I’m just getting into detailed research about these enrichment technologies and it seems that direct capture on arrays is having much more success than that technique from the Church lab (the molecular inversion probe study that you referenced).

In that same Nat Methods issue there are two other studies that seemed to have much greater success with what seems like a much simpler protocol.

I’ve attempted a preliminary analysis on my site:
http://seqanswers.com/forums/showthread.php?t=8

Volunteers should be aware of the ways in which knowledge of their genome and phenotype might be used against them. For example, in principle, anyone with sufficient knowledge could take a volunteer’s genome and/or open medical records and use them to (1) infer paternity or other features of the volunteer’s genealogy, (2) claim statistical evidence that could affect employment or insurance for the volunteer, (3) claim relatedness of the volunteer to infamous villains, (4) make synthetic DNA corresponding to the volunteer and plant it at a crime scene, (5) revelation of disease lacking a current cure.

If you are interested in the technical side (and have access), here is a reference for the Church group’s version of the technology:

Porreca GJ et al. Multiplex amplification of large sets of human exons. Nat Methods. 2007 Nov;4(11):931-6.

A new generation of technologies is poised to reduce DNA sequencing costs by several orders of magnitude. But our ability to fully leverage the power of these technologies is crippled by the absence of suitable ‘front-end’ methods for isolating complex subsets of a mammalian genome at a scale that matches the throughput at which these platforms will routinely operate. We show that targeting oligonucleotides released from programmable microarrays can be used to capture and amplify approximately 10,000 human exons in a single multiplex reaction. Additionally, we show integration of this protocol with ultra-high-throughput sequencing for targeted variation discovery. Although the multiplex capture reaction is highly specific, we found that nonuniform capture is a key issue that will need to be resolved by additional optimization. We anticipate that highly multiplexed methods for targeted amplification will enable the comprehensive resequencing of human exons at a fraction of the cost of whole-genome resequencing.