MET Exon 14 Alterations and New Resistance Mutations to Tyrosine Kinase Inhibitors: Risk of Inadequate Detection with Current Amplicon-Based NGS Panels

Abstract

Introduction: Targeted therapies such as tyrosine kinase inhibitors (TKIs) have dramatically improved the treatment of lung adenocarcinoma, and detection of activating mutations of genes such as EGFR or anaplastic lymphoma kinase gene (ALK) is now mandatory in the clinical setting. However, additional targetable alterations are continuously being described and forcing us to adapt our detection methods. Here we have evaluated the ability of eight amplicon-based next-generation sequencing (NGS) panels to detect the recently described mesenchymal epithelial transition factor (MET) exon 14 (METex14) alterations or new mutations conferring resistance to TKIs.

Methods: A total of 191 tumor samples from patients with NSCLC were screened for METex14 mutations by Sanger sequencing, and 62 additional cases were screened by Sanger sequencing and two amplicon-based NGS panels. In silico comparison of eight commercially available targeted NGS panels was also performed for the detection of METex14 alterations or ALK, ROS1, or EGFR resistance mutations.

Results: NGS analysis of the positive METex14 cases revealed a false-negative case because of amplicon design. Moreover, in silico analysis revealed that none of the eight panels considered would be able to detect more than 63% of literature-reported cases of METex14 mutations and similar limitations would be expected with new ALK, ROS1, or EGFR resistance mutations.

Conclusions: We have illustrated major limitations of commercially available amplicon-based DNA NGS panels for detection of METex14 and recently described resistance mutations to TKIs. Documented choice of available panels and their frequent reevaluation are mandatory to deliver the most accurate data to the clinician for therapeutic decisions.

Keywords: Molecular testing; NGS cancer panels; Non–small cell lung cancer; Targeted therapies.