Brief Report: DNA-based versus RNA-based detection of MET exon 14 skipping events in lung cancer.

INTRODUCTION: Genomic variants that lead to MET exon 14 skipping represent a potential targetable molecular abnormality in non-small cell lung cancer (NSCLC). Consequently, reliable molecular diagnostic approaches that detect these variants are vital for patient care.

METHODS: We screened NSCLC patient tumor samples for MET exon 14 skipping via two distinct approaches: a DNA-based next-generation sequencing (NGS) assay that employs an amplicon-mediated target enrichment, and an RNA-based NGS assay that employs anchored multiplex PCR for target enrichment.

RESULTS: The DNA-based approach detected MET exon 14 skipping variants in 11 of 856 NSCLC samples (1.3%). The RNA-based approach detected MET exon 14 skipping in 17 of 404 samples (4.2%), a statistically significant increase compared to the DNA-based assay. Among 286 samples tested by both assays, RNA-based testing detected 10 positives, 6 of which were not detected by the DNA-based assay. Examination of primer binding sites in the DNA-based assay in comparison with published MET exon 14 skipping variants revealed genomic deletion involving primer binding sequences as the likely cause of false negatives. Two samples positive via the DNA-based approach were uninformative in the RNA-based approach due to poor quality RNA.

CONCLUSIONS: By circumventing an inherent limitation of DNA-based amplicon-mediated testing, RNA-based analysis detected a higher proportion of MET exon 14 skipping cases. However, RNA-based analysis was highly reliant on RNA quality, which can be suboptimal in some clinical samples.