Table 1.

Definitions of mutation categories and the ratio of mutation categories.

$\text{Compound}\text{mutations}=\mathrm{missense}+\mathrm{complex}+\mathrm{inframe}+\mathrm{nonstop}-\mathrm{LoFI}$

$\text{Loss}\text{of}\text{Function}\left(\mathrm{LOF}\right)=\mathrm{nonsense}+\mathrm{frameshift}$

$\mathrm{Damaging}=\mathrm{HiFI}+\mathrm{MiFI}$

$\mathrm{Benign}=\mathrm{silent}+\mathrm{LoFI}$

$ratio{(A/B)}_g=\left\{\begin{array}{cc}\frac{A_g}{B_g}\hfill & if{B}_g\ne 0\hfill \\ 2\ast \max (A)\hfill & if{B}_g=0\hfill \end{array}\right)$

Along with mutation categories annotated by COSMIC, we define additional categories which combine multiple mutation types. These categories together with the 11 mutation categories defined in “Ratio-metric features” section are used to define ratio-metric features. The ratio of two mutation types A and B is defined for a given gene, where A and B are any two mutation categories.