PMID- 37067589 OWN - NLM STAT- MEDLINE DCOM- 20230609 LR - 20230610 IS - 1432-2307 (Electronic) IS - 0945-6317 (Print) IS - 0945-6317 (Linking) VI - 482 IP - 6 DP - 2023 Jun TI - Comparison of NTRK fusion detection methods in microsatellite-instability-high metastatic colorectal cancer. PG - 983-992 LID - 10.1007/s00428-023-03538-1 [doi] AB - Tropomyosin receptor kinase (TRK) inhibitors have been approved for metastatic solid tumors harboring NTRK fusions, but the detection of NTRK fusions is challenging. International guidelines recommend pan-TRK immunohistochemistry (IHC) screening followed by next generation sequencing (NGS) in tumor types with low prevalence of NTRK fusions, including metastatic colorectal cancer (mCRC). RNA-based NGS is preferred, but is expensive, time-consuming, and extracting good-quality RNA from FFPE tissue is challenging. Alternatives in daily clinical practice are warranted. We assessed the diagnostic performance of RNA-NGS, FFPE-targeted locus capture (FFPE-TLC), fluorescence in situ hybridization (FISH), and the 5'/3' imbalance quantitative RT-PCR (qRT-PCR) after IHC screening in 268 patients with microsatellite-instability-high mCRC, the subgroup in which NTRK fusions are most prevalent (1-5%). A consensus result was determined after review of all assay results. In 16 IHC positive tumors, 10 NTRK fusions were detected. In 33 IHC negative samples, no additional transcribed NTRK fusions were found, underscoring the high sensitivity of IHC. Sensitivity of RNA-NGS, FFPE-TLC, FISH, and qRT-PCR was 90%, 90%, 78%, and 100%, respectively. Specificity was 100% for all assays. Robustness, defined as the percentage of samples that provided an interpretable result in the first run, was 100% for FFPE-TLC, yet more limited for RNA-NGS (85%), FISH (70%), and qRT-PCR (70%). Overall, we do not recommend FISH for the detection of NTRK fusions in mCRC due to its low sensitivity and limited robustness. We conclude that RNA-NGS, FFPE-TLC, and qRT-PCR are appropriate assays for NTRK fusion detection, after enrichment with pan-TRK IHC, in routine clinical practice. CI - (c) 2023. The Author(s). FAU - Schraa, Suzanna J AU - Schraa SJ AD - Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands. FAU - Stelloo, Ellen AU - Stelloo E AD - Cergentis BV, Utrecht, Netherlands. FAU - Lacle, Miangela M AU - Lacle MM AD - Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands. FAU - Swennenhuis, Joost F AU - Swennenhuis JF AD - Cergentis BV, Utrecht, Netherlands. FAU - Brosens, Lodewijk A A AU - Brosens LAA AD - Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands. FAU - Fijneman, Remond J A AU - Fijneman RJA AD - Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands. FAU - Feitsma, Harma AU - Feitsma H AD - Cergentis BV, Utrecht, Netherlands. FAU - Koopman, Miriam AU - Koopman M AD - Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands. FAU - de Leng, Wendy W AU - de Leng WW AD - Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands. FAU - Vink, Geraldine R AU - Vink GR AD - Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands. AD - Department of Research and Development, Netherlands Comprehensive Cancer Organisation (IKNL), Utrecht, Netherlands. FAU - Bol, Guus M AU - Bol GM AUID- ORCID: 0000-0002-4021-3823 AD - Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands. G.M.Bol-2@umcutrecht.nl. LA - eng PT - Journal Article DEP - 20230417 PL - Germany TA - Virchows Arch JT - Virchows Archiv : an international journal of pathology JID - 9423843 RN - EC 2.7.10.1 (Receptor, trkA) RN - 0 (Oncogene Proteins, Fusion) SB - IM MH - Humans MH - Receptor, trkA/genetics MH - In Situ Hybridization, Fluorescence MH - *Neoplasms/genetics MH - *Colonic Neoplasms/genetics MH - Microsatellite Repeats MH - Oncogene Proteins, Fusion/genetics MH - Gene Fusion PMC - PMC10247849 OTO - NOTNLM OT - FISH OT - Fusion detection OT - Immunohistochemistry OT - NTRK fusions OT - Sequencing COIS- S.J. Schraa reported grants from Personal Genome Diagnostics (PGDx) outside the submitted work. E. Stelloo, J.F. Swennenhuis, and H. Feitsma are employees of Cergentis BV, the company that invented and owns the FFPE-TLC technology. R.J.A.F. reported public private partnership consortia grants in collaboration with Cergentis BV, Personal Genome Diagnostics, Delfi Diagnostics, MERCK BV, outside the submitted work. In addition, R.J.A.F. has several patents pending. M. Koopman reported institutional scientific grants from Bayer, Bristol Myers Squibb, Merck, Personal Genome Diagnostics (PGDx), Pierre Fabre, Roche, Sirtex and Servier, has an advisory role for Nordic Farma, Merck-Serono, Pierre Fabre, and Servier outside the submitted work and is principal investigator from the international cohort study PROMETCO with Servier as sponsor. W.W. de Leng reported grants from Roche, BMS, and Pfizer and was involved in advisory boards for BMS, Janssen, and Novartis outside the submitted work. G.R. Vink reported grants from BMS, Merck, Servier, Personal Genome Diagnostics (PGDx), Bayer, Sirtex, Pierre Fabre, Lilly, and Delfi Diagnostics outside the submitted work. G.M. Bol reports institutional scientific grants from Bayer, Pierre Fabre, and Terumo. No other disclosures were reported. EDAT- 2023/04/18 06:00 MHDA- 2023/06/09 06:41 PMCR- 2023/04/17 CRDT- 2023/04/17 11:15 PHST- 2023/02/14 00:00 [received] PHST- 2023/03/27 00:00 [accepted] PHST- 2023/03/15 00:00 [revised] PHST- 2023/06/09 06:41 [medline] PHST- 2023/04/18 06:00 [pubmed] PHST- 2023/04/17 11:15 [entrez] PHST- 2023/04/17 00:00 [pmc-release] AID - 10.1007/s00428-023-03538-1 [pii] AID - 3538 [pii] AID - 10.1007/s00428-023-03538-1 [doi] PST - ppublish SO - Virchows Arch. 2023 Jun;482(6):983-992. doi: 10.1007/s00428-023-03538-1. Epub 2023 Apr 17.