Computational Analysis of SNPs and Codons for cancerous genes

Breast cancer, liver cancer (hepatocellular carcinoma, intrahepatic cholengiocarcinoma, gallbladder cancer), and lung cancers all are multi-genic diseases. As not all the genetic changes in the genomic data causes a disease to occur, but there are a very few number of variations in the codons of specific genes which cause any lethal effect. Thus, with the objective of statistical evaluation of significance of nucleotide positions in codons through SNPs in gene sequences implicated in cancers, and statistical analysis of codon expression level, reported genes for mentioned cancers were studied. ACUA (Automated Codon Usage Analysis) software is used for the codon and SNP analysis studies, which helped to study different parameters (percentage of AT and GC; codon adaptive index (CAI); ENc (Effective Number of Codon); and number of all four nucleotides with respect to all three positions of the codons). By the results of analysis, CAI (Codon Adaptive Index) and ENC( Effective Number of Codon) values are proved to be an important parameter to evaluate the involvement of a gene causing cancer, on the other hand, these studies could be helpful in gene targeting.