Genome sequencing and depth of coverage

Question

[kdx80v45]

Hello,

I wanted to ask some questions about genome sequencing and this forum seems to have a lot of knowledgable people.

I noticed there are several different levels of coverage available such as 15x,30x etc

What effect do those numbers have on the sensitivity of the test?

Would 30x be much more powerful in terms of detecting variants or genes associated with health conditions?

What about chromosome deletions, translocations, and mosaicism?

Would those be detected better by 30x over 15x.

Thanks

Answer 1

[trausch]

Higher coverage is indeed more powerful in terms of detecting variants, see PMID: 18987734 - Figure 5.

In cancer genomics, you in addition need to take into account tumor purity, ploidy and heterogeneity (sub-clonality), e.g., for a tumor purity of only 50% you loose half your coverage for the "contaminating" normal sample.