Targeted sequence capture - Nimblegen + GS Junior

[sutree]

Hello all, first time here...

I am attempting to put together a proposal that involves sub-genomic sequencing experiments and need some help. Here is how I envision it working:

I would like to take 40-50 primary tumors and extract genomic DNA, create a custom array chip that will capture my regions of interest (three well-characterized genes that are 50-100kb in length).

Sequence these regions across all tumors and look at the genetic variation present therein.

I am hoping to use a GS Junior to do the sequencing (that works right?) and they recommend NimbleGen capture arrays.

Does this sound feasible??

Much obliged!

[Zaag]

It does, I would look into LR-PCR instead of sequence capture first, could be cheaper for those few genes (depending on if you want to sequence the whole gene or only the exons, if only the exons arrays are probably cheaper).