Question: sciClone + clonEvol on WES
0
gravatar for Kasthuri
20 months ago by
Kasthuri240
United States
Kasthuri240 wrote:

I have WES data for 3-time points - germline, diagnosis, and relapse. I can call "somatic" mutations between germline & diagnosis and diagnosis & relapse, that will enable me to do two time-point analysis using sciClone and clonEvol. However, I can call just SNPs in each of these time points and do a sciClone+clonEvol analysis, which will not be based on somatic mutations, yet it will give me cellular clones. I can then superimpose somatic mutations on these clones. Is this a right way to do analysis since I have only three time-points? Any help will be much appreciated. Thanks!

clonality analysis • 1.1k views
ADD COMMENTlink modified 20 months ago by Samuel Brady280 • written 20 months ago by Kasthuri240
1
gravatar for Samuel Brady
20 months ago by
Samuel Brady280
Samuel Brady280 wrote:

The best thing here would be to not consider the germline sample as a timepoint. You have essentially two tumor timepoints: diagnosis and relapse.

So first identify the somatic variants in the diagnosis sample (relative to germline).

Next identify the somatic variants in the relapse sample (relative to germline).

Then plot the somatic variant VAFs in the diagnosis sample on one axis, and the somatic variant VAFs in the relapse sample on the other axis. This is called a 2d comparison plot here: https://github.com/genome/sciclone

ADD COMMENTlink modified 20 months ago • written 20 months ago by Samuel Brady280

Thanks! I did that. I was trying to get some cool fishplots - thinking that increasing the time points will give me better ones. But unfortunately, not :-(

ADD REPLYlink written 20 months ago by Kasthuri240
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 745 users visited in the last hour