Molecular Diagnostic Assays and Clinicopathologic Implications of MET Exon 14 Skipping Mutation in Non–small-cell Lung Cancer

Recent studies revealed MET exon 14 skipping (METex14) as a biomarker that predicts the response to MET inhibitors in non–small-cell lung cancer (NSCLC). However, METex14 genomic alterations exhibit a highly diverse sequence composition, posing a challenge for clinical diagnostic testing. This study aimed to find a reasonable diagnostic assay for METex14 and identify its clinicopathologic implications. We performed a comprehensive analysis of METex14 in 414 EGFR/KRAS/ALK/ROS1-negative (quadruple negative) surgically resected NSCLCs. We used real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Sanger sequencing for the first assay, followed by next-generation sequencing (NGS; hybrid-capture targeted DNA/RNA sequencing). Clinicopathologic implications of the METex14 group were analyzed in a total of 880 NSCLCs. METex14 was confirmed in 13 (3.1%) patients by DNA- and RNA-NGS. After comparison of assay results, qRT-PCR and NGS demonstrated the highest concordance rate. The mean variant allele frequency was 10.5% and 49% in DNA- and RNA-NGS, respectively. DNA-NGS revealed various lengths of indel and substitutions around and in exon 14. Moreover, METex14 was associated with adenocarcinoma (4.8%; 11/230) or sarcomatoid carcinoma (9.5%; 2/21), old age, never-smokers, and early stage of disease. METex14 occurs in about 3% of NSCLCs and has characteristic clinicopathologic features. NGS should be the first assay of choice as a multiplex testing. Sanger sequencing can detect METex14, but sensitivity can be hampered by large deletions or low allele frequency. qRT-PCR, an mRNA-based method, is sensitive and specific and can be appropriate for screening METex14 as a single gene testing. MET exon 14 skipping (METex14) has been reported as a biomarker that predicts the response to MET inhibitors. However, METex14 alterations exhibit a highly diverse sequence composition, posing a challenge for diagnostic testing in clinics. The present study showed that next-generation sequencing can be the first assay of choice as a multiplex testing and real-time quantitative reverse transcription polymerase chain reaction can be appropriate as a single gene testing. METex14 also had characteristic clinicopathologic features.