International Journal of Molecular Medical Science, 2025, Vol.15, No.1, 9-19 http://medscipublisher.com/index.php/ijmms 15 on recurrence risk and overall survival rate. The detection of ctDNA (circulating tumor DNA) is one of the key steps, and NGS can be used to analyze ctDNA or tumor nuclear DNA isolated from plasma or tumor tissue, thereby detecting genetic variations such as mutations, amplifications, or deletions. Through these tests, mutations in specific genes such as TP53 or changes in other tumor suppressor genes can be associated with an increased risk of poor prognosis in OSCC patients (Figure 2) (Sumbal et al., 2018). In addition, the presence of ctDNA in postoperative blood may also indicate the risk of residual disease or recurrence, thereby further assisting doctors in prognosis assessment and treatment decision-making. Figure 2 Schematic representation of ctDNA analysis and clinical implications using NGS (Adapted from Sumbal et al., 2018) Image caption: A specimen taken from either plasma or tumor tis- sue can be subjected to NGS. Then whole-exome sequencing or targeted sequences in ctDNA isolated from plasma can be performed. Genetic variations can be assessed for prospective clinical utilization and prognosis. Mutations can be identified in patient’s plasma for ctDNA detection at the time of diagnosis or later after surgery (Adapted from Sumbal et al., 2018) Additionally, protein markers in saliva and serum, such as cytokines and specific growth factors, are associated with tumor aggressiveness and metastatic potential. These biomarkers can help predict the course of the disease and guide treatment decisions, enabling clinicians to develop more targeted therapeutic approaches based on the patient’s risk profile (Blatt et al., 2023). Integrating multiple genomic biomarkers provides a comprehensive molecular profile of the tumor, facilitating precise risk assessment. This biomarker-based stratification approach supports the implementation of personalized treatment, allowing clinicians to adjust therapy according to the patient’s specific genetic profile, thereby enhancing treatment efficacy and improving long-term prognosis(Wang, 2024). 6 Challenges and Limitations 6.1 Technical limitations One of the major technical challenges in the application of genomic biomarkers is the accuracy and sensitivity of detection methods. Technologies like Next-Generation Sequencing (NGS) and liquid biopsy techniques, while powerful, often struggle with detecting low-frequency mutations in early-stage tumors due to the small amount of circulating tumor DNA (ctDNA) present in the bloodstream (Sumbal et al., 2018). This low abundance of ctDNA can lead to false negatives, which poses a risk in early cancer detection where sensitivity is critical.
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