201P RNA-based plus DNA-based analysis of METexon 14 skipping in a non-small cell lung cancer increases diagnostic performance

MET exon 14 skipping mutations (METex14 skip) are found in approximately 3–5% of non-small cell lung cancer (NSCLC) and typically occur in the absence of other driver mutations. The recent approvals of MET-tyrosine kinase inhibitors (TKIs) capmatinib and tepotinib have significantly changed clinical outcomes in this subgroup of patients. Consequently, reliable molecular diagnostic approaches that detect these variants are vital for patient care. This study assessed the potential advantages of running an RNA-sequencing assay on top of DNA-based next-generation sequencing (NGS) for METex14 skip detection. All NSCLC samples tested at Oncoclínicas Precison Mecidine (OCPM) from March 2020 to December 2022 were retrospectively evaluated. Archived formalin-fixed paraffin-embedded (FFPE) tumor material underwent DNA/RNA extraction followed by NGS with in-house developed GS180 panel (Anchored Multiplex PCR [AMP™] DNA and RNA assay, Archer Dx). From 548 samples, RNA seq failed in 142 cases (26%). Prevalence of METex14 skip in samples tested with DNA seq only was 4.9% and in the entire cohort with DNA and/or RNA seq was 7%. Out of the 28 cases with METex 14 skip DNA alterations, in 7 cases (25%) we found deep intronic events outside the canonical splice site. In 12 out of 37 cases (32%) the diagnosis of METex14 skip was contingent on RNA sequencing results (DNA failure or hidden deep intronic event). From 26 cases with informative DNA plus RNA sequencing results, the discordance rate was 46%, with METex 14 skip being detected by DNA only in 7 cases (27%) and RNA only in 5 cases (19%). The prevalence of METex14 skip in Brazilian patients with nsNSCLC is slightly higher than published literature. Unlike other oncogenic drivers, METex14 skip present unique analytical challenges due to variant complexity that require high-quality NGS and optimized bioinformatics pipelines for accurate detection. RNA-based assays increase sensitivity for METex14 skip and support the interpretation of complex intronic events detected by DNA seq. However, RNA-based assays are highly reliant on RNA quality, which can be suboptimal in some clinical samples.