Whole-exome sequencing analysis of oral squamous cell carcinoma delineated by tobacco usage habits

Oral squamous cell carcinoma (OSCC) is a common cancer of oral cavity in India. Cigarette smoking and chewing tobacco are known risk factors associated with OSCC. However, genomic alterations in OSCC with varied tobacco consumption history is not well-characterized. In this study, we carried out whole-exome sequencing to characterize the mutational landscape of OSCC tumors from subjects with different tobacco consumption habits. DNA was extracted from 30 primary OSCC tumor samples. Libraries were constructed and sequenced using Illumina Hiseq 2500 platform. Data obtained were processed using Samtools, Picard and GATK pipeline. Somatic variants were identified using Strelka and annotated using Varimat. Copy number alterations were assessed using OncoCNV.