ORIGINAL RESEARCH article
Front. Genet.
Sec. Cancer Genetics and Oncogenomics
This article is part of the Research TopicAdvancements in head and neck tumor treatment strategy driven by the perspective of precision oncologyView all 6 articles
Genomic Landscape of Oral Squamous Cell Carcinoma from the Southwest Coast of Karnataka: Insights from FFPE-Based Next-Generation Sequencing
Provisionally accepted
Hafeeda Kunhabdulla1Riaz Abdulla1*
Divya Lakshmanan Mangalath2
Rohan Thomas3Devika Jayarajan1Vipul Jain3Fahizah A1Muhammed S Mustak4
Ranajit Das2*- 1Yenepoya (Deemed to be University) Dental College, Mangaluru, India
- 2Yenepoya Research Centre, Yenepoya University, Mangalore, India
- 3Yenepoya Medical College Hospital, Mangaluru, India
- 4Mangalore University, Mangalagangotri, India
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Background: Oral squamous cell carcinoma (OSCC) remains a major health burden in India, yet region-specific genomic data are limited. This study aimed to characterize the mutational landscape of OSCC patients from the southwest coast of Karnataka using FFPE tissues and assess potential clinical correlations. Methods: Whole-exome sequencing was performed on tumor and adjacent normal FFPE samples from 21 OSCC patients. Variants were annotated using multiple clinical databases, and stratified analyses were conducted across clinicopathological parameters including age, sex, tumor site, and TNM stage. Results: We identified extensive inter-patient variability in clinically relevant mutations, with intronic and missense variants being most frequent. A core set of 21 genes including ABCB1, CD44, IL6, PADI2, and VKORC1—carried pathogenic or drug-response variants in all patients. Ten tumor-exclusive mutations were observed, including TLR1 rs5743618, present in 100% of tumors. Pathway and network analyses highlighted enrichment in p53 signaling, immune pathways, and platinum-drug resistance. Stratified analyses showed no significant differences in mutation burden across TNM stages (Kruskal– This is a provisional file, not the final typeset article Wallis p = 0.952), nodal status (p = 0.460), age, or sex. Polygenic risk score estimation revealed that 15 of 21 patients belonged to the highest-risk quartile, suggesting strong inherited susceptibility. Conclusion: FFPE-based genomic profiling successfully captured key OSCC-associated alterations and revealed region-specific mutation signatures. The predominance of germline and pharmacogenomic variants and strong PRS enrichment underscore the potential of incorporating hereditary risk assessment and targeted therapy selection into OSCC management strategies in this population.
Keywords: FFPE, Genomic profiling, India, Karnataka, Mutational landscape, Next-generation sequencing, oral squamous cell carcinoma
Received: 05 Nov 2025; Accepted: 28 Jan 2026.
Copyright: © 2026 Kunhabdulla, Abdulla, Mangalath, Thomas, Jayarajan, Jain, A, Mustak and Das. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Riaz Abdulla
Ranajit Das
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