depth of coverage for WES of germline DNA

Question

[Chiara.Caprioli]

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

Answer 1

[Kevin Blighe]

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

[Chiara.Caprioli]

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

[Kevin Blighe]

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