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Background   BCOR-CCNB3  sarcoma (BCS) is a group of undifferentiated small round cell sarcomas harboring the  BCOR  gene rearrangement which shares morphology with the Ewing sarcoma family as well as other malignant round blue cell tumors, thus making them difficult to diagnose. The aim of this study was to explore the role of molecular techniques in the diagnosis of BCS.    Methods  Twenty-three cases of  EWSR1  rearrangement-negative undifferentiated small round cell sarcomas (Ewing-like sarcoma) were analyzed for the presence of  BCOR  gene rearrangement by Fluorescence in situ hybridization (FISH) and Reverse Transcription -Polymerase Chain Reaction (RT-PCR). The clinicopathological features of the positive cases were also reviewed. Fifteen additional cases were used as negative controls.    Results  Eight cases were found with  BCOR  gene rearrangement by FISH and reappraised as BCS. The patients ranged in age from 8 to 20 years old, with a male predominance (M:F = 6:2). All tumors were located in the lower extremities. The tumor locations were more common in bone ( n  = 6) than deep soft tissue ( n  = 2). Histologically, 7 of 8 tumors were predominately composed of spindle or ovoid cells. The tumor cells were usually arranged in solid hypercellular sheets without a distinct architectural pattern. IHC showed expression of TLE1 (100%), CCNB3 (88%), BCOR (71%). RT-PCR for  BCOR-CCNB3  fusion transcript was positive in 7 of 8 cases. Pre-operative chemotherapy resulted in eradication of tumors in 5 patients after a follow-up of 7 to 42 months.    Conclusions  Efficient diagnosis of  BCOR  rearranged sarcomas is achieved by the using a combination of FISH and RT-PCR assays.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13000-021-01114-2.

Detection of BCOR gene rearrangement in Ewing-like sarcoma: an important diagnostic tool