FACETS cellular fraction

[ghost]

Hi,

I am wondering how exactly interpret the cellular fraction returned by FACETS. Let's say for example we have cf.em = {1,0.6,0.3,0.2}

• 1 correspond to events with no changes between tumor and normal since we are not interested in these we can exclude them.
• 0.6 is the cellular fraction for all the clonal events and the tumour purity
• 0.4 and 0.3 are the cellular fraction for the two sub clones identified.

Shall we look at the cell fraction for the sub clones straight or do we have to adjust for tumor purity i.e. sub clonal cell frac = 0.4*0.6=0.24 and 0.3*0.6=0.18 ?

Many thanks for your help

[veseshan]

The cellular fraction (cf) is fraction of tumor cells with that event i.e it is already corrected for tumor purity.

Venkat

[ghost]

Thank for your answer! So If I want to compare the cellular fraction of each sub clones between 2 samples from the same donor (2 different runs of facets), I can compare the cf directly, right ? Sorry I am new in the field

[veseshan]

That would be reasonable.