<i>MYC</i> amplification as a prognostic biomarker in osteosarcoma: A report from the Children’s Oncology Group.

Abstract

10045 Background: Osteosarcoma is characterized by complex chromosomal alterations and genomic instability. MYC copy number (CN) gains are observed in 10%-60% of cases, and MYC amplification is associated with poor outcomes in single-center cohorts and genomic studies of relapsed or high-risk patients. This study aimed to validate the prognostic role of MYC amplification in a large, multi-center cohort of patients enrolled on Children’s Oncology Group (COG) up-front treatment and biobanking protocols. We also assessed other genes linked to survival. Methods: This retrospective, IRB-approved case-control study used banked FFPE DNA from 137 osteosarcoma samples from the COG biorepository for SNP microarray (Affymetrix OncoScan). Patients were enrolled on INT-0133, P9754, AOST0331 and APEC14B1 from 1993-2024. Amplifications of MYC, CCNE1 , CDK4 , and the 6p21.1 locus, as well as chromosome 6, 8, 12, and 19 ploidy were assessed. Gene amplification was defined as the ratio of gene to chromosome copies (e.g. MYC CN/chr8 CN) &gt; 2.0. The primary outcome was occurrence of event-free survival (EFS) event. Patients were matched on metastatic status and follow-up time. Univariate conditional logistic regression models were fit for each genetic feature to obtain the odds ratio (OR) of EFS event associated with amplification (95% confidence interval (CI)) and to conduct one-sided tests for the null hypothesis OR £ 1 at the 5% level. Results: Sixty-five case-control pairs for MYC, CDK4 , and 6p21.1, and 63 for CCNE1 were analyzed. MYC amplification was estimated to have a 1.87-fold increase in odds of EFS event (95% CI: 0.79, 4.42; p = 0.08). CDK4 amplification was associated with a 5-fold increase in odds of event (95% CI: 1.10, 22.82; p = 0.02). Neither amplification of 6p21.1 or CCNE1 were associated with increased odds of event, with ORs of 1.33 (95% CI 0.56, 3.16; p = 0.26) and 0.73 (95% CI: 0.29, 1.81; p = 0.25), respectively. Conclusions: MYC amplification may be associated with increased odds of EFS event in this cooperative group cohort. Though the result did not reach statistical significance, this finding aligns with prior studies demonstrating increased EFS-event risk for patients with MYC amplification. While our selection of a ratio cut point &gt; 2.0 to define amplification was informed by prior studies, the optimal cut point has not been determined and cut points may be assay dependent. Although CDK4 amplification appears associated with increased odds of event, confidence in this finding is limited by a sparse-data bias, due to a low number of control patients with CDK4 amplification. Future analyses will explore MYC and CDK4 copy number ratio as a continuous variable and assessing the relationship between additional genomic features and EFS events in this population.