Sequencing Depth And Mutation Frequency

Question

[Luca Beltrame]

Hello,

the group I work in will soon start a focused sequencing approach over a certain number of genes in tumor samples using the Ion Torrent platform. One of the questions that came up when designing the experiment is the depth of coverage needed for specific mutation frequencies, as the budget only allows a limited number of Ion Torrent sequencing chips to be bought.

Basically, I would like to ask if there is literature, or experience, on the minimum depth required to detect mutations with a frequency less than 20%, 10%, or smaller, as like this we could fine-tune the experiment with the appropriate depth (and number of chips).

Thanks in advance.

Answer 1

[JC]

Maybe this paper could help you: http://bioinformatics.oxfordjournals.org/content/26/12/i318.full