Hospital for Sick Kids in Toronto researchers are reporting that focused RNA sequencing can detect clinically actionable alterations in 87% of tumors and supply decisive findings the place DNA-seq both fails, returns no variant, or isn’t informative.
Most cancers therapies have seen large enhancements lately, partly resulting from extremely particular concentrating on and diagnostic methods.
DNA-based strategies dominate molecular most cancers diagnostics however wrestle to detect gene fusions and assess splice website penalties. RNA sequencing permits delicate fusion detection and direct evaluation of transcript-level disruption brought on by splicing mutations.
Within the research, “Medical utility of focused RNA sequencing in most cancers molecular diagnostics,” revealed in Nature Drugs, researchers carried out a focused RNA-seq assay to judge 2,310 tumors throughout central nervous system, strong, and hematopoietic cancers.
Of the two,310 tumors submitted for evaluation, 110 (4.8%) failed high quality management, primarily resulting from inadequate RNA. Amongst samples assembly high quality thresholds, sequencing was profitable in 99.6%.
Oncogenic variants had been recognized in 74% of tumors, with an extra 13% labeled as pertinent negatives—bringing complete medical utility to 87%.
Amongst optimistic circumstances, 40% carried single nucleotide variants (SNVs) or indels, 32% fusions, 2.5% different structural variants, and 5% confirmed a number of courses. Fusions had been 1.8 occasions extra frequent in youngsters, whereas SNVs had been 1.6 occasions extra frequent in adults.
Amongst 103 samples with matched DNA sequencing, RNA-seq detected 93.3% of oncogenic variants. Variant allele frequencies between RNA-seq and DNA-seq confirmed sturdy correlations.
Amongst tumors sequenced with diagnostic intent, 37 acquired new diagnoses, representing 1.9% of evaluable circumstances. A further 11 tumors had been reclassified primarily based on the presence or absence of diagnostic alterations, bringing the whole to 48 revised diagnoses.
Central nervous system tumors accounted for 30 of the 48 revised diagnoses. In 13 circumstances, RNA-seq reclassified ependymoma as glioma, astroblastoma, or paraganglioma. Seven low-grade gliomas had been re-diagnosed as diffuse midline glioma, H3 K27-altered, primarily based on identification of H3K27M mutations.
5 strong tumors had been reclassified, together with one initially identified as metastatic Wilms tumor, re-identified as clear cell sarcoma of the kidney following detection of a BCOR inside tandem duplication. One other case, beforehand examined with detrimental fusion outcomes, was revised to dermatofibrosarcoma protuberans after RNA-seq recognized a canonical COL1A1::PDGFB fusion.
Eight tumors had been reclassified not by detection of a brand new alteration however by ruling out anticipated diagnostic options. In every case, RNA-seq excluded defining molecular markers of the histologic prognosis, resulting in re-evaluation of tumor classification.
In complete, 94 of 104 sufferers thought of for focused remedy acquired therapy primarily based on RNA-seq findings. MAPK pathway inhibitors, tyrosine kinase inhibitors, and immune checkpoint therapies had been mostly used.
Fusions alone defined oncogenesis in 86% of fusion-driven tumors, lots of which lacked extra alterations. RNA-seq succeeded throughout all tumor sorts and tissue codecs, together with degraded FFPE samples.
Researchers conclude that focused RNA-seq can function a stand-alone molecular diagnostic with excessive yield, minimized value, and broad medical applicability.
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Extra info: Robert Siddaway et al, Medical utility of focused RNA sequencing in most cancers molecular diagnostics, Nature Drugs (2025). DOI: 10.1038/s41591-025-03848-8
