NGS data provides information on variant allele frequency which is to be used for calculating copies of total cf-DNA, variant copies of cf-DNA per ml. I have used the method described in Annals of Oncology 27: 862–867, 2016 Detection of ubiquitous and heterogeneous mutations in cell-free DNA from patients with early-stage non-small-cell lung cancer authors in this paper, based on the assumption that there are 3.3 pg DNA per haploid copy of the genome, have calculated the total cf-DNA, variant copies of cf-DNA per ml. Is there any other method available for calculating copies of ct-DNA?
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sunilpachakar •
I recently looked around for methods to determine copy number aberration (CNA) using shallow whole genome sequencing (sWGS) and came across this paper:
https://www.ncbi.nlm.nih.gov/pubmed/28710315
But that's all I know.
I've running sWGS to detect CNAs at ~0.05X from tumor samples (not from blood).
Good luck!
I'm using UMI(Unique Molecular Identifier), which is a random sequence binding to your library before PCR.
Since the UMI bind to your library before PCR, you can count UMI copies as your ct-DNA copies and variant copies.
BUT library conversion ratio plays an important role, original ct-DNA never perfectly convert to library, take care.
I appreciate your response, but my query is not related to sequencing things. It moreover deals with identifying/calculating mutant copies present in the sample.
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