Targeted RNA analysis (RNA-seq) in solid tumours: a key tool in diagnostic dead-end situations

Targeted RNA analysis (RNA-seq) in solid tumours: a key tool in diagnostic dead-end situations 

High‑throughput sequencing has become a major tool in oncology, with diagnostic, theranostic and prognostic applications. DNA‑ and RNA‑based NGS analyses (RNA‑seq) are complementary: DNA sequencing enables the detection of point mutations and small insertions/deletions (indels), while RNA analysis detects fusion transcripts and certain splice variants resulting from large deletions. These various alterations in tumor tissue have become essential biomarkers. 

Why perform RNA analysis using NGS? 

• Superior sensitivity for fusion detection 

FISH is a targeted technique that detects known and previously described fusions using specific probes. 
RNA sequencing makes it possible to identify fusion transcripts, including those involving rare or unexpected partner genes. Unlike FISH, RNA‑seq enables the simultaneous detection of all potential fusion partners in a single sequencing run. This approach therefore provides significantly higher sensitivity than FISH (22% additional fusions not detected by FISH, RT‑PCR or DNA panels) [aacrjournals.org] [thelancet.com]. 

• Detection of large deletions 

RNA‑seq can detect deletions located deep within intronic regions that affect exon splicing. It allows the identification of MET exon 14 skipping events, observed in non‑small cell lung cancer, as well as EGFRvIII deletions found in glioblastomas.