Hi everyone!

I am a graduate student, and my lab models breast cancer in mice. The mice have an oncogene that is amplified, and a floxed p53 allele. The idea is that when the mice reach a certain age, the oncogene is over-amplified (part of a big amplicon) and the floxed p53 is lost (LOH). Then, on certain occasions (individual mouse), the wild-type allele will be lost. Thus, the mouse will be -/- for p53 and have a great advantage; the tumour cells should be predominantly p53 -/-. We have floxed sites in introns 1 and 10.

When I run JISITC, the oncogene is greatly amplified (as expected). However, p53 is not significantly deleted. Yet, protein levels clearly show it is. Hence, I was wondering, what could happen? I was thinking that maybe it's because the deleted region is not a deleted amplicon, but a deletion within a gene. Hence, JISTIC would not pick it up since it's not a deletion that covers the entire gene. Has anyone worked with floxed genes and acGH data and experienced such thing?

Thank you very much for your time and your help.