PMID- 31652375
OWN - NLM
STAT- MEDLINE
DCOM- 20201005
LR  - 20201005
IS  - 1098-2264 (Electronic)
IS  - 1045-2257 (Linking)
VI  - 59
IP  - 3
DP  - 2020 Mar
TI  - Testing NTRK testing: Wet-lab and in silico comparison of RNA-based targeted 
      sequencing assays.
PG  - 178-188
LID - 10.1002/gcc.22819 [doi]
AB  - 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.
CI  - (c) 2019 Wiley Periodicals, Inc.
FAU - Pfarr, Nicole
AU  - Pfarr N
AUID- ORCID: 0000-0002-5977-5375
AD  - Institute of Pathology, Technical University Munich (TUM), Munich, Germany.
FAU - Kirchner, Martina
AU  - Kirchner M
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 - Leichsenring, Jonas
AU  - Leichsenring J
AD  - Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
FAU - Merkelbach-Bruse, Sabine
AU  - Merkelbach-Bruse S
AD  - Institute of Pathology, University Hospital Cologne, Cologne, Germany.
FAU - Glade, Julia
AU  - Glade J
AD  - Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
FAU - Hummel, Michael
AU  - Hummel M
AD  - Institute of Pathology, Charite University Hospital, Berlin, Germany.
FAU - Stogbauer, Fabian
AU  - Stogbauer F
AD  - Institute of Pathology, Technical University Munich (TUM), Munich, 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  - Gerhard-Domagk-Institute of Pathology, and Division of Translational Pathology, 
      Gerhard-Domagk-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 - 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  - Gerhard-Domagk-Institute of Pathology, and Division of Translational Pathology, 
      Gerhard-Domagk-Institute of Pathology, University Hospital Munster, Munster, 
      Germany.
FAU - Lassen, Ulrik
AU  - Lassen U
AD  - Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, 
      Denmark.
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  - Quality 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.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20191118
PL  - United States
TA  - Genes Chromosomes Cancer
JT  - Genes, chromosomes & cancer
JID - 9007329
RN  - 0 (Biomarkers, Tumor)
RN  - 0 (Receptors, Nerve Growth Factor)
SB  - IM
MH  - Adolescent
MH  - Adult
MH  - Aged
MH  - *Biomarkers, Tumor
MH  - Child
MH  - Child, Preschool
MH  - Clinical Decision-Making
MH  - Disease Management
MH  - Female
MH  - *Genetic Testing/methods
MH  - *High-Throughput Nucleotide Sequencing/methods/standards
MH  - Humans
MH  - Immunohistochemistry
MH  - In Situ Hybridization, Fluorescence
MH  - Infant
MH  - Male
MH  - Middle Aged
MH  - Neoplasms/diagnosis/genetics/metabolism
MH  - Receptors, Nerve Growth Factor/*genetics/metabolism
MH  - Reproducibility of Results
MH  - Workflow
MH  - Young Adult
OTO - NOTNLM
OT  - FFPE
OT  - NGS
OT  - NTRK
OT  - RNA sequencing
OT  - gene fusion
EDAT- 2019/10/28 06:00
MHDA- 2020/10/06 06:00
CRDT- 2019/10/26 06:00
PHST- 2019/09/20 00:00 [received]
PHST- 2019/10/19 00:00 [revised]
PHST- 2019/10/22 00:00 [accepted]
PHST- 2019/10/28 06:00 [pubmed]
PHST- 2020/10/06 06:00 [medline]
PHST- 2019/10/26 06:00 [entrez]
AID - 10.1002/gcc.22819 [doi]
PST - ppublish
SO  - Genes Chromosomes Cancer. 2020 Mar;59(3):178-188. doi: 10.1002/gcc.22819. Epub 
      2019 Nov 18.