Satellite DNA fragility accompanies complex genome rearrangements and ecDNA oncogene amplification in canine osteosarcomas.

Canine osteosarcoma (OS) is an aggressive bone cancer with remarkable similarity to human OS. Despite its value as a comparative oncology model, the drivers of genomic instability remain poorly defined, hindering cross-species insights into disease progression. We applied long-read PacBio HiFi whole genome sequencing to matched tumor and blood samples from four purebred dogs to generate high-resolution maps of somatic structural variants (SVs). Tumor genomes showed extensive rearrangement complexity, with satellite repeat regions, particularly SAT1_CF, enriched near somatic SV breakpoints and occurring within genomic contexts marked by focal hypomethylation. We also identified multiple extrachromosomal DNA (ecDNA) elements carrying oncogenes indicating ecDNA-mediated oncogene amplification. Together, these data provide an integrated genomic and epigenomic view of canine OS, implicating satellite repeats as recurrent substrates for rearrangement and ecDNA as a prominent mode of genome remodeling. This work advances our understanding of OS genome dynamics and establishes a comparative framework for investigating repeat-driven instability and oncogene amplification across species.