Breast cancer is ranked the first cancer in women worldwide and the second leading cause of death after cervical cancer particularly in developing countries. Specific genes are associated with breast cancer risk in human genome. Understanding the codon usage bias (CUB) with compositional dynamics of coding sequence is of great importance in gaining clues to predict the level of gene expression and genome characterization. In this study, we have analyzed the complete nucleotide coding sequences of fifteen breast cancer risk genes with the help of various genetic indices. Our analysis revealed that both neutral mutation and selective constraint play major roles in the codon usage patterns of breast cancer risk genes. Our results further show that gene expression level is linked with alterations in the nucleotide skewness. Breast cancer gene products showed the dominance of three amino acids namely serine, leucine and glutamate in their composition but the least usage of two amino acids namely tryptophan and methionine. Moreover, the level of breast cancer gene expression measured by RCBS revealed a significant negative correlation with highly used amino acids. In addition, highly used amino acids had negative impact on the expression of breast cancer risk genes.

Background: The non uniform usage of synonymous codons during translation makes codon usage bias i.e some codons are used more frequently than others. However the synonymous codon usage pattern differs among the genes of an organism and also among different organisms. Mitochondrial genome is small, highly conserved and maternally inherited with high mutation rate. The study of codon usage bias pattern is useful for better understanding the process of evolution in terms of molecular biology. Methods and Result: In this study we analyzed codon usage pattern of genes encoding mitochondrial ATPase 6 and ATPase 8 in different species of mammals. From our study it was evident that leucine is the most frequent amino acid in both genes in the mammalian species. ENC value ranged from 57 to 60 with a mean of 59.25 in ATPase 6. In ATPase 8, ENC value ranged from 42 to 60 with a mean of 54.1. In ATPase 6, a significant positive correlation was observed between overall A and A3% (r =0.9065, p<0.001), C and C3% (r = 0.9238, p< 0.001), GC and GC3% (r = 0.9244, p<0.001). ENC showed a highly significant positive correlation with overall GC content (r =0.9479, p<0.001) and GC3 (r = 0.9387, p<0.001) in ATPase 6. But in ATPase 8, significant positive correlations were observed between A% and A3% (r=0.6502, p<0.05), C% and C3% (r =0.9804, p< 0.001), GC% and GC3% (r =0.9732, p<0.001). In addition, a highly positive correlation was found between ENC and GC (r = 0.9333 p<0.001), ENC and GC3 (r = 0.9811, p<0.001) in ATPase 8. Conclusion: In our findings, we observed the codon usage bias in ATPase 6 and ATPase 8 in mammalian species is not remarkable. However in both the genes, the frequent codons favour A or C at the 3rd codon position. Our results supported that mutation pressure plays a major role in the codon usage pattern in mitochondrial ATPase 6 and ATPase 8 in addition to natural selection in some mammalian species.