Thanks for the useful comments, especially wrt to the clear definition of resequencing.

First, on the pedantic side, is that “resequencing” is not synonymous with second generation sequencing. Resequencing is sequencing a target genome for which you already have one or more reference sequences. Contrast this with “de novo sequencing”, which generates such a reference sequence when none is available.

Second, a key bit of information is copy number, and while it is suggestive that at least some exome sequencing approaches preserve this, they may not do so fully (i.e. introduce some distortion).

Third, it may soon be a moot point. Exome sequencing adds additional steps, whose cost is worth it if you save money on everything else. The cost of whole genome sequencing is coming down very rapidly, whereas the cost of various exome selection methods is not on such a trend. If the added cost of selection outweighs downstream efficiencies, then targeted sequencing won’t be competitive. For whole exome sequencing — barring some major improvements in the cost — that point of lost economy is probably less than 2 years away.