학술논문
Development, testing and validation of a targeted NGS-panel for the detection of actionable mutations in lung cancer (NSCLC) using anchored multiplex PCR technology in a multicentric setting.
Document Type
Academic Journal
Author
Kumbrink J; Institute of Pathology, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), Munich, Germany.; German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.; Demes MC; Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany.; Jeroch J; Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany.; Bräuninger A; Institute of Pathology, Justus Liebig University Giessen, Giessen, Germany.; Hartung K; Institute of Pathology, Justus Liebig University Giessen, Giessen, Germany.; Gerstenmaier U; Institute of Pathology, University Ulm, Ulm, Germany.; Marienfeld R; Institute of Pathology, University Ulm, Ulm, Germany.; Hillmer A; Institute of Pathology, University Hospital Cologne, Cologne, Germany.; Bohn N; Archer, Boulder, CO, United States.; Lehning C; Archer, Boulder, CO, United States.; Ferch F; Archer, Boulder, CO, United States.; Wild P; Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany.; Gattenlöhner S; Institute of Pathology, Justus Liebig University Giessen, Giessen, Germany.; Möller P; Institute of Pathology, University Ulm, Ulm, Germany.; Klauschen F; Institute of Pathology, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), Munich, Germany.; German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.; Jung A; Institute of Pathology, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), Munich, Germany.; German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.
Source
Publisher: Frontiers Media S. A Country of Publication: Switzerland NLM ID: 9706087 Publication Model: eCollection Cited Medium: Internet ISSN: 1532-2807 (Electronic) Linking ISSN: 12194956 NLM ISO Abbreviation: Pathol Oncol Res Subsets: MEDLINE
Subject
Language
English
Abstract
Lung cancer is a paradigm for a genetically driven tumor. A variety of drugs were developed targeting specific biomarkers requiring testing for tumor genetic alterations in relevant biomarkers. Different next-generation sequencing technologies are available for library generation: 1) anchored multiplex-, 2) amplicon based- and 3) hybrid capture-based-PCR. Anchored multiplex PCR-based sequencing was investigated for routine molecular testing within the national Network Genomic Medicine Lung Cancer (nNGM). Four centers applied the anchored multiplex ArcherDX-Variantplex nNGMv2 panel to re-analyze samples pre-tested during routine diagnostics. Data analyses were performed by each center and compiled centrally according to study design. Pre-defined standards were utilized, and panel sensitivity was determined by dilution experiments. nNGMv2 panel sequencing was successful in 98.9% of the samples ( N = 90). With default filter settings, all but two potential MET exon 14 skipping variants were identified at similar allele frequencies. Both MET variants were found with an adapted calling filter. Three additional variants ( KEAP1 , STK11 , TP53 ) were called that were not identified in pre-testing analyses. Only total DNA amount but not a qPCR-based DNA quality score correlated with average coverage. Analysis was successful with a DNA input as low as 6.25 ng. Anchored multiplex PCR-based sequencing (nNGMv2) and a sophisticated user-friendly Archer-Analysis pipeline is a robust and specific technology to detect tumor genetic mutations for precision medicine of lung cancer patients.
Competing Interests: AJ received honoraria for scientific talks, participance in adboards and reimbursement of travel as well as accommodation expenses from Amgen, AstraZeneca, Bayer Pharmaceuticals, BMS, Biocartis, Boehringer Ingelheim, Merck KgA, Lilly, MSD, Novartis, QuIP GmbH, Roche Pharma, Stemline, Takeda. M-CD has received consulting fees and honoraria for lectures by Biocartis, Roche, Bayer, Janssen-Cilag, Novartis, Thermo Fisher Scientific, Molecular Health, Qiagen and Astra Zeneca. Research Support was provided by Astra Zeneca, Roche and Thermo Fisher. RM received a research grant from BMS and participated in adboards from BMS and AstraZeneca. CL, FF, and NB are affiliated with ArcherDx which supported the study. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
(Copyright © 2024 Kumbrink, Demes, Jeroch, Bräuninger, Hartung, Gerstenmaier, Marienfeld, Hillmer, Bohn, Lehning, Ferch, Wild, Gattenlöhner, Möller, Klauschen and Jung.)
Competing Interests: AJ received honoraria for scientific talks, participance in adboards and reimbursement of travel as well as accommodation expenses from Amgen, AstraZeneca, Bayer Pharmaceuticals, BMS, Biocartis, Boehringer Ingelheim, Merck KgA, Lilly, MSD, Novartis, QuIP GmbH, Roche Pharma, Stemline, Takeda. M-CD has received consulting fees and honoraria for lectures by Biocartis, Roche, Bayer, Janssen-Cilag, Novartis, Thermo Fisher Scientific, Molecular Health, Qiagen and Astra Zeneca. Research Support was provided by Astra Zeneca, Roche and Thermo Fisher. RM received a research grant from BMS and participated in adboards from BMS and AstraZeneca. CL, FF, and NB are affiliated with ArcherDx which supported the study. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
(Copyright © 2024 Kumbrink, Demes, Jeroch, Bräuninger, Hartung, Gerstenmaier, Marienfeld, Hillmer, Bohn, Lehning, Ferch, Wild, Gattenlöhner, Möller, Klauschen and Jung.)