Celleular prevalence or cancer cell fraction?

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Steffen Larsen

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Jun 5, 2023, 5:19:36 AM6/5/23

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Hi all.

I just reread the documentation on the GitHub page for Pyclone VI. Under the output format, it states that cellular prevalence is equal to cancer cell fraction. I wonder if this is widely accepted in the oncology community - I am relatively new to this.

When I started, a colleague recommended a method paper from Boutros et al. in which cellular prevalence is treated as the fraction of both cancer cells and admixed normal cells in a sample that carries an SNV - or a set of SNVs. CCF can thus be calculated from this by dividing with the purity.

I have been following this and has therefore routinely divided the cellular prevalence calculated by PyClone with the purity in order to get CCF, but given that the PyClone developers state that it is already equal to CCF, I guess this is wrong? I am also having troubles with downstream clonal evolution inference and I wonder if this could have something to do with it. I’ll be grateful for any insight on this.

Thanks,

Steffen

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