Mutational landscape of head and neck squamous cell carcinomas in a south asian population

Kulsoom Ghias, Sadiq S. Rehmani, Safina A. Razzak, Sarosh Madhani, M. Kamran Azim, Rashida Ahmed, Mumtaz J. Khan

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer type globally and contributes significantly to burden of disease in South Asia. In Pakistan, HNSCC is among the most commonly diagnosed cancer in males and females. The increasing regional burden of HNSCC along with a unique set of risk factors merited a deeper investigation of the disease at the genomic level. Whole exome sequencing of HNSCC samples and matched normal genomic DNA analysis (n=7) was performed. Significant somatic single nucleotide variants (SNVs) were identified and pathway analysis performed to determine frequently affected signaling pathways. We identified significant, novel recurrent mutations in ASNS (asparagine synthetase) that may affect substrate binding, and variants in driver genes including TP53, PIK3CA, FGFR2, ARID2, MLL3, MYC and ALK. Using the IntOGen platform, we identified MAP kinase, cell cycle, actin cytoskeleton regulation, PI3K-Akt signaling and other pathways in cancer as affected in the samples. This data is the first of its kind from the Pakistani population. The results of this study can guide a better mechanistic understanding of HNSCC in the population, ultimately contributing new, rational therapeutic targets for the treatment of the disease.

Original languageEnglish
Pages (from-to)526-542
Number of pages17
JournalGenetics and Molecular Biology
Issue number3
StatePublished - 1 Jul 2019


  • Driver mutation
  • Head and neck squamous cell carcinoma (HNSCC)
  • Novel mutation
  • Pakistani population
  • Whole exome sequencing


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