RNA-seq outperforms DNA methods in detecting actionable cancer mutations

Researchers at the Hospital for Sick Children in Toronto report that targeted RNA sequencing can detect clinically actionable alterations in 87% of tumors, offering decisive results when DNA sequencing is inconclusive. While DNA-based methods dominate molecular cancer diagnostics, they often miss gene fusions and fail to assess splice site consequences. RNA sequencing enables sensitive fusion detection and direct assessment of transcript-level disruptions from splicing mutations.

In a study published in Nature Medicine, “Clinical utility of targeted RNA sequencing in cancer molecular diagnostics,” researchers evaluated 2,310 tumours from central nervous system, solid, and hematopoietic cancers. Of these, 4.8% failed quality control, mostly due to insufficient RNA; sequencing succeeded in 99.6% of the remaining samples. Oncogenic variants were found in 74% of tumours, with another 13% classified as pertinent negatives, totalling 87% clinical utility. Fusions were 1.8 times more common in children, while single nucleotide variants were 1.6 times more common in adults. Among 103 tumours with matched DNA sequencing, RNA-seq detected 93.3% of oncogenic variants, with strong allele frequency correlations. The method also enabled reclassification of 48 tumours, including 37 new diagnoses. Central nervous system tumours accounted for 30 of these, with notable re-diagnoses such as ependymoma to glioma and low-grade glioma to diffuse midline glioma, H3 K27-altered.

Of 104 patients considered for targeted therapy, 94 received treatment based on RNA-seq findings, most commonly MAPK pathway inhibitors, tyrosine kinase inhibitors, and immune checkpoint therapies. The study concludes that targeted RNA-seq is a high-yield, cost-effective stand-alone diagnostic applicable across tumour types and sample formats.