Targeted resequencing/enrichment for low complexity regions

[tracecakes]

Hi all,

I am looking into methods that would be able to resequence ~0.5 - 1 Mb region which contains repetitive/GC rich regions. I would like to do this to see if there is a large structural variation going on in here (large inversion). I only have a few samples that I would like to do this on (at most 4) so it does not have to be scaled, but still cost effective and not requiring massive amounts of DNA.

Does any one have any recommendation/experience on how to go about this ? In particular, can anyone comment on mate pair sequencing vs 454 pyrosequencing, as well as hybrid capture and long range for enrichment ?

Any ideas greatly appreciated , thanks !

[SNPsaurus]

It is challenging to do this--most pulldown methods expect to reduce the per sample cost by having many samples. My lab did a BAC pulldown approach (http://www.genetics.org/content/189/3/767.short) when mapping mutants with the Bowerman group, but we happened to have BAC resources around. In general, for small-scale projects I'd say MYcroarray MYbaits is a good choice (http://www.mycroarray.com/mybaits/mybaits-custom.html). For $2,400 you can tile across the 1 Mb region and pulldown 12 samples. Pretty pricey for 4 samples, I guess, but cheaper than WGS.

Mate pair libraries can be difficult to make with large inserts, but you'd be fine with 3 kb and get better efficiency sequencing from it, or even a 500 bp paired-end run. These days, I'd look into a PacBio run for structural changes. I don't know if you can capture 10 kb fragments with MYbaits, though. Sorry these ramblings are so vague!