I have some query regarding mutation call with VarScan2. I have whole exome data for samples of normal blood with its corresponding tumor pair and 2 clones isolated from the tumor which are reprogrammed to derive induced pluripotent stem cells(IPSC).
Now the idea is if using VarScan2 I call the SNPs from normal/tumor pair and normal/IPSC pair , I can retrieve the germline and somatic variants for both the calls and can check the somatic variants or the germline variants that are shared between the normal/tumor pair and normal/iPSC pair. Pretty straight forward approach, this approach should also enable me to find variants that are acquired during reprogramming process as well. However I do not have sequencing done for the IPSC at different time points so whatever variants I have in the IPSC if it does not match with the somatic variants for normal/tumor pair I would presume they are acquired during reprogramming and are also masking most of the mutations that were in tumor. Fair enough. I want to ask the viability of another approach. I would like to know if the approach sound feasible or not.
Instead of calling the germline and somatic variants in Normal/IPSC pair if I call as Tumor /IPSC pair, then the somatic variations in this case is specific mutations that have happened during the reprogramming from tumor to its clone. Then the germline for this pair should have : Germline Tumor/IPSC pair= Sum of Germline Normal/Tumor variants+ Somatic Normal/Tumor+ Somatic Normal/IPSCs.
Now if I remove the Germline Normal/Tumor of Call 2 with the Germline Normal/Tumor of the Call 1 then am left with mutations of somatic Normal/Tumor + somatic Normal/IPSCs. I want to know use this to understand the extent of mutation that were carried from tumor to IPSCs , thus giving an idea of the background that the genomic aberrations are maintained from tumor to its IPSCs even after reprogramming. Can this be done from the somatic variants in Call2 highlighted in Bold? Is this a viable approach? I tried to overlap these with the variants found in call1 for the somatic normal/tumor pair and somatic normal/IPSC pair with the results of Call 2 but the overlap is too small. Does not give any idea if the tumor mutational background conservation in IPSC even after reprogramming. I would like to get some inputs on this . Please let me know your comments for the above mentioned approach and also suggests if there is any such approach close to this that can help me in resolving the mutational background sharing between a tumor and its IPSCs.
Thanks a lot.