The impact of next generation sequencing on sarcoma diagnosis.

Abstract

e23528 Background: The rarity and heterogeneity of sarcoma has been complicating the diagnosis of sarcoma for years. Even expert pathologists of sarcoma could make mistakes in the diagnosis of this disease. The availability of Next Generation Sequencing (NGS) data enabled more accurate diagnosis of sarcoma. In this study, we systematically described the application of NGS on the diagnosis of sarcoma and the contribution of NGS to the diagnostic accuracy of sarcoma. Methods: A multi-center, retrospective study included 235 sarcoma patients’ tumor and paired normal samples that were sent from 56 hospitals to a College of American Pathologists (CAP) accredited and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory, at Shanghai, China for Next Generation Sequencing (NGS) was performed. Using next generation sequencing based YS panel consisting 450 genes, these 235 sarcoma patients’ sample were sequenced and the NGS data was analyzed. The initial diagnosis without NGS information was reconsidered by expert pathologists. Results: Taking into consideration both the initial diagnosis and the NGS results, the final diagnosis of these 235 sarcoma cases included 8 low grade malignant fibromyxoid tumors, 11 dermatofibrosarcoma protuberans (DFSP), 38 myxoliposarcomas, 22 alveolar rhabdomyosarcomas, 11 alveolar soft tissue sarcoma, 2 desmoplastic small round cell tumors, 37 NTRK rearrangement spindle cell tumors, 40 Ewing’s sarcoma and 66 synoviosarcomas. In total, 29% initial diagnoses were changed according to NGS identified fusions, including 13% low grade malignant fibromyxoid tumors (1 FUS- CREB3L2 fusion), 27% DFSPs (3 COL1A1- PDGFB fusions), 11% myxoliposarcomas (3 FUS- DDIT3 fusions and 1 EWSR1- DDIT3 fusion), 14% alveolar rhabdomyosarcomas (2 PAX7- FOXO1 fusions and 1 FOXO1- LINC00598 fusion), 18% alveolar soft tissue sarcomas (2 ASPSCR1- TFE3 fusions), 50% desmoplastic small round cell tumor (1 EWSR1- WT1 fusion), 95% NTRK rearrangement spindle cell tumors, 13% Ewing’s sarcomas (3 EWSR1- FLI1 fusions and 2 EWSR1- ERG fusions) and 21% synoviosarcomas (9 SS18- SSX1 fusions and 5 SS18- SSX2 fusions). Conclusions: NGS would be highly recommended for accurate diagnosis of sarcoma, especially for NTRK rearrangement spindle cell tumor, the majority of which were confirmed according to NGS identified fusions.