5500 EZ Exome Hybridisation Enhancers

[JPC]

When using the 5500 adapters and the Roche EZ Exome capture kit should I block the whole sequence of the P1 (41bp) and Standard (53bp) adapters during hybridisation? or can I just block the 3' end of each adapter...or just the Library PCR section?

I know Baylor used truncated adapters with their SOLiD 4 protocol and I could use this at the P1 end but they don't use the P2/barcode/IA.

[jimmyinfrance]

Ran into the same problem, we are testing blocking the whole thing, but haven't got results yet (capture done, seq next week). This post is a few weeks old, do you have an update?
ABI's TargetSeq uses no 3' end modification in their blockers, which also differs to the Baylor protocol

[JPC]

No update sorry, we are awaiting a firmware upgrade before running the machine. I have ordered oligos to block the whole sequence, but this will become expensive when multiplexing. We can then try using N's across the barcode section or possibly to batches of barcodes where R, Y, K, M etc can be utilised (as recommended by a contact in Liverpool CGR).