Whole-Exome Sequencing Reveals the Mutational Landscape of Head and Neck Squamous Cell Carcinoma: A Pilot Study from Northeast India

Background Head and neck squamous cell carcinoma (HNSCC) is a major cancer burden in India, with Northeast India reporting the highest male incidence nationally (31.7/100,000), driven largely by tobacco use. The region is almost absent from reference genomic cohorts, with current The Cancer Genome Atlas (TCGA)-HNSCC data including only minimal representation of South/Southeast Asian populations. Methods We performed whole-exome sequencing on ten treatment-naive HNSCC tumours from Northeast India (five tobacco-exposed, five non-exposed), using tumour-only variant calling (DRAGEN, GRCh38) and VEP annotation. Variants were tiered against ClinVar and AMP/ASCO/CAP guidelines, benchmarked against TCGA-HNSCC (n = 618) and the database of genomic variants of oral cancer (dbGENVOC; n = 100), and mutational signatures were extracted using SigProfilerExtractor. A tobacco-exposed vs. non-exposed case–control comparison identified differentially represented variants. Results Joint calling yielded 57,234 variants, including 28 ClinVar-annotated pathogenic/oncogenic variants concentrated in TP53 , CDKN2A , TERT , and HRAS . Across the top 50 OncoKB genes, this cohort showed markedly higher mutation frequencies than TCGA-HNSCC and dbGENVOC. NOTCH1 was the most recurrently altered established driver gene. Mutational signature analysis was dominated by SBS5 and SBS26, with no dominant tobacco-associated signature detected. Case–control analysis between tobacco and non-tobacco cohorts identified 170 enriched variants across 116 genes differentially enriched in tobacco-exposed tumours; the sole HIGH-impact candidate was a frameshift variant in MICA , while ELP2 was the only variant classified likely pathogenic by AlphaMissense and CADD = 25.0. Conclusion This pilot cohort reveals a genomic architecture that diverges substantially from existing reference datasets, generating hypotheses for tobacco-specific mutagenesis in an understudied population that warrant validation in larger, matched-normal, whole-genome-sequenced cohorts.