I'm working in a cancer center where we use PDTX (Patient-Derived Tumor Xenograft) so the principle is to graft human tumors in mice. We recently reached a dead-end as we wanted to performed some RNA-seq (75bp; paired-ends) on these tumors. The problem is that there always is a cellular contamination of the tumor sampling with surrounding mouse tissues.
Some papers described the (obvious?) possibility to remove sequenced mouse reads based on the SNP that differ between these species. However, none of these papers clearly demonstrate whether the transcriptome profiling is correlated with a mouse-free sample doing this method. Due to sequence similarity I really doubt the resulting transcriptome data will provide a good estimation of tumor RNAs. AFAIK, the mouse genome (and consequently the transcriptome) is relatively similar to the human one with highly conserved sequences across these species (particularly for coding regions). I suspect such regions to not have different SNPs and not be able to correctly assess if a read is a mouse one or a human one.
Is anyone familiar with this situation? Is there a method to reliably get the tumor gene expression while removing the contamination from mouse RNAs? Should we just sort human cells by flow cytometry and establish a cell line to make sure no mouse cells survived?