Question: sciClone + clonEvol on WES
0
gravatar for Kasthuri
2.4 years ago by
Kasthuri260
United States
Kasthuri260 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 • 1.5k views
ADD COMMENTlink modified 2.4 years ago by Samuel Brady300 • written 2.4 years ago by Kasthuri260
1
gravatar for Samuel Brady
2.4 years ago by
Samuel Brady300
Samuel Brady300 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 2.4 years ago • written 2.4 years ago by Samuel Brady300

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 2.4 years ago by Kasthuri260
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