Abstract 3556: Assessing patterns of genomic instability in recurrent osteosarcoma
Authors: Kinnaman Michael David , Zaccaria Simone , Makohon-Moore Alvin , Gundem Gunes , Ossa Juan E. Arango , Dela Cruz Filemon S. , Meyers Paul A. , Hameed Meera , Tap William D. , Bender Julia Lynne Glade , Papaemmanuil Elli , Kung Andrew , Donahue Christine Iacobuzio 
Published: April 2023

Objective: The osteosarcoma genome is characterized by high levels of genomic instability, however whether there is pervasive ongoing genomic instability, or instability introduced by an early catastrophic event, is still unsettled.

Methods: We performed 30-80x whole genome sequencing (WGS) of 37 tumor samples from 8 patients with relapsed or refractory osteosarcoma. Each patient had at least one sample from a primary site and one sample from a metastatic or relapse site. A set of high confidence single nucleotide variants (SNV), copy number alterations (CNA), structural variations (SV) were called for each sample using our pediatric expanded genomics pipeline and an analysis focused on markers of genomic instability was performed using a custom pipeline of computational tools.

Results: Of the 8 patients in our cohort, 4 had localized disease at diagnosis (OSCE4, OSCE5, OSCE6, OSCE9) and 4 had metastatic disease at diagnosis (OSCE1, OSCE2, OSCE3, OSCE10). There were 17 samples from primary sites, 7 pretreatment biopsies, 10 on therapy primary resections, 20 metastatic sites, 15 of which were from lung metastases. We have previously reported on the clonal evolution regarding SNVs and CNAs within this cohort. TP53 structural variants involving intron 1/2 were seen in 6/8 patients (OSCE2, OSCE3, OSCE4, OSCE6, OSCE9, OSCE10). No new structural variants in consensus driver genes emerged in metastatic or relapse samples. Comparing the earliest sample to most recent sample in each patient, only OSCE1, OSCE9, and OSCE10 demonstrated an increase of ≥100 structural variants at the final timepoint. In OSCE2, OSCE5, and OSCE6, there were less structural variants identified at the final timepoint when compared to the earliest timepoint. Homologous recombination deficiency (HRD) scores were calculated for each sample. Only 4/8 patients (OSCE3, OSCE4, OSCE9, OSCE10) had an HRD score in the most recently acquired sample higher than the score from the primary site. Regions of hypermutation consistent with kataegis were identified for each sample, with the number of kataegis events remaining unchanged or decreasing in some instances. Kataegis events co-localized with rearrangement events a majority of the time (range 50-100%, Avg= 72.6%). Complex rearrangements such as chromothripsis and chromoplexy were assesed. In 6 patients there were &gt; 9 chromosomal arms involved in complex rearrangements that were shared between primary sites and metastatic/recurrent sites, while ≤ 4 chromosomal arms were involved with new complex rearrangements unique to the metastatic sites.

Conclusion: The patterns observed in our cohort reveal that osteosarcoma is relatively stable from diagnosis through subsequent relapses, supporting the model that an early catastrophic event accounts for the genomic instability observed in osteosarcoma.

Citation Format: Michael David Kinnaman, Simone Zaccaria, Alvin Makohon-Moore, Gunes Gundem, Juan E. Arango Ossa, Filemon S. Dela Cruz, Paul A. Meyers, Meera Hameed, William D. Tap, Julia Lynne Glade Bender, Elli Papaemmanuil, Andrew Kung, Christine Iacobuzio Donahue. Assessing patterns of genomic instability in recurrent osteosarcoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3556.