WES data - first exon

Question

[anatopf]

A very simple question - why is it that it's difficult to get good coverage/WES data for the first exon of a gene?

Is this simply related to the GC composition, or there is something else to it?

Thanks!

[russhh]

are you sure the first exons that you have looked at are present in your targetting library?

Answer 1

[User 59]

Short answer, yes! GC content bias is the problem. Whilst it is possible to ameliorate this with some clever bait design for custom panels, most exome kits will generally have issues. I suspect not all first exons are coding exons however, which probably helps some genes..

[Katie D'Aco]

Interesting, I never knew that. Is it because of the GC box in the promoter region?

[User 59]

This paper is an interesting read on the topic.