Target enrichment technologies for ABI SOLiD

Q:my group is involved in a national project to develop a genomic platform for cancer research. while Nimblegen has developed target enrichment chip for the Genome Sequencer 20, nothing similar has been done for the SOLiD system, as far as I know. Does anybody know something more about this topic?

A:You can concatamerise the Nimblegen Seqcap 500-mers and shear them with a Covaris instrument down to <= 100 bp then ligate on P1 and P2. You can bioinformatically remove the partially sequenced Nimblegen adaptors later in silico. Pretty damn messy solution but size reduction is required to get high density sequencing from Solexa and SOLiD after Nimblegen seqcap (see Hodges et al., 2007 in Nat Meth). BTW, the Covaris costs $$$. Also, 454/Roche will have the "Titanium" upgrade available soon for 454 FLX with over 5x more bases sequenced for less money.

We were investigating post-capture size reduction methods to use Solexa/SOLiD but decided to ditch that idea after we heard about Titanium. We have access to a 454 FLX machine - so that also swayed our judgement.

A:The Agilent method looks interesting to us as well. Also, the Covaris usually comes with the SOLiD so no extra cost there and the amount of data is still 1-2 orders of magnitude more for SOliD than even Titanium per run - albeit some increase is needed to get same coverage.