Identification of cancer cell fraction

For each mutation we calculated the mutation copy number as previously described, using the mutant allele burden, tumor cellularity and locus specific copy number in the tumor and matched normal⁴⁹. The mutation copy number reflects the percentage of tumor cells within a sample carrying that mutation, and permits the cross-comparison of the mutation in related samples despite differences in tumor purity and/ or copy number profiles. Mutations present on multiple copies of a chromosomal segment will have a mutation copy number greater than 1. To group mutations according to the percentage of cells containing it, or cancer cell fraction (CCF), the number of chromosomes carrying the mutation must be determined. For all mutations within amplified regions with a major allele copy number, the observed fraction of mutated reads was compared to the expected fraction of mutated reads resulting from a mutation present assuming a binomial distribution³⁷.