Question: depth of coverage for WES of germline DNA
0
gravatar for Chiara.Caprioli
7 days ago by
Chiara.Caprioli0 wrote:

Hi,

I'm performing WES on tumor/germline DNA couples to score driver cancer mutations, using ~200x coverage for tumor samples. My doubt and question for you is about the minimum reliable coverage we can use for sequencing the germline DNA. In theory, lowering the coverage for the germline would minimize the possibility of misclassifying somatic variants, at the same time optimizing the cost of seq. Have you any references to share?

Thanks a lot

sequencing genome • 70 views
ADD COMMENTlink modified 7 days ago by Kevin Blighe65k • written 7 days ago by Chiara.Caprioli0
1
gravatar for Kevin Blighe
7 days ago by
Kevin Blighe65k
Kevin Blighe65k wrote:

For germline variants where the frequency is expected to be 0%, 50%, or 100%, you just need 18 minimal, but 30 is ideal. We derived these numbers from our benchmarking in a clinical setting in the UK: A: DP in VCF files?

To detect somatic mutations, higher read depth over each position over which variants are being called is obviously ideal. Even at 200, you will miss mutations in rare clones that exist in a tumour bulk biopsy sample.

Kevin

ADD COMMENTlink modified 7 days ago • written 7 days ago by Kevin Blighe65k

Thanks! the "shallow" coverage of the tumor sample is fine for me, in the context of my project.

For general interest, I share this http://dx.doi.org/10.1016/j.jmoldx.2017.01.011

ADD REPLYlink written 6 days ago by Chiara.Caprioli0

Great, so, their figure 2 is more or less in line with what I said.

ADD REPLYlink written 6 days ago by Kevin Blighe65k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1174 users visited in the last hour