Testing NTRK testing: Wet-lab and in silico comparison of RNA-based targeted sequencing assays.
Adolescent
Adult
Aged
Biomarkers, Tumor
Child
Child, Preschool
Clinical Decision-Making
Disease Management
Female
Genetic Testing
/ methods
High-Throughput Nucleotide Sequencing
/ methods
Humans
Immunohistochemistry
In Situ Hybridization, Fluorescence
Infant
Male
Middle Aged
Neoplasms
/ diagnosis
Receptors, Nerve Growth Factor
/ genetics
Reproducibility of Results
Workflow
Young Adult
FFPE
NGS
NTRK
RNA sequencing
gene fusion
Journal
Genes, chromosomes & cancer
ISSN: 1098-2264
Titre abrégé: Genes Chromosomes Cancer
Pays: United States
ID NLM: 9007329
Informations de publication
Date de publication:
03 2020
03 2020
Historique:
received:
20
09
2019
revised:
19
10
2019
accepted:
22
10
2019
pubmed:
28
10
2019
medline:
6
10
2020
entrez:
26
10
2019
Statut:
ppublish
Résumé
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.
Substances chimiques
Biomarkers, Tumor
0
Receptors, Nerve Growth Factor
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
178-188Informations de copyright
© 2019 Wiley Periodicals, Inc.
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