Question: SciClone: Why cluster in non-CN neutral region considering it infers only on CN neutral region
0
gravatar for CY
12 weeks ago by
CY140
United States
CY140 wrote:

I have been using SciClone to check clonality changes between pre- and post- treatment tumor. It is an impressive tools and the figure generated seems reasonable and easy to interpret.

However, SciClone paper claims that it only makes clonality inference from variants' VAF within CN neutral region. Then why do I see clusters on non-CN neutral region (1 copy and 3 copies)? How are they inferred? Is it that SciClone only uses VAF within CN neutral region to establish the baseline and later infers clusters on non-CN neutral region after adjusting the VAF based on the ploidy?

sciclone clonality • 195 views
ADD COMMENTlink modified 11 weeks ago • written 12 weeks ago by CY140
1
gravatar for Chris Miller
11 weeks ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

Then why do I see clusters on non-CN neutral region (1 copy and 3 copies)?

They're plotted by default in a 1d view (in the appropriate row), but not utilized for clustering. I'd need more information on exactly what your inputs and outputs are to offer more help.

ADD COMMENTlink written 11 weeks ago by Chris Miller20k

My input is pretty standard. A variant list with VAF and a CNV list generated by VarScan. The output is 1D view and 2D view.

The 1 copy and 3 copy plot in the 1D view is exactly what I am talking ab out. So you mean the clusters on 1 / 3 copy plot are just plotting based on the variant and CNV input. No actually clustering is performed on them, right? So just need to focus on the 2 copy clustering for clonality changes.

ADD REPLYlink written 11 weeks ago by CY140
1

Yep, you've got it. Just look at the 2 copy plot for clustering. There's also an option to show just the CN2 regions in the plotting command.

ADD REPLYlink written 11 weeks ago by Chris Miller20k
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