How to calculate copies of circulating tumour DNA from sequencing data?

Question

[sunilpachakar]

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?

Answer 1

[maduh17]

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!

Answer 2

[liangzebin5566]

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.

[sunilpachakar]

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.