Clavé Safont, SergiSalido Galeote, MartaGibert Fernandez, Joan, 1988-Hardy-Werbin, MaxRocha, Pedro P.Riera, XèniaTorres, EricaTaus García, ÁlvaroPijuan Andujar, LaraBellosillo Paricio, BeatrizArriola Aperribay, Edurne2024-05-142024-05-142023Clavé S, Jackson JB, Salido M, Kames J, Gerding KMR, Verner EL, et al. Comprehensive NGS profiling to enable detection of ALK gene rearrangements and MET amplifications in non-small cell lung cancer. Front Oncol. 2023 Oct 20;13:1225646. DOI: 10.3389/fonc.2023.12256462234-943Xhttp://hdl.handle.net/10230/60126Introduction: Next-generation sequencing (NGS) is currently widely used for biomarker studies and molecular profiling to identify concurrent alterations that can lead to the better characterization of a tumor's molecular landscape. However, further evaluation of technical aspects related to the detection of gene rearrangements and copy number alterations is warranted. Methods: There were 12 ALK rearrangement-positive tumor specimens from patients with non-small cell lung cancer (NSCLC) previously detected via fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and an RNA-based NGS assay, and 26 MET high gene copy number (GCN) cases detected by FISH, selected for this retrospective study. All 38 pre-characterized cases were reassessed utilizing the PGDx™ elio™ tissue complete assay, a 505 gene targeted NGS panel, to evaluate concordance with these conventional diagnostic techniques. Results: The detection of ALK rearrangements using the DNA-based NGS assay demonstrated excellent sensitivity with the added benefit of characterizing gene fusion partners and genomic breakpoints. MET copy number alterations were also detected; however, some discordances were observed likely attributed to differences in algorithm, reporting thresholds and gene copy number state. TMB was also assessed by the assay and correlated to the presence of NSCLC driver alterations and was found to be significantly lower in cases with NGS-confirmed canonical driver mutations compared with those without (p=0.0019). Discussion: Overall, this study validates NGS as an accurate approach for detecting structural variants while also highlighting the need for further optimization to enable harmonization across methodologies for amplifications.application/pdfeng© 2023 Clavé, Jackson, Salido, Kames, Gerding, Verner, Kong, Weingartner, Gibert, Hardy-Werbin, Rocha, Riera, Torres, Hernandez, Cerqueira, Nichol, Simmons, Taus, Pijuan, Bellosillo and Arriola. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/articlehttp://dx.doi.org/10.3389/fonc.2023.1225646ALK rearrangementMET amplificationBiomarkersFluorescence in situ hybridization (FISH)Molecular testingNext generation sequencing (NGS)Non-small cell lung cancer (NSCLC)info:eu-repo/semantics/openAccess