Blood Based Biomarkers for Minimal Residual Disease Detection in Pediatric Sarcomas

Blood Based Biomarkers for Minimal Residual Disease Detection in Pediatric Sarcomas Primary Objective To test whether continuing detection of cell-free plasma tumor DNA (ptDNA) when a patient is in radiographic remission 2-3 weeks after local control can predict recurrence in pediatric sarcomas which include fusion positive sarcomas and osteosarcomas. To test whether the continuing presence of circulating tumor cells (CTC), when a patient is otherwise in radiographic remission 2-3 weeks after local control, can predict recurrence of pediatric sarcomas. Secondary Objectives To test whether the decrease of ptDNA burden following the initial cycle of therapy, can predict the five-year recurrence free survival of patients with pediatric sarcomas. To test whether the CTC or ptDNA burden detected in newly diagnosed patients before local control or chemotherapy can predict the five-year recurrence free survival of patients with pediatric sarcomas. Exploratory Objectives To characterize the plasma cytokine levels in patients with high-risk pediatric sarcoma patients. To demonstrate the feasibility of discovering the clonal evolution in pediatric sarcoma patients through plasma tumor DNA and tumor analysis. To explore the feasibility of performing single cell RNA-seq on CTC samples collected through a multi-center consortium. To explore the feasibility of detecting fusion genes such as, but not limited to SYT-SSX1/SSX2, EWS-WT1, CIC-DUX4, and BCOR-CCNB3 from the ptDNA of patients with fusion gene positive sarcomas. To explore the detailed kinetics of ptDNA release during early stage chemotherapy administration. Inclusion Criteria 1 Patients must be ≤ 40 years of age 2 Patients must be newly diagnosed. They must not have received any systemic agents for therapy for this new diagnosis 3 Patients with a suspected or confirmed diagnosis of one of the following solid tumors listed below. Histologic or cytological confirmation of the diagnosis is not required at enrollment, but must be resulted within 1 month of enrollment, which will be used to stratify patients into the five separate cohorts listed below. The assigned cohorts are used only for statistical analysis. • Cohort 1, Ewing sarcoma: confirmed or suspected diagnosis of Ewing sarcoma with a t(11;22) EWS-FLI1 or t(21;22) EWS-ERG translocation. • Cohort 2, Fusion gene positive rhabdomyosarcoma: confirmed or suspected diagnosis of a rhabdomyosarcoma with a t(2;13) PAX3-FOXO1 or t(1;13) PAX7-FOXO1 translocation.