Genomic analyses have quantified the importance of known and novel 'rules of nonsense-mediated mRNA decay (NMD)', allowing accurate prediction of whether premature termination codon (PTC)-containing mRNAs are degraded or not. NMD can both aggravate and alleviate the effects of PTCs that cause genetic disease, and this varies across both diseases and individuals. NMD frequently inactivates tumor suppressor genes and silences the expression of neoantigens.
Either an increase in the global mutation rate or a redistribution of mutations from inactive to active DNA can increase the rate at which consequential mutations are acquired. Environmental carcinogens and intrinsic mechanisms operating in tumor cells can cause cancer by this second mechanism: by specifically increasing the mutation rate in active regions of the genome.
Comparative analyses of genomes, from bacteria across fungi to humans and human tumors have revealed many links between genes' biological roles and the accrual of synonymous mutations. The evolutionary trace of codon bias patterns across homologous genes may be examined to learn about a gene’s relevance to various phenotypes, or, more generally, its function in the cell.