Abstract 3175: Copy number gains of clinically relevant genes in advanced non small cell lung cancer patients
Authors: Ariza Núria Jordana- , Garzón Mónica , García-Peláez Beatriz , Román Ruth , Alamillo Jordi Bertrán- , Rodriguez Sonia , Aldeguer Erika , García-Román Silvia , Viteri Santiago , Aguilar Andrés , Cao María González , Bueno Alejandro Martínez- , Vila Miguel Angel Molina , Costa Rafael Rosell , de las Casas Clara Mayo 
Published: September 2020

Abstract
Background: Somatic copy number gains (CNGs; i.e. amplifications) have been related to tumorogenesis and some of them are designated targets for therapies, such as HER2 amplification in breast cancer. In the case of NSCLC, MET alterations are receiving increasing attention as targets in precision medicine and several clinical trials of anti-MET agents are ongoing. Routine testing for CNGs on formalin-fixed paraffin embedded (FFPE) samples is usually carried out by in-situ hybridization (FISH) covering a single gene. Although this methodology is still the gold standard of CNG detection, it presents several drawbacks and cannot be used in liquid biopsies. Here we aimed to determine the potential of next generation sequencing (NGS) to simultaneously determine CNGs across many genes in FFPE and liquid biopsy samples in NSCLC patients.
Methods: FFPE biopsies (n=137) and blood samples (n=24) at presentation from NSCLC patients (p) of our institutions were prospective tested. In addition, 40 tumor and 19 blood samples at relapse were also analyzed, most of them from p progressing to tyrosine kinase inhibitors. DNA was purified and submitted to NGS using the 16-gene QIAact Lung Panel (Genereader®, Qiagen). For each sample, CNGs were determined using an algorithm developed in house.
Results: Validation analyses in 8 cell lines showed 100% concordance between FISH and NGS for detection of EGFR, MET and HER2 amplifications. Among the 137 NSCLC biopsies at presentation, MET was the gene showing a higher frequency of CNGs (11%), followed by PIK3CA, KRAS and EGFR (7% each). Regarding tumor tissues at progression, the frequency of MET amplification raised to 15%, and HER2 was the second most common gene with CNGs (13%). CNGs were associated with sensitizing mutations only in the case of EGFR, with 6 samples showing both alterations concomitantly. Of the 24 blood samples at presentation, CNGs were detected only in one case, corresponding to an EGFR-mut patient with EGFR amplification. In contrast, MET and EGFR amplification were the most frequent CNGs (16% each) of liquid biopsies at progression to EGFR TKIs. Additionally, ALK amplification was detected in a 11% of cases progressed to ALK therapies. Paired tumor-blood samples were available for 9 patients and concordance in CNG detection was 70 %.
Conclusions: CNGs in clinically relevant genes are present in a significant percentage of advanced NSCLC patients. However, with the only exception of EGFR, they are not concomitant with driver mutations in the same gene. NGS can be used to determine CNGs in multiple genes in both tumor tissue and liquid biopsy samples and further research is warranted to determine the clinical implications of these findings.
Citation Format: Núria Jordana- Ariza, Mónica Garzón, Beatriz García-Peláez, Ruth Román, Jordi Bertrán- Alamillo, Sonia Rodriguez, Erika Aldeguer, Silvia García-Román, Santiago Viteri, Andrés Aguilar, María González Cao, Alejandro Martínez- Bueno, Miguel Angel Molina Vila, Rafael Rosell Costa, Clara Mayo de las Casas. Copy number gains of clinically relevant genes in advanced non small cell lung cancer patients [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3175.