Identification Of CDKN2A Somatic Mutations in HCC Patients: Insights from NGS in An Egyptian Cohort | ||
| African Journal of Biological Sciences | ||
| Articles in Press, Accepted Manuscript, Available Online from 26 September 2025 | ||
| Document Type: Original Article | ||
| DOI: 10.21608/ajbs.2025.424967.1137 | ||
| Authors | ||
| Aya Abdelwahab* 1; Randa M Talaat2; Moustafa A. Sakr3; Mohamed K Khalifa4; Ehab A. Ahmed5; mohamed A. selim6; Ghada M. Nasr7; Manal O. El Hamshary7 | ||
| 1Molecular diagnostics, University of Sadat city | ||
| 2Department of Molecular Diagnostics and Therapeutics, Genetic Engineering & Biotechnology Research Institute, University of Sadat City. | ||
| 3epartment of Molecular Diagnostics and Therapeutics, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat City 32897, Egypt | ||
| 4Technical advisor molecular pathology lab. children cancer hospital 57357. Chief scientific officer omicsense company | ||
| 5Chemistry Department, Faculty of Science, Cairo University, Cairo, Egypt Medical Genome Center Faculty of Medicine, Cairo University, Cairo, Egypt, | ||
| 6Immunology Botany and Microbiology Department, Faculty of Science (boys), AL-Azhar University, Egypt. | ||
| 7Department of Molecular Diagnostics and Therapeutics, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat City 32897, Egypt | ||
| Abstract | ||
| Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality worldwide, most often arising in the setting of cirrhosis associated with chronic hepatitis B or C virus infection. While curative treatment is possible at early stages, advanced disease is marked by high recurrence rates and poor prognosis. A deeper understanding of the molecular mechanisms underlying HCC is essential for improving therapeutic outcomes. Cyclin-dependent kinase inhibitor 2A (CDKN2A) is a tumor suppressor gene central to cell cycle regulation, and its alterations have been linked to several malignancies. In this study, circulating cell-free DNA from 21 Egyptian HCC patients was analyzed using targeted next-generation sequencing (NGS) with full CDKN2A coverage. Mutations were detected in 6 patients (28.6%), with 10 somatic variants identified: 40% were single-nucleotide variants (SNVs), 50% copy number variants (CNVs), and 10% multi-nucleotide variants (MNVs). Among SNVs, half were synonymous, while the remainder included non-synonymous and splice-site variants. Predicted functional impacts ranged from deleterious to uncertain or likely tolerated. No significant association was observed between CDKN2A mutation status and clinicopathological features. These findings highlight CDKN2A as a potential contributor to hepatocarcinogenesis and underscore the need for larger studies to clarify its prognostic and therapeutic relevance. | ||
| Keywords | ||
| HCC, CDKN2A; NGS; SNV and Somatic mutation | ||
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