I was just wondering how feasible it is to look for mutations in RNA-seq data from FFPE mutations. I know that the FFPE process may cause base changes to the RNA so I was wondering if it would be at all meaningful to look for stuff like variants in the data? If so what does the pipeline seem to look like? Unfortunately I don't think I would be able to DNA sequencing for these samples so I wanted to know if it was all possible with RNA
My sequencing depth is high as I only focused the RNA-seq on a panel of genes (targeted sequencing). So based on that I guess it might be alot more possible. I have never analysed DNA sequencing but would the pipeline be similar for RNA-seq data?
Have you been able to identify the FFPE samples in the TCGA? - how did you do that? FFPE DNA suffers fragmentation, cross-linking, and bases can 'decay' into other bases. So, it is frought with issues.
If anything, it would be a useful PLoS ONE or Scientific Reports manuscript to compare the TCGA FFPE versus fresh tissue data.
I haven't done that comparison yet but I believe there have been a few studies to compare paired FFPE and fresh frozen samples but there have been some mixed results.
https://pubmed.ncbi.nlm.nih.gov/26202458/ https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170632#pone.0170632.ref015