Can RNA-seq data from a surgical tumor specimen, without matched normal DNA/RNA from the same individual, allow for analysis of relative frequency of non-synonymous mutational load (ML) in the sample? The goal would then be to compare relative frequency of a sample's ML to expression level of a specific, unrelated gene.
Confounding factors identified to date:
Somatic mutational load will be over estimated in each sample because some germline mutations will be included due to reference being publicly available genome vs the individual's genome.
Mutational load will be under estimated because mutations that do not produce highly expressed transcripts will not be identified.
At the suggestion of @sam, I am converting this question to a Forum, since I was erroneously answering my own post, so others may have not been aware of the discussion that is ongoing. I apologize for this error, I am new to the forum.
For previous discussion, and proposed experimental design, please see my original post
Any thoughts would be very helpful!