RNA Sequencing Outperforms DNA Techniques in Detecting Critical Cancer Mutations

Recent research from Toronto's Hospital for Sick Children highlights the superior efficacy of targeted RNA sequencing (RNA-seq) over traditional DNA-based methods in identifying actionable cancer mutations. The study demonstrates that RNA-seq can detect clinically significant alterations in 87% of tumor samples, providing crucial insights especially when DNA sequencing fails or yields inconclusive results.

While DNA methods dominate molecular diagnostics for cancer, they often struggle with detecting gene fusions and analyzing splice site impacts. In contrast, RNA-seq offers heightened sensitivity for gene fusion detection and direct assessment of transcript disruptions caused by splicing mutations, enhancing diagnostic precision.

In the comprehensive study titled "Clinical utility of targeted RNA sequencing in cancer molecular diagnostics," researchers evaluated 2,310 tumors spanning various cancer types, including central nervous system, solid, and hematopoietic cancers. Although 4.8% of samples failed quality control due to insufficient RNA, the remaining samples achieved a success rate of 99.6%. Among these, oncogenic variants were identified in 74% of tumors, with an additional 13% classified as relevant negatives, resulting in a total clinical utility of 87%.

The findings also revealed that RNA-seq detected 93.3% of oncogenic variants in 103 cases with matched DNA sequencing, showing a strong correlation between RNA and DNA variant allele frequencies. Notably, 37 cases received new diagnoses, with 13 reclassified based on RNA findings, including CNS tumors like gliomas and low-grade gliomas reclassified as more aggressive forms. In solid tumors, diagnoses of Wilms tumor and dermatofibrosarcoma were revised after RNA analysis identified specific genetic fusions.

Targeted RNA-seq not only refined current diagnoses but also guided more personalized treatment options. About 94 patients received targeted therapies, mainly involving MAPK pathway inhibitors, tyrosine kinase inhibitors, and immune therapies. The method proved effective across all tumor types and sample formats, including degraded FFPE tumor tissues, underscoring its broad applicability.

Overall, this research suggests that targeted RNA sequencing can serve as a standalone diagnostic tool, offering high diagnostic yield with reduced costs and wide clinical relevance. It exemplifies a significant advancement in molecular cancer diagnostics, promising improved patient management and treatment outcomes.