ORIGINAL RESEARCH article
Front. Oncol.
Sec. Thoracic Oncology
Volume 15 - 2025 | doi: 10.3389/fonc.2025.1618509
This article is part of the Research TopicReal-World Data and Real-World Evidence in Lung Cancer Volume IIView all 3 articles
NGS Coverage Accurately Predicts MET and HER2 (ERBB2) Gene Amplifications in a Real-World Non-Small Cell Lung Cancer Cohort
Provisionally accepted
Adam Kowalewski1,2,3*
Janna Siemanowski-Hrach1Thomas Stehle1
Jan Rehker1Udo Siebolts1Sabine Merkelbach-Bruse1Carina Heydt1- 1Faculty of Medicine, University of Cologne, Cologne, North Rhine-Westphalia, Germany
- 2Faculty of Medical Sciences, Bydgoszcz University of Science and Technology, Bydgoszcz, Pomeranian, Poland
- 3Department of Tumor Pathology, Oncology Centre Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Pomeranian, Poland
Select one of your emails
You have multiple emails registered with Frontiers:
Notify me on publication
Please enter your email address:
If you already have an account, please login
You don't have a Frontiers account ? You can register here
Background: Fluorescence in situ hybridization (FISH) is the current standard for detecting gene amplifications, yet its low throughput and practical constraints call for alternative methods. This study evaluates next-generation sequencing (NGS) as a potential tool for accurately predicting gene amplifications.We analyzed 66 primary non-small cell lung cancer (NSCLC) samples, tested by both NGS and FISH. FISH was conducted to detect gene amplifications in MET in 26 samples, in HER2 (ERBB2) in 21 samples, in PIK3CA in 9 samples, and KRAS in 9 samples, with one tumor tested for both MET and ERBB2. NGS fold changes, reflected by gene coverage, were calculated as the ratio of the highest gene-specific coverage to the mean coverage across all genes.Results: Amplification was detected in 46 (68.7%) samples. NGS fold changes correlated strongly with FISH Gene/CEN ratios (Spearman's ρ = 0.720, p < 0.001) and gene copy number per cell (Spearman's ρ = 0.847, p < 0.001). Among FISH-negative cases, NGS fold change ranged from 0.57 to 1.95, while in FISH-positive cases, it ranged from 2.11 to 25.08.NGS fold changes demonstrate significant correlation with FISH metrics, supporting NGS as a promising marker for gene amplification. A fold change cutoff of 2.0 effectively distinguishes amplified from non-amplified cases, with NGS achieving a high degree of predictive reliability across the tested genes.
Keywords: NGS, coverage, Amplification, Met, HER2, Lung, Cancer, NSCLC
Received: 26 Apr 2025; Accepted: 07 Jul 2025.
Copyright: © 2025 Kowalewski, Siemanowski-Hrach, Stehle, Rehker, Siebolts, Merkelbach-Bruse and Heydt. 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) or licensor 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.
* Correspondence: Adam Kowalewski, Faculty of Medicine, University of Cologne, Cologne, 50931, North Rhine-Westphalia, Germany
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.