Comprehensive NGS profiling to enable detection of ALK gene rearrangements and MET amplifications in non-small cell lung cancer

Sergi Clavé; Jennifer B Jackson; Marta Salido; Jacob Kames; Kelly M R Gerding; Ellen L Verner; Eric F Kong; Elizabeth Weingartner; Joan Gibert; Max Hardy-Werbin; Pedro Rocha; Xènia Riera; Erica Torres; James Hernandez; Gustavo Cerqueira; Donna Nichol; John Simmons; Álvaro Taus; Lara Pijuan; Beatriz Bellosillo; Edurne Arriola

doi:10.3389/fonc.2023.1225646

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.2023.1225646. eCollection 2023.

Authors

Sergi Clavé^{1

2

3}, Jennifer B Jackson⁴, Marta Salido^{1

2

3}, Jacob Kames⁴, Kelly M R Gerding⁴, Ellen L Verner⁴, Eric F Kong⁴, Elizabeth Weingartner⁴, Joan Gibert², Max Hardy-Werbin^{2

5}, Pedro Rocha^{2

3

5}, Xènia Riera^{1

2}, Erica Torres¹, James Hernandez⁴, Gustavo Cerqueira⁴, Donna Nichol⁴, John Simmons⁴, Álvaro Taus^{2

5}, Lara Pijuan¹, Beatriz Bellosillo^{1

2

3}, Edurne Arriola^{2

3

5}

Affiliations

¹ Pathology Department, Hospital del Mar, Barcelona, Spain.
² Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain.
³ Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
⁴ Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States.
⁵ Medical Oncology Department, Hospital del Mar, Barcelona, Spain.

Abstract

Introduction: 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.

Keywords: ALK rearrangement; MET amplification; biomarkers; fluorescence in situ hybridization (FISH); molecular testing; next generation sequencing (NGS); non-small cell lung cancer (NSCLC).

Copyright © 2023 Clavé, Jackson, Salido, Kames, Gerding, Verner, Kong, Weingartner, Gibert, Hardy-Werbin, Rocha, Riera, Torres, Hernandez, Cerqueira, Nichol, Simmons, Taus, Pijuan, Bellosillo and Arriola.

Grants and funding

The submitted manuscript has been read and approved by all contributing authors. This work was partially supported with an unrestricted research grant from Pfizer S.L.U. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication. This work was also supported by grants from Agència de Gestió d’Ajuts Universitaris i de Recerca (2021-SGR-776 and 2021-SGR-628) and Fondo de Investigación Sanitaria-Instituto de Salud Carlos III co-funded by the European Union (CB16/12/00241 and PI22/00105).