SciClone: Which Variant to Which Clone

Question

[A Soggy Waffle]

Do you think what I want to do is possible? I have not yet run SciClone and want some input from more experienced folks.

Say I run SciClone and find three clonal populations. Is there a way I can take the output vaf and know which variants are in clone X? i.e. Could find which variants belong to which clonal populations from the results of a SciClone analysis?

Answer 1

[Chris Miller]

Yes, that is exactly the point of SciClone. :)

That said, there are always some caveats.

• Variants in CN-altered regions are more difficult to place because of VAF-shifts and will require some manual intervention.
• the possibility of "cryptic" subclones is always there. That is, multiple subclones at near-identical frequencies that can't be resolved from single-sample sequencing. We talk about this in the paper - give it a read.

[CY]

Hi Chris

Actually I have been using SciClone have having the same question regarding figuring out which variants belonging to which cluster. Is there any intermediate or functions within SciClone that can generate this for me?

Also, I have another question regarding the cluster inference within non-CN neutral region. Could you please share some comments here: SciClone: Why cluster in non-CN neutral region considering it infers only on CN neutral region. Really appreciate