Study Design

[gavin.oliver]

Hi,

Is anyone aware of a decent reference that might provide some information on good study design for a NGS project (exome sequencing).

Obviously a clear idea of what questions you want to address is required from the outset to ensure the correct protocols and level of coverage etc.

Just wondering if such a reference exists or if I'm being too optimistic Alternatively it would be great if someone with experience could suggest the major questions I should be asking about the study design at the outset.

Best,

Gavin

[niceday]

what exactly are you looking for?
If you can be a bit more specific.

[gavin.oliver]

Maybe I asked the question a little too early - I'm still trying to get some more details from the person organising the study.

All I know at the moment is that they are interested in exome sequencing and variant detection related to cancer.

I guess with exome sequencing/variant calling the major questions will be what to use for exome capture, what sequencing platform is best for the application, what level of coverage is required (x30 seems standard?) and what software is best to use for the analysis. Also what service provider to use...