Mutational landscape of ESCC tumors from tobacco users and non-users

Esophageal squamous cell carcinoma (ESCC) is one of the most common causes of cancer-related mortality in India. Tobacco and alcohol consumption are the major risk factors associated with high incidence of ESCC. Genomic profiling of ESCC tumors from Indian cohort is not studied so far. In this study, we have performed whole exome sequencing analysis of 28 ESCC samples from an Indian cohort to understand genomic alterations associated with esophageal squamous cell carcinoma. We have analyzed tumors from tobacco users and non-users to investigate genetic differences associated with tumors from these two groups. DNA was extracted from 28 primary ESCC 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.