Abstract / Summary
Abstract Background Sarcomas are rare and heterogeneous mesenchymal neoplasms in which accurate classification can be challenging because of overlapping histologic and immunophenotypic features. We evaluated the diagnostic contribution of clinical next-generation sequencing (NGS) in a real-world sarcoma cohort and further characterized genomic and fusion findings and their clinical implications. Methods We retrospectively reviewed 106 patients with suspected or pathologically confirmed bone and soft tissue tumors who underwent 110 clinical NGS assays. Diagnostic impact was determined by integrated review of histomorphology, immunohistochemistry, molecular findings, and ancillary tests and categorized as reclassification, refinement, molecular confirmation, or no direct diagnostic impact. Differences in altered-gene counts between genomic classes were assessed using Mann–Whitney U tests with Benjamini–Hochberg correction, and outcomes of matched therapy were evaluated. Results NGS provided diagnostically relevant information in 61 of 106 patients (57.5%), including reclassification or refinement in 37 (34.9%) and molecular confirmation in 24 (22.6%). Nineteen of the 23 refined tumors had initially been classified as sarcoma, not otherwise specified, or undifferentiated round/small cell sarcoma. Genomically complex or other tumors had more genes affected by short variants (q = 0.002) and copy-number alterations (q < 0.001) than translocation-associated sarcomas. RNA sequencing detected fusion transcripts in 35 of 53 evaluable patients (66.0%); EWSR1 fusions involved seven partner genes across eight histologic diagnoses. A candidate novel SFXN1::NRG2 fusion in pleomorphic liposarcoma was supported by concordant RNA and genomic breakpoint findings. Treatment-relevant alterations or biomarkers were identified in 35 patients, of whom 11 (31.4%) received matched therapy; among 10 response-evaluable patients, three achieved partial response and six had stable disease. Conclusions Clinical NGS was particularly useful for resolving diagnostically ambiguous sarcomas. Partner-level characterization of EWSR1 fusions provided classification information beyond rearrangement status alone, and treatment-relevant molecular findings further linked diagnostic profiling to matched therapy in selected patients.