I am a bioinformatician, not a biologist hence my question may appear very naive. Here is my case:
I was given exome data of several transgenic mice. Some have been additionally treated to develop certain types of tumors, a single transgenic mice has been kept as control. I have been asked to look for tumor genome variation.
Most studies on tumor genome variation I know of use paired samples (a sample from the tumor and a control from a healthy tissue of the same animal or individual). This is still not trivial as the tumor is often a mix of different subclonal populations but, at least, there are plenty of bioinformatics tools that try to elucidate the tumor mutations vs the healthy tissue and all the differences which are found are atributed to the tumor.
What I don't know is whether I can treat the different transgenic mice from the same strain as having the same genome, i.e. attribute any differences between genome of the tumor of animal A and the genome of healthy animal B to the tumor alone, rather than to genome variation between A and B?