Targeted RNA sequencing enhances the integrated diagnosis of bone and soft tissue tumors.
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BACKGROUND: The diagnosis of bone and soft tissue tumors is challenging due to their rarity, overlapping morphology, and limited access to specialized immunohistochemistry (IHC) in routine practice. Because many of these tumors are fusion-driven, targeted RNA sequencing may improve diagnostic accuracy, but its use is not yet established in Japan. METHODS: We retrospectively analyzed 90 cases of bone and soft tissue tumors, including benign lesions, using the TruSight RNA Pan-Cancer Panel (1385 genes) on FFPE samples. Fusion detection was combined with expression-based clustering. Diagnostic impact was assessed by comparing initial histological impressions with integrated diagnoses incorporating targeted RNA panel findings. RESULTS: Fusion transcripts were detected in 63 cases (69.2 %), of which 46 were in-frame. Twenty-five cases harbored well-characterized pathogenic fusions that directly contributed to diagnostic confirmation or refinement. Twenty-one cases showed fusion transcripts of uncertain significance, and ten of these were reclassified as likely pathogenic after additional validation. Three cases exhibited complex fusion patterns suggestive of chromothripsis or chromoplexy, warranting further genome-wide analysis. RNA expression clustering distinguished several tumor subtypes and provided complementary support for diagnostically challenging cases, such as undifferentiated pleomorphic sarcoma. CONCLUSIONS: Targeted RNA panel testing enabled robust detection of clinically relevant fusions and provided expression-based insights into tumor classification. When integrated with histopathology, this approach improved diagnostic accuracy in rare tumors and offered a practical triage strategy for extended genomic analysis, highlighting its clinical utility in pathology practice.