New research published in The Journal of Molecular Diagnostics on Jul. 23 shows that RNA-based testing can improve the detection and interpretation of clinically actionable genomic alterations leading to MET exon 14 skipping in lung cancer patients, which are important biomarkers that may be missed by DNA-only approaches. The study, published by Elsevier, is expected to lead to improved diagnostic accuracy and help determine patients' eligibility for MET-targeted therapies.
Mutations leading to MET exon 14 skipping occur in 3% to 4% of non-small cell lung cancer (NSCLC) patients. These mutations are highly heterogeneous and appear across a broad splice-site region, creating significant analytical challenges for both DNA- and RNA-based next-generation sequencing assays.
The researchers aimed to improve assay design, variant interpretation, and diagnostic workflows in molecular pathology laboratories. In a large real-world cohort of NSCLC patients, they systematically characterized the spectrum of MET exon 14-associated alterations encountered in routine clinical practice. They assessed their functional consequences at the RNA level, identified potential diagnostic pitfalls, and evaluated laboratory performance through multinational external quality assessment schemes.
The study identified a total of 171 distinct mutations affecting the MET exon 14 splice region. RNA analysis confirmed exon 14 skipping for more than 100 different alteration types and showed that certain clinically relevant events—including large genomic deletions and a synonymous variant affecting splicing—may be missed or incorrectly interpreted by DNA-based testing alone.
External quality assessment schemes using both tissue and liquid biopsy samples demonstrated excellent laboratory performance for tissue-based testing with an overall success rate of 98%. However, liquid biopsy testing was more challenging; while performance improved from a success rate of 37.5% in the first round (2022) to 63% in the second round (2024), detection remains technically demanding.
Dr. Heydt said, "To improve diagnostic accuracy, incorporating RNA-based confirmation, where feasible, can improve sensitivity and specificity for identifying true exon-skipping events." Dr. Heydt concluded, "Our study provides evidence supporting the complementary role of RNA-based testing in the assessment of MET exon 14 alterations and highlights the value of EQA programs in monitoring assay performance, identifying analytical limitations, promoting harmonization of testing strategies, and ensuring accurate and reproducible results for patient selection for MET-targeted therapies."
