Optimization of Routine Testing for MET Exon 14 Splice Site Mutations in NSCLC Patients

Clotilde Descarpentries, Frédéric Leprêtre, Fabienne Escande, Zoulika Kherrouche, Martin Figeac, Shéhérazade Sebda, Simon Baldacci, Valérie Grégoire, Philippe Jamme, Marie-Christine Copin, David Tulasne, Alexis B Cortot

Genomic alterations affecting splice sites of MET exon 14 were recently identified in non-small cell lung cancer (NSCLC) patients. Objective responses to MET tyrosine kinase inhibitors have been reported in these patients. Thus, detection of MET exon 14 splice site mutations represents a major challenge. So far, most of these alterations were found by full-exome sequencing or large capture-based NGS panels, which are not suitable for routine diagnosis. Aiming to provide a molecular testing method applicable in routine practice, we first developed a fragment-length analysis for detecting deletions in introns flanking MET exon 14. Second, we designed an optimized targeted next generation sequencing (NGS) panel called CLAPv1, covering the MET exon 14 and flanking regions in addition to the main molecular targets usually covered in genomic testing. In patients with MET exon 14 mutations, MET gene amplification, gene copy number and MET receptor expression were also determined. Among 1514 formalin-fixed paraffin-embedded NSCLC samples, non optimized NGS allowed detection of MET exon 14 mutations in only 0.3% of the patients, and fragment length analysis detected deletions in 1.1% of the patients. Combined, the optimized CLAPv1 panel and fragment length analysis implemented for routine molecular testing revealed MET exon 14 alterations in 2.2% of 365 additional NSCLC patients. MET gene amplification or high gene copy number were observed in 6 out of 30 patients (20%) harboring MET exon 14 mutations. These results demonstrate that optimized targeted NGS and fragment-length analysis improve detection of MET alterations in routine practice.