Pathway Study of Gene Variants of Pancreatic Cancer Detected by Whole Exome Sequencing Data Analysis

Author(s): M. L. Patil*, S. B. Madagi and J.Hoskeri

Abstract: Whole Exome sequencing, an application of next generation sequencing involves sequencing protein coding regions of genome. In current work WES data analysis was carried out on human pancreatic cancer genome using Ubuntu linux platform where the potential gene variants were identified. The human pancreatic genome sequence pairs from ENA database ERR232253, ERR232254 and ERR232254 with accession number were used for analysis where quality check of samples was performed using FastQC tool. Followed by the alignment of quality checked samples with reference genome hg38 using Bowtie2, resulting in SAM format file and was further converted to BAM format using SAMtools. The BAM file is sorted and the duplicates were removed using Picard tool, then generation of VCF file using BCF tools that predicts the possible gene variants found in the samples. The result revealed that gene HRNR showed average of 21 mutations indicating potential gene variant in pancreatic cancer. Also among the nonsynonymous mutations in samples 97 genes are found to be common, possessing 5 and more mutations. The work showed domain analysis, involvement of genes in biological process, pathway analysis and gene function. Investigation showed that 18 genes affected Protein Biosynthesis and 26 were specific to Nucleus tissue location.

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