Cancer Cell Fraction
Cancer cell fraction (CCF) is the proportion of cancer cells in a sample that carry a specific somatic mutation. It is the fundamental metric for clone abundance in subclonal-reconstruction.
Calculation
CCF is derived from the observed variant-allele-fraction by correcting for sample purity (ρ) and local copy number:
CCF = VAF × (ρ × NT + 2 × (1 − ρ)) / (m × ρ)
Where NT is the total copy number at the locus in tumor cells and m is the multiplicity — how many allelic copies carry the mutation (Tarabichi et al., 2021).
Clonal vs. Subclonal
A mutation with CCF = 1.0 (or close to it, after accounting for uncertainty) is clonal — present in 100% of cancer cells. It is likely a truncal mutation that occurred early in the tumor’s evolutionary history, before the most recent common ancestor of the sampled cells. A mutation with CCF < 1.0 is subclonal — present in only a fraction of cancer cells. It occurred later, after the divergence of the sampled population into multiple subclonal lineages.
CCF and Phylogenetics
The CCFs of different mutations constrain the possible phylogenetic-tree. A mutation present in all cells of clone A cannot have a higher CCF than a mutation present in all cells of clone A’s ancestor. In multi-sample data, the crossing-rule applies: if clone A has higher CCF than clone B in one sample but lower in another, they must be sibling clones, not ancestor and descendant.
Detection Limits
At standard sequencing depths (~100×), mutations with CCF < 0.05–0.10 are typically undetectable, meaning minor subclones below this threshold are invisible to bulk sequencing (Tarabichi et al., 2021).