Tumor evolution tool for reconstructing a phylogenetic tree

Question

[Ikram]

Hello everyone,

I have previously worked with gene tree/species tree evolution tools but not tumor evolution so if it looks like a silly question, I beg your pardon.

I have variant calling data (using Mutect and VarScan) for whole-exome sequencing data. In the review paper, such as http://sysbio.oxfordjournals.org/content/64/1/e1, the authors say that, for instance, for PyClone, Phylosub and SciClone, the input data is single nucleotide variant (SNV). When I check, for instance, in test data in PyClone, it has a nicely formatted input file which is used to generate the output.

I am wondering if someone has worked with any pipeline for phylogenetic tree reconstruction using "any" of tumor evolution software? I would be grateful if you can share your experience (and, if possible, the steps).

Thanks in advance

[Sean Davis]

You are asking for an approach to running multiple software packages, or something different?

[Ikram]

I am interested in sub-clonal evolution in primary tumor and secondary (metastasis) sites using one or more phylogenetic tools.

Answer 1

[Chris Miller]

Once you've clustered your data to identify subclonal populations (with the algorithms you list above), there are a few different tools that will attempt to construct evolutionary trees. The ones I'm aware of are below:

ClonEvol: https://github.com/hdng/clonevol

SubcloneSeeker: http://www.genomebiology.com/2014/15/8/443

Schism: http://karchinlab.org/apps/appSchism.html