Comparison of NTRK fusion detection methods in microsatellite-instability-high metastatic colorectal cancer

Suzanna J Schraa, Ellen Stelloo, Miangela M Laclé, Joost F Swennenhuis, Lodewijk A A Brosens, Remond J A Fijneman, Harma Feitsma, Miriam Koopman, Wendy W de Leng, Geraldine R Vink, Guus M Bol*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

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.

Original languageEnglish
Pages (from-to)983-992
Number of pages10
JournalVirchows Archives
Volume482
Issue number6
Early online date17 Apr 2023
DOIs
Publication statusPublished - Jun 2023

Keywords

  • FISH
  • Fusion detection
  • Immunohistochemistry
  • NTRK fusions
  • Sequencing

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