OBJECTIVE Osteosarcoma (OS) is the most common primary bone malignancy among adolescents and young adults. It is characterized by a high mortality rate, though it remains a relatively rare disease overall. The treatment protocols can be complex and challenging. We conducted a comparative genomic variation study to identify genes involved in the metabolism of chemotherapy drugs that are affected by various genomic alterations. METHODS This study analyzed the germline and tumor genomes of three OS patients who responded poorly to chemotherapy, developed lung metastases, and ultimately succumbed to the disease. Genes of interest were identified through a systematic review of apoptosis, autophagy, necroptosis, and chemotherapy-related databases. Whole-genome sequencing (WGS) revealed deleterious single nucleotide polymorphisms (SNPs), copy number variations (CNVs), and structural variations (SVs) in genes linked to cancer and chemotherapy. Protein association network analyses were used to highlight both shared and unique biological processes associated with OS in these patients. RESULTS Pathogenic SNPs were identified exclusively in patients P1 and P3. Patient P1 exhibited a missense
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