!!Urgent help: identifying CNV of an interesting region by targeted sequencing

[mrfox]

Hi all,
My collaborator is interested in a region (about 8M bp long), that has been reported to susceptible to amplification/deletions.

Our goal is to perform sequencing experiments to specifically study the copy number variation of this region.

Whole-exome sequencing of course can help but most of the information will be wasted since our collaborator is not interested in other regions.

I wonder if we could capture the 8M region plus 3M up-stream and 3M down-stream region and then perform deep sequencing on the total 14M-bp region. Ideally, the up- and down-stream regions have no copy number change while it will be easy to quantify the copy numbers of the middle region.

I am not sure if the above strategy is feasible. Please help if you have a better idea of detecting copy number variation for a targeted region or if you have any advice for sequencing the above described region.

THanks a lot!

[SNPsaurus]

Probably a MYbaits custom pulldown would be a good way to access the region.

http://www.mycroarray.com/mybaits/MYbaits+sequence+capture+target+enrichment+kit.html

[Brian Bushnell]

If you want to detect potential large indels in that area, I suggest mapping with BBMap, using the flag "maxindel=200000" (or however long you wish, though bear in mind that higher numbers reduce accuracy).