Question: SciClone: Which Variant to Which Clone
gravatar for stphnwist
3 months ago by
stphnwist0 wrote:

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?

genotype sciclone • 219 views
ADD COMMENTlink modified 3 months ago by Chris Miller19k • written 3 months ago by stphnwist0
gravatar for Chris Miller
3 months ago by
Chris Miller19k
Washington University in St. Louis, MO
Chris Miller19k wrote:

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.
ADD COMMENTlink written 3 months ago by Chris Miller19k
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