In the near future, I will have to deal with circulating cell-free DNA in the context of finding cancer biomarkers - I have read up on methylation, biomarkers, cancer, though I must admit I haven't read too much about cfDNA yet.
In this context, it seems strange that I can't find (450k) methylation data of circulating cell-free DNA.
- Where would I find this kind of data - or why doesn't it exist/isn't it being used?
Can't find is a big thing to say - I have tried several keywords, TCGA does not provide it AFAIK, I have tried on GEO and just by googling. I think GEO returns methylcap/seq data and 27k data for
I would think that if an epigenetic marker is to be used against the background of cfDNA, it would be useful to have a 'universal reference' to test against, instead of finding markers by testing against normal tissue first, and then testing the potential of any/all markers without knowing their status in cfDNA. You don't need to do this when you're trying to find genetic alterations - these 'should' be present in circulating tumor DNA.
Since I'm new to cfDNA I don't know if a universal reference is a good idea, if it's possible, or what the caveats would be.