# VAF - variant allele frequency

Variant allele fraction or frequency (VAF): the fraction of mutated reads for a given variant, which is a readout for the proportion of DNA mutated in the sequenced tissue.

# CCF - cancer cell fraction

Cancer cell fraction (CCF): the fraction of cancer cells from the sequenced sample carrying a set of SNVs.

$$CCF = VAF *\frac{1}{p}[pCN_t + CN_n(1-p)]$$

VAF: corresponds to the variant allele frequency at the mutated base

p: the tumor purity肿瘤纯度

CNt: the tumor locus specific copy number所在位置的拷贝数

CNn: the normal locus specific copy number (CNn was assumed to be 2 for autosomal chromosomes)正常样本的拷贝数

# Clonal and subclonal mutation

https://www.sciencedirect.com/science/article/pii/S0002929719303878

For clonality, a mutation with a probability of >50% or the lower bound of the 95% confidence interval of its CCF >90% was classified as clonal and subclonal otherwise.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538405/

A clonal SNV will have a CCF of 1.0 (i.e., 100% of tumor cells). A subclonal mutation has a CCF less than 1.0 (for example, 0.4, or 40% of tumor cells).

https://www.nature.com/articles/s41467-019-09255-1

Mutations were classified as subclonal if the upper bound of CCF 95% confidence interval was less than 1.

https://www.nature.com/articles/s41591-020-0900-x

the dominant subclones (cancer cell fraction (CCF) ≥75%), minor clone (CCF < 75%)

# 参考

Principles of Reconstructing the Subclonal Architecture of Cancers

A practical guide to cancer subclonal reconstruction from DNA sequencing

Tracking the Evolution of Non-Small-Cell Lung Cancer

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#Author: Jason

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