Table 1.

Biological Information Is Integrated into Statistical Models

Biological Knowledge	Statistical Interpretation
transcript isoforms	sum aggregate of CDS from multiple isoforms of the same gene
variation in mutation types	consider 11 different mutation types
background mutation rates	beta prior of ${\eta }_{ij}$ which is background rate of mutation type j in individual i
differences in background mutation rates	estimate separate mutation rates ${\eta }_{ij}$ for each individual tumor
redundancy of the genetic code	define $N_{jk}$ and $M_{jk}$ as the number of base pairs in CDS of gene k that can give rise to nonsilent and silent mutations
multiple mutations in one gene	addressed by the Poisson process
sequencing coverage	$c_{ik}$ is the proportion of CDS with a minimum eight sequence coverage in both a tumor and its matched normal DNA from individual i
CDS size	${\sum }_j\left({\text{N}}_{\text{jk}}+{\text{M}}_{\text{jk}}\right)=3\text{L}$ where L is length of CDS for gene k