Is there public (DNA methylation) data on circulating cell-free DNA - why not?
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4.1 years ago
Mathias ▴ 90

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.

epigenetics circulating cell-free DNA biomarker • 1.6k views
Entering edit mode
4.1 years ago

I did my PhD on cfDNA back in 2010-2012 where I was looking at copy number alterations and SNPs (in a breast cancer setting). I'm now back in cancer after avoiding it through most of my postdoctoral years, but mainly now focusing on immunotherapy. Epigenetic studies of cfDNA are showing promise in terms of having the ability to infer the tissue of origin of the cfDNA through te analysis of, for example, nucleosome spacing, or indeed methylation patterns. Obviously, by doing this and in addition scanning for mutations in known oncogenes, one could potentially identify where a tumour is beginning to form in the body without the need to perform expensive screens like MRI, or other invasive procedures.

There are indeed not many studies out there for methylation of cfDNA. For next generation sequencing studies on methylation, I found these:

Then there are 3 methylation microarray studies that I found:

Best of luck,



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