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PURPOSE: Chondrosarcomas are the second most common primary malignant bone tumors. While histologic grade is the most important factor predicting the clinical outcome of chondrosarcoma, it is subject to interobserver variability. IDH1 and IDH2 hotspot mutations were recently found to be frequently mutated in central chondrosarcomas. However, a few published articles have been controversial regarding the association between IDH1/IDH2 mutation status and clinical outcomes in chondrosarcomas. EXPERIMENTAL DESIGN: We performed hotspot sequencing of IDH1 and IDH2 genes in 89 central chondrosarcomas and targeted next-generation sequencing in 54 of them, then correlated the IDH1/IDH2 mutation status with the patient’s clinical outcome. RESULTS: Although no association was discovered between IDH mutation status and the patient’s overall survival, IDH1/IDH2 mutation was found to be associated with longer relapse free and metastasis free survival in high-grade chondrosarcomas. Genomic profiling reveals TERT gene amplification and ATRX mutation, for the first time, in addition to TERT promoter mutation in a subset (6/30, 20%) of high-grade and dedifferentiated chondrosarcomas. These abnormalities in telomere genes are concurrent with IDH1/IDH2 mutation, and with CDKN2A/2B deletion or TP53 mutation, suggesting a possible association and synergy among these genes in chondrosarcoma progression. We found twenty-one percent of chondrosarcoma patients also had histories of second malignancies unrelated to cartilaginous tumors, suggesting possible unknown genetic susceptibility to chondrosarcoma. CONCLUSIONS: IDH1/IDH2 mutations are associated with longer relapse free and metastasis free survival in high-grade chondrosarcomas and they tend to co-occur with TERT mutations, and with CDKN2A/2B and TP53 alterations in a subset of high-grade chondrosarcomas.