I have been working with an exome data for quite a while now where I have tumors of 2 different histopathological conditions. One is a high grade tumor and other is low grade tumor and derived iPSCs from them. Now We have sequenced the tumor/, its corresponding normal and the iPSCs at exome level and tried to look for the mutational landscapes. In fact the CNV calls on the exome data gave use much better picture in understanding to what extent the similar CNV regions in tumor pass on to the iPSCs. Note that I did the CNV calls with Control-FREEC using normal samples as well. So they are somatic CNVs. Recently I figured out that when I try to match the exact CNV regions of a high grade iPSCs to that of low grade iPSCs , I see a lot of similar regions. Infact 40% regions called as CNV (exact regions 100% identity) are shared between high grade iPSCs and low grade iPSCs. Is not that a bit strange? I am providing the images for the different overlap. I calculate the overlap using bedtools intersect with -u -f parameter with -f = 1.0. I would like to know is this usual or is it something unusual. In fact the these are 2 different tumors from 2 different persons.
S_313_tumor is high grade
S_333_tumor is low grade
Can you see them now?
could you have contaminated the ipsc clones during cell culture?
I dont think so that the iPSCs are that contaminated. Their efficiencies were checked and also the teratoma assays were done. Yes they might have been a bit less tumorous for the low grade since the low grade tumor is having stromal contamination. In that case clone which is selected and reprogrammed might have less tumorigenic features. But again this was elucidated when I called the somatic CNVs from the low grade tumor , if you can see the first image, I believe the lest number of CNV is low grade tumor is due to the fact of contamination. But iPSCs contamination , I dont think so. Anyone else have seen such events?
I can't see either of your images, and your description is rather opaque; I'm not even sure if the two tumours are from two separate patients..
I have tried to edit the post. Can you let me know if you can see them now or not? Yes the two tumors are different and from each tumor I have 2 iPSCs created . I have already mentioned which sample corresponds to which tumor. Anyway why do you think it is opaque? If you need more clarification am there to clarify. Please let me know