Question: Tumor clonality algorithms
5
gravatar for kezcleal
5.4 years ago by
kezcleal160
United Kingdom
kezcleal160 wrote:

I am interested in assessing the clonality of a tumor sample I have which is also paired with a normal tissue control from the same patient (~30x coverage). Specifically, I would like to know if there are any significant sub-clones present within the tumor sample.

I have come across numerous tools which look like they may be able to help me, including: cloneHD, SubcloneSeeker, ABSOLUTE, CITUP, THetA2, PhyloWGS .. others?

Does anybody have an experience using any of these tools, or any thoughts on which one I should try out?

 

sequencing snp ngs • 5.4k views
ADD COMMENTlink modified 2.2 years ago by sm.hashemin90 • written 5.4 years ago by kezcleal160

My initial hunch was to use PhyloWGS

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by kezcleal160

I suggest CLONET

ADD REPLYlink written 5.4 years ago by Nicola Casiraghi450

If it is not urgent, I would keep an eye out for this project

ADD REPLYlink written 5.4 years ago by Ying W4.0k
  1. Is there one of which does not need normal or blood control? 2. does any of them work with 0.3x coverage for CNV bases heterogeneity?
ADD REPLYlink written 2.2 years ago by sm.hashemin90
5
gravatar for Brad Chapman
5.4 years ago by
Brad Chapman9.5k
Boston, MA
Brad Chapman9.5k wrote:

We've been working on integrating clonality and heterogeneity estimation tools into bcbio (https://github.com/chapmanb/bcbio-nextgen). It's still a work in progress but we've been evaluating against internal datasets where we have external predictions of normal contamination. We've had the most success with:

We also looked at THetA2, but didn't have good luck with it, so spent more time with the above three tools.

Hope this helps provide some useful directions.

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by Brad Chapman9.5k
3
gravatar for Eric T.
5.4 years ago by
Eric T.2.6k
San Francisco, CA
Eric T.2.6k wrote:

I've had decent results with THetA2, but it's designed for exome or targeted sequencing. It sounds like you're using WGS so another choice like SciClone (code) might be better for you.

If you you're handy with a VCF you can just plot the variant allele frequencies, ideally just the somatic SNVs, and look for a cluster or just a few believable variants with frequency below 0.5 (scaled down for a less-pure tumor sample).

ADD COMMENTlink modified 5.4 years ago by Malachi Griffith18k • written 5.4 years ago by Eric T.2.6k
2
gravatar for Malachi Griffith
5.4 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith18k wrote:

We use SciClone (code) a lot.  Some thoughts.  It should be noted that tools like this infer clonal architecture by examining (clustering) the distribution of variant allele frequencies (VAFs) of somatic variants.  To do this accurately relies on several things.  First the VAF estimates must be accurate.  With only 30x coverage, you will probably have a lot of variance in your VAF estimates.  Other things also influence observed VAFs.  For example copy number events.  These can alter VAFs and confound clonality estimation if they are not properly corrected or excluded.  You need to have observed enough variants across a range from 'dominant' to sub-clonal to get a good picture.  If your variant calls are full of false positives you may get a misleading picture.  Having multiple time points can be powerful.  Good luck.

ADD COMMENTlink written 5.4 years ago by Malachi Griffith18k
1
gravatar for sxl919
5.4 years ago by
sxl91910
United States
sxl91910 wrote:

How about SciClone (code)?

ADD COMMENTlink modified 5.4 years ago by Malachi Griffith18k • written 5.4 years ago by sxl91910
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