Clonal evolution prediction tool

Question

[saurabhyadav15]

Hello Everyone,

I have obtained the Simple somatic mutation data from exome sequencing study (ICGC) for my cancer of interest for more than 200 patients. I can get variant allele frequency however I don't have copy number data. I am interested in predicting sub clonal structure of the tumor (intra-tumor heterogeneity). Please suggest me tools. I am confused between so many option such PyClone, SciClone, PhyloWGS etc

Thanks in advance. Saurabh

Answer 1

[Chris Miller]

a) You can call copy number from exomes using one of many widely available tools (cn.mops, varscan, many others)

b) any of the algorithms you list for clonal structure inference would be a fine choice. Read up on them and understand what inputs you'll need first.

Answer 2

[saurabhyadav15]

Thanks a lot, Chris, a) I can't use these tools use mentioned since I don't have the access to raw sequencing data. b) I will use these tools.

Since I don't have somatic mutation copy number information for all the mutations. I am thinking of excluding all the mutation that fall in the significantly copy number altered regions and assume all others as CN un-affected mutations. CN altered regions are quite a few for my cancer of interest so I won't be excluding lot of mutations. What do you think?

Also please let me know minimum read-depth threshold for SSM data. I have on an average 200 SSMs from exome seq. 50% are filtered out at 100X.