogene Proteins, Fusion/*genetics MH - RNA-Seq/*methods/standards MH - Receptor Tyrosine Kinase-like Orphan Receptors/*genetics MH - Sensitivity and Specificity MH - Tissue Preservation/methods OTO - NOTNLM OT - FISH OT - NGS OT - NTRK OT - NTRK fusion variants OT - RNA sequencing EDAT- 2020/04/23 06:00 MHDA- 2021/07/07 06:00 CRDT- 2020/04/23 06:00 PHST- 2020/03/17 00:00 [received] PHST- 2020/04/16 00:00 [revised] PHST- 2020/04/17 00:00 [accepted] PHST- 2020/04/23 06:00 [pubmed] PHST- 2021/07/07 06:00 [medline] PHST- 2020/04/23 06:00 [entrez] AID - 10.1002/gcc.22853 [doi] PST - ppublish SO - Genes Chromosomes Cancer. 2020 Aug;59(8):445-453. doi: 10.1002/gcc.22853. Epub 2020 May 9.