I have cfDNA samples which were sequenced (at about 300-1000X) on a 30-gene panel via a capture-seq protocol for the purposes of calling variants on circulating tumour DNA.

However, the resulting variant calls (from both varscan and Mutect2) are dominated by transversions from C>A and G>T at low allele frequencies, which are characteristic of DNA oxidation of guanine to 8-oxoguanine, and which I suspect are artefacts.

I have matched baseline tumour samples from the same patients, sequenced in the same way, (and there are a few C>A/G>T transversions at low AFs in these samples that I can filter out by a direct allele fraction filter).

My question is this, what is the best way of filtering out the false positive mutations derived from the 8-oxoG formation and retaining the true positives (which will be at low allelic fraction)?

Some background: I do have serial (cfDNA) time points for some patients, so I am loath to just look at mutations called in the baseline tumour samples, as any (true) novel variants appearing later in the time points would be missed.


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.