Agilent SureSelect enrichment

[javier]

hello All,

we're trying Agilent All Exon capture kit, and are unsure of the enrichment efficiency degree (as measured by qPCR).
the system seems to be working (loss of intergenic/intronic regions, gains in exonic regions... tested on a few loci).
Agilent says one could expect to see 8 cycle Ct differences (post vs pre-hyb libraries) but we don't get that much.
(reluctant to risk a 2x76bp PE run just to find out we are mostly sequencing intergenic regions).
anyone out there having lower Ct differences? any worry? what sorts of results?
any suggestion to maximise enrichment? (you may have tested increase/decrease input DNA, hyb time...)?

best wishes, Javier

[MYselect]

We did some work where we used microarrays to test samples post-enrichment without spending the money on sequencing. Since the results looked great we went for sequencing after. We presented these results on a poster at the San Diego Xgen conference, March 2010. You can get a pdf of the poster at this location:

http://www.mycroarray.com/products/myselect.html