Estimating a gene's mutation burden by the number of observed synonymous base substitutions

A common goal of tumor sequencing projects is the identification of genes whose mutations are selected for during tumor development. This is accomplished by finding genes that have more nonsynonymous mutations than expected by an estimated background mutation frequency. While this frequency is unknown, it can be estimated using both the observed synonymous mutation frequency, and the nonsynonymous to synonymous mutation ratio. The synonymous mutation frequency can be determined across all genes, or in a gene-specific manner. This choice introduces an interesting tradeoff. A gene-specific frequency is difficult to estimate given small or missing synonymous mutation counts, but adjusts for an underlying mutation load bias. Using a genome-wide synonymous frequency is more robust, but is less suited for adjusting for the same bias. Studying three evaluation criteria for identifying genes with high nonsynonymous mutation burden (preferential selection of expressed genes, genes with mutations in conserved bases, and genes that show loss of heterozygosity), we find that the gene-specific synonymous frequency is superior in the gene expression and conservation tests, while both frequencies perform similarly for the loss of heterozygosity test. In conclusion, we believe that the use of the gene-specific synonymous mutation frequency is well suited for estimating a gene's nonsynonymous mutation burden.