Evaluating Targeted Next-Generation Sequencing Assays and Reference Materials for NTRK Fusion Detection

Christina Bormann Chung, Jeeyun Lee, Marc Barritault, Pierre Paul Bringuier, Zhaolin Xu, Weei Yuarn Huang, Andrea Beharry, Joseph Castillo, Jason Christiansen, Jennifer C. Lin, Brandon S. Sheffield

Producción científica: Contribución a una revistaArtículorevisión exhaustiva

18 Citas (Scopus)

Resumen

Neurotrophic tyrosine receptor kinase (NTRK1/2/3) fusions are oncogenic drivers in approximately 0.3% of solid tumors. High-quality testing to identify patients with NTRK fusion-positive tumors who could benefit from tropomyosin receptor kinase inhibitors is recommended, but the current NTRK testing landscape, including next-generation sequencing (NGS), is fragmented and availability of assays varies widely. The analytical and clinical performance of four commonly available RNA-based NGS assays, Archer's FusionPlex Lung panel (AFL), Illumina's TruSight Oncology 500 (TSO500), Thermo Fisher's Oncomine Precision Assay and Oncomine Focus Assay (OFA), were evaluated. Experiments were conducted using contrived samples [formalin-fixed, paraffin-embedded cell lines and SeraSeq formalin-fixed, paraffin-embedded reference material], NTRK fusion-negative clinical samples, and NTRK fusion-positive clinical samples, according to local assays. Estimated limit of detection varied across the four assays: 30 to 620 fusion copies for AFL (cell lines), versus approximately 30 to 290 copies for TSO500 and approximately 1 to 28 copies for OFA and Oncomine Precision Assay. All assays showed 100% specificity for NTRK fusions detection, but quality control pass rate was variable (AFL, 43%; TSO500, 77%; and OFA, 83%). The NTRK fusion detection rate in quality control–validated clinical samples was 100% for all assays. This comparison of the strengths and limitations of four RNA-based NGS assays will inform physicians and pathologists regarding optimal assay selection to identify patients with NTRK fusion-positive tumors.

Idioma originalEnglish
Páginas (desde-hasta)18-32
Número de páginas15
PublicaciónJournal of Molecular Diagnostics
Volumen24
N.º1
DOI
EstadoPublished - ene. 2022
Publicado de forma externa

Nota bibliográfica

Funding Information:
Supported by Genentech, Inc . Third-party medical writing assistance, under the direction of the authors, was provided by Laura Vergoz, Ph.D., of Ashfield MedComms, an Ashfield Health company, and was funded by F. Hoffmann-La Roche Ltd. NTRK fusion-positive clinical samples were provided by the clinical team and biobank of Samsung Medical Center, Seoul, Republic of Korea; Les Hospices Civils de Lyon, France; Nova Scotia Health Authority, Halifax, NS, Canada; and William Osler Health System, Brampton, ON, Canada. Reagents for the Oncomine Precision Assays were provided by Thermo Fisher, Inc. Experiments were executed, under the direction of the authors, by Q 2 Solutions | EA Genomics LLC in Morrisville, NC. Formalin-fixed, paraffin-embedded cell lines were prepared by Allison Cordrey, Mark Merchant, and the Research Pathology/Histology Lab at Genentech, Inc., South San Francisco, CA.

Funding Information:
Supported by Genentech, Inc. Third-party medical writing assistance, under the direction of the authors, was provided by Laura Vergoz, Ph.D., of Ashfield MedComms, an Ashfield Health company, and was funded by F. Hoffmann-La Roche Ltd. NTRK fusion-positive clinical samples were provided by the clinical team and biobank of Samsung Medical Center, Seoul, Republic of Korea; Les Hospices Civils de Lyon, France; Nova Scotia Health Authority, Halifax, NS, Canada; and William Osler Health System, Brampton, ON, Canada. Reagents for the Oncomine Precision Assays were provided by Thermo Fisher, Inc. Experiments were executed, under the direction of the authors, by Q2 Solutions | EA Genomics LLC in Morrisville, NC. Formalin-fixed, paraffin-embedded cell lines were prepared by Allison Cordrey, Mark Merchant, and the Research Pathology/Histology Lab at Genentech, Inc., South San Francisco, CA. Disclosures: C.B.C. reports employment from Genentech; shareholder/stockholder/stock options from Roche, Illumina; and work on projects cofunded by F. Hoffmann-La Roche Ltd and Illumina. J.L. reports advisory/consultancy fees from Oncologie, Seattle Genetics; and research grant/funding from AstraZeneca, Eli Lilly & Company, and Merck Sharp & Dohme. M.B. reports employment from Hospices Civils de Lyon; and honoraria from Genentech, Inc. P.-P.B. reports no conflict of interest. Z.X. reports advisory/consultancy fees, research grant/funding from F. Hoffmann-La Roche Ltd, Pfizer, Merck, AstraZeneca, Bayer, Boehringer Ingelheim, EMD Serono, and Novartis. W.-Y.H. reports advisory/consultancy fees and research funding from Bayer. A.B. reports employment from William Osler Health System. J.Ca. reports employment from Genentech, Inc.; and work on projects cofunded by F. Hoffmann-La Roche Ltd and Illumina. J.Ch. reports employment from Roche Sequencing Solutions, Inc., at the time of the study and from Boundless Bio, Inc., currently. J.C.L. reports employment from Genentech, Inc., at the time of study and from Merck & Co, Inc., currently. B.S.S. reports advisory/consultancy fees, research grant/funding, and travel/accommodation/expenses from Amgen, AstraZeneca, Bayer, Biocartis, Boehringer Ingelheim, Eli Lilly, EMD Serono, Merck, Novartis, Pfizer, F. Hoffmann-La Roche Ltd, and Thermo Fisher.

Funding Information:
Disclosures: C.B.C. reports employment from Genentech; shareholder/stockholder/stock options from Roche, Illumina; and work on projects cofunded by F. Hoffmann-La Roche Ltd and Illumina. J.L. reports advisory/consultancy fees from Oncologie, Seattle Genetics; and research grant/funding from AstraZeneca, Eli Lilly & Company, and Merck Sharp & Dohme. M.B. reports employment from Hospices Civils de Lyon; and honoraria from Genentech, Inc. P.-P.B. reports no conflict of interest. Z.X. reports advisory/consultancy fees, research grant/funding from F. Hoffmann-La Roche Ltd, Pfizer, Merck, AstraZeneca, Bayer, Boehringer Ingelheim, EMD Serono, and Novartis. W.-Y.H. reports advisory/consultancy fees and research funding from Bayer. A.B. reports employment from William Osler Health System. J.Ca. reports employment from Genentech, Inc.; and work on projects cofunded by F. Hoffmann-La Roche Ltd and Illumina. J.Ch. reports employment from Roche Sequencing Solutions, Inc., at the time of the study and from Boundless Bio, Inc., currently. J.C.L. reports employment from Genentech, Inc., at the time of study and from Merck & Co, Inc., currently. B.S.S. reports advisory/consultancy fees, research grant/funding, and travel/accommodation/expenses from Amgen, AstraZeneca, Bayer, Biocartis, Boehringer Ingelheim, Eli Lilly, EMD Serono, Merck, Novartis, Pfizer, F. Hoffmann-La Roche Ltd, and Thermo Fisher.

Publisher Copyright:
© 2022 Association for Molecular Pathology and American Society for Investigative Pathology

ASJC Scopus Subject Areas

  • Pathology and Forensic Medicine
  • Molecular Medicine

PubMed: MeSH publication types

  • Journal Article

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