(P 76) MOLECULAR AND CHROMOSOMAL MICROARRAY PROFILING OF OSTEOSARCOMA IN CHILDREN, ADOLESCENTS AND YOUNG ADULTS: A SINGLE INSTITUTION REPORT

Objective: Metastatic disease at diagnosis and histologic response to neoadjuvant-chemotherapy have been the main predictors for poor outcome in patients with osteosarcoma (OST). Although next-generation sequencing (NGS) allowed a deeper molecular understanding of OST genomics, there have been limited studies characterizing the molecular features and genome-wide copy number variations (CNVs) of OST and their evolution through treatment.

Methods: After IRB approval, the clinical, molecular features, and CNVs of patients with OST treated at Children’s Hospital Los Angeles who had NGS performed with OncoKids® panel and chromosomal microarray (CMA) performed with OncoScan® formalin fixed paraffin embedded (FFPE) Array (Affymetrix) were reviewed. Read data was mapped to the human genome (GRCh37/hg19). Each chromosome was binned with segments of10^7 base pairs and weighted geometric means of CNVs per segment were calculated and ranked.

Results: Seventy patients with OST median age 13 years (range 7-19) including 23 with metastases had 91 NGS panels performed. Majority had extremity primaries; 3 pelvis, 4 head and neck. Most (n=65) received cisplatin/doxorubicin/methotrexate (MAP). Pathogenic variants of clinical significance (VCS) identified at diagnosis (n=23) were TP53, RB1, ATRX, PTEN, TSC1; significant gene amplifications ( 8 copies) (SGA) were MYC, IGF1R, CCND3. Additional VCS identified at local control (n=3) were PTCH1 and TP53. The VCS and SGA identified at first relapse (n=10) were RB1, TP53, ATRX, PIK3CA and PDGFRA, KIT, KDR respectively. The VCS at 2nd relapse (n=1) included TP53, at 3rd relapse (n=1) was CDKN2A and at 4th relapse (n=1) was TP53. Twelve patients had longitudinal OST samples with NGS, and all preserved their original tumor’s VCS/SGA. Interestingly 9 of these patients had either loss or addition of variants of uncertain significance (VUS) at tumor recurrence.

A total of 37 patients with localized OST and CMA samples from primary diagnosis were analyzed revealing intra- and inter-tumoral CNV heterogeneity (Figure 1). Chromosomes (Chr) with the highest average number of CNVs include chr 1, 5, 6, 8, 17, and 19. Chromosomes with the lowest average number of CNVs include chr X, 6 and 13. Chromosomes with the most variable CNVs include chr 4, 5, 6, 7, 8, 13, 15, 17, and 19. Chromosomes with the least variable CNVs include chr 5, 9, 10, 13, 17, 21, and 22. The chromosomes noted to have the most variable CNVs code for the genes reported as VCS identified on OncoKids, such as chr 4 (KIT, PDGFRA, and KDR), chr 6 (CCND3), chr 8 (MYC), chr 13 (RB1), and chr 17 (TP53). Of note, Chr 13 had different segments that involved the most variable CNVs and least variable CNVs.

Conclusion: TP53, RB1, ATRX, CDKN2A are the most common VCS in OST similar to previous reports. VCS at diagnosis were preserved at the time of recurrence with the loss or addition of VUS. Further analyses of CMAs are underway in order to gain insight into the relevance of CNV changes through treatment. Moreover, better characterization of the evolution of genomic landscape in OST with treatment may offer opportunities for molecular prognostication, understanding resistance mechanisms and opportunities for targeted therapies.