Supplementary Data

Genomic alterations in chemotherapy genes detected in three model Thai adolescent patients with fatal osteosarcoma at Maharaj Nakorn Chiang Mai Hospital, Thailand.OBJECTIVE: Osteosarcoma is the most common primary bone malignancy among adolescents and young adults, 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 investigated the germline and tumor genomes of three primary osteosarcoma patients who responded poorly to chemotherapy, later developed lung metastases, and ultimately succumbed to the disease. Whole Genome Sequencing (WGS) data for both the germline and tumor genomes of these patients were analyzed to identify deleterious single nucleotide polymorphisms (SNPs), copy number variations (CNVs), and structural variations (SVs) in genes associated with chemotherapy and cancer. An in silico analysis of protein association networks was performed on the affected genes of each patient to identify both common and unique biological processes associated with osteosarcoma.RESULTS: All patients shared a stop-gained mutation in the tumor suppressor gene MLH1 and a frameshift mutation in REV3L, present in both their germline and tumor genomes. Additionally, a high-impact variant in a splice donor site of the tumor suppressor gene TP53 was found in their tumor genomes. The tumor genome of patient OS0059 was extensively affected by CNVs, whereas the tumor genomes of patients OS0061 and OS0081 demonstrated relatively moderate CNVS. Structural variations were detected in all three tumor genomes and affect different key genes involved in platinum drug resistance and DNA repair. All identified mutated genes were also correlated with the clinical features of the patients.CONCLUSIONS: The genetic makeup of osteosarcoma is complex and varies from patient to patient, potentially affecting processes related to cell death or resistance to chemotherapy. Our investigations suggest that structural alterations, such as copy number variations (CNVs) and structural variations (SVs), in genes involved in chemotherapy metabolism and DNA repair mechanisms in tumor biopsies, could be useful for clinicians to design chemotherapy regimens suitable for different osteosarcoma (OS) patients.