Research
Print page Print page
Switch language
The Capital Region of Denmark - a part of Copenhagen University Hospital
Published

Testing NTRK testing: Wet-lab and in silico comparison of RNA-based targeted sequencing assays

Research output: Contribution to journalJournal articleResearchpeer-review

DOI

  1. Putative new childhood leukemia cancer predisposition syndrome caused by germline bi-allelic missense mutations in DDX41

    Research output: Contribution to journalJournal articleResearchpeer-review

  2. Blocking protein quality control to counter hereditary cancers

    Research output: Contribution to journalReviewResearchpeer-review

  3. Novel fusion genes and chimeric transcripts in ependymal tumors

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Trisomy 8 in pediatric acute myeloid leukemia: A NOPHO-AML study

    Research output: Contribution to journalJournal articleResearchpeer-review

  1. Angiotensinogen promoter methylation predicts bevacizumab treatment response of patients with recurrent glioblastoma

    Research output: Contribution to journalJournal articleResearchpeer-review

  2. Tisotumab Vedotin in Previously Treated Recurrent or Metastatic Cervical Cancer

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Entrectinib for ROS1 fusion-positive NSCLC and NTRK fusion-positive solid tumours

    Research output: Contribution to journalComment/debateResearchpeer-review

  • Nicole Pfarr
  • Martina Kirchner
  • Ulrich Lehmann
  • Jonas Leichsenring
  • Sabine Merkelbach-Bruse
  • Julia Glade
  • Michael Hummel
  • Fabian Stögbauer
  • Annika Lehmann
  • Marcel Trautmann
  • Jörg Kumbrink
  • Andreas Jung
  • Wolfgang Dietmaier
  • Volker Endris
  • Daniel Kazdal
  • Matthias Evert
  • David Horst
  • Hans Kreipe
  • Thomas Kirchner
  • Eva Wardelmann
  • Ulrik Lassen
  • Reinhard Büttner
  • Wilko Weichert
  • Manfred Dietel
  • Peter Schirmacher
  • Albrecht Stenzinger
View graph of relations

NTRK fusions involving three neurotrophic tyrosine receptor kinase genes NTRK1, NTRK2, and NTRK3 and a variety of fusion partners were identified as oncogenic drivers across many cancer types. Drugs that target the chimeric protein product require the identification of the underlying gene fusion. This advocates the diagnostic use of molecular assays ranging from fluorescence in situ hybridization (FISH) and reverse transcription polymerase chain reaction (RT-PCR)/Sanger approaches to targeted next-generation sequencing (NGS). Immunohistochemistry may be used as a screening tool and adjunct diagnostic assay in this context. Although FISH and RT-PCR/Sanger approaches are widely adopted in routine diagnostics, current experience with targeted RNA-based NGS is limited. Here, we report on the analysis of major assays (TruSight TST170 and TruSight RNA Fusion [Illumina]; Archer FusionPlex Solid Tumor, Archer FusionPlex Lung, and Archer FusionPlex Oncology [Archer]; Oncomine Comprehensive Assay v3 RNA and Oncomine Focus RNA [Thermo Fisher Scientific]) that are commercially available. The data set includes performance results of a multicentric comparative wet-lab study as well as an in silico analysis on the ability to detect the broad range of NTRK fusions reported until now. A test algorithm that reflects assay methodology is provided. This data will support implementation of targeted RNA sequencing in routine diagnostics and inform screening and testing strategies that have been brought forward.

Original languageEnglish
JournalGenes, Chromosomes & Cancer
Volume59
Issue number3
Pages (from-to)178-188
Number of pages11
ISSN1045-2257
DOIs
Publication statusPublished - Mar 2020

    Research areas

  • FFPE, gene fusion, NGS, NTRK, RNA sequencing

ID: 58970198