Clinical utility of DNA and RNA next-generation sequencing (NGS) for accurate diagnosis (Dx) and sub-classification of bone and soft tissue tumors (BST).

Abstract

e23521 Background: BST account for only 1-2% of adult cancers but encompass >100 distinct entities with diverse histology, genomics, prognosis, and clinical management. This rarity and heterogeneity make accurate dx and sub-classification challenging. We evaluated the clinical utility of concurrent DNA-/RNA-NGS for dx of BST. Methods: DNA/RNA co-extracted from tumor tissue were profiled with hybrid-capture NGS assays FoundationOne CDx (DNA), which interrogates alterations in 324 genes, and FoundationOne RNA which detects fusions in 318 genes. Fusions were filtered using a list of known dx fusions from NCCN guidelines, and all cases underwent central review by a board-certified pathologist. Results: Between Jun-Dec 2024, 270 bone (8%, n=22) and soft tissue (92%, n=248) tumors from unique patients underwent parallel DNA-/RNA-NGS during routine clinical care. Reportable results were obtained for both analytes in 90% of cases (n=244). The most common submitted pathology dx were sarcoma NOS (23%), GIST (12%), non-uterine leiomyosarcoma (10%), angiosarcoma (7%), and liposarcoma (5%). Dx fusions were identified in 24% (n=64) of cases, which confirmed the submitted dx in 21% (n=57), refined the classification in 2% (n=4), and corrected a misdiagnosis in 1% (n=3; Table). The most common recurrent fusions included NAB2 :: STAT6 (n=8), PAX3 :: FOXO1 (n=6), EWSR1 :: FLI1 (n=4), and SS18 :: SSX1 (n=4). Notably, 75% (43/57) of confirmed dx and 100% (7/7) of revised dx were based on fusions detected in RNA only. In addition, therapeutically targetable fusions were detected in 5 cases (2%; ALK n=2, BRAF , FGFR2 , NTRK1 ). Conclusions: Concurrent DNA-/RNA-NGS provided dx utility in 24% of BST, leading to revised diagnoses for 7 patients. Inclusive of targetable fusions, RNA-NGS added incremental value to DNA-NGS alone for 19% (51/270) of patients. These findings support a multimodal dx strategy combining morphology, immunohistochemistry, and both DNA- and RNA-NGS for accurate classification and management of BST. Reclassified BST N=7. Case Submitted Pathology Dx Dx Fusion (All RNA Only) Revised Integrated Dx Dx Corrected 1 Epithelioid Angiosarcoma YAP1 :: TFE3 Epithelioid Hemangioendothelioma 2 Uterine EndometrialStromal Sarcoma COL1A1 :: PDGFB COL1A1-PDGFB Fusion‐AssociatedUterine Fibrosarcoma 3 Atypical CellularFibrous Meningioma NAB2 :: STAT6 Solitary Fibrous Tumor Dx Refined 4 Spindle Cell Neoplasm w/ Vaguely Fibromyxoid Stroma, Differential Incl. Ossifying Fibromyxoid Tumor PRRX1 :: NCOA2 PRRX-NCOAx -Rearranged Fibroblastic Tumor 5 Undifferentiated Round Cell Sarcoma, Possible BCOR Sarcoma MGA :: NUTM1 NUTM1 -Rearranged Spindle Cell Sarcoma 6 Undifferentiated Uterine Sarcoma w/ Osteosarcomatous Component JAZF1 :: SUZ12 Uterine Endometrial Stromal Sarcoma 7 Differential Incl. MPNST, BCOR Lesion, Other Primitive Sarcoma SS18 :: SSX2 Synovial Sarcoma