Hi

For each variant, the `variant allele frequency (VAF)`

depends on the local copy number of the tumor `(CPNmut)`

, the `purity (p)`

, the local copy number of the normal sample `(CPNnorm)`

and also the `cancer cell fraction (CCF)`

, defined as the proportion of cancer cells harboring the mutations. The expected `VAF`

, given the `CCF`

, can be calculated as follows:

```
VAF (CCF) = p*CCF / CPNnorm (1-p) + p*CPNmut
```

Then saying

For a given mutation with `āaā alternative reads`

, and a `depth of āNā`

, the probability of a given `CCF`

can be estimated using a binomial distribution `P(CCF) = binom(a|N, VAF(CCF))`

. CCF values can then be calculated over a uniform grid of 100 CCF values (0.01,1) and subsequently normalized to obtain a posterior distribution

I got confused here: in the below formula assuming they have CCF, they then calculate VAF based on the CCF

```
VAF (CCF) = p*CCF / CPNnorm (1-p) + p*CPNmut
```

Then why again they are going to calculate CCF by saying

*CCF values can then be calculated over a uniform grid of 100 CCF values (0.01,1) and subsequently normalized to obtain a posterior distribution*

I totally lost the context

Can you help me?

They are calculating

`VAF(CCF)`

, which I am guessing is a prior probability of the expected VAF for a given CCF.They then obtain a posterior distribution based on the prior assumption, so the CCF they're calculating is based on the actual observed VAF and not on a theoretical "this should be the VAF for a given CCF" assumption. This needs the first step (prior probability determination) though. Ideally, they should use different notations for CCF

_{expected}/CCF_{actual}and VAF_{expected}/VAF_{actual}I cannot be completely confident about this answer. If you could point me to the source, I can read up and clarify better.

Thank you so much, here

https://stm.sciencemag.org/highwire/filestream/196992/field_highwire_adjunct_files/0/7-283ra54_SM.pdf

In second page,

`Estimating the cancer cell fraction and mutation copy number`

sectionIn my own data I have

`VAF (alternative allele read counts /total depth)`

for each variantI also have tumour copy number

My concerns are:

1- If the

`actual VAF`

is my own`VAF(alternative allele read counts /total depth)`

?2- What is

`actual CCF`

?For this if I am not wrong, I have used

`CCF function`

in`cDriver R package`

to calculate CCF (actual ?) using my own VAF (actual VAF?)3- Which CCF I should use for getting expected VAF?

4- They want expected CCF for getting 95% confidence interval to call a mutation clonal or sub-clonal, so are these all steps required for getting confidence interval? Can not I simply use naive quantile bootstrap 95% confidence intervals (with 10,000 re-sampled averages) on my actual CCF or VAF to call a mutation clonal or sub-clonal?

I have read this document many times but I am just getting more confused

I need some time to read this article. I'll get back to you once I understand what's going on.

I sincerely apologize - I have not been able to pay this sufficient attention. Were you able to figure anything out?

Thank you for your time and attention; Actually I am just realising this issue is not that easy and demands much efforts from mysids than a simple communication. I started to know about clonality topic in last recent few weeks and I am just trying to find a software compatible with what input information I can provide

I am not sure, but I'd use purity as cancer cell fraction. "Tumor purity is defined as the proportion of cancer cells in the tumor tissue." Absolute does that - I'd try to make it working.