best way to re-sequence a few Mb of genomic sequences

[NanYu]

Hi,
If I want to re-sequence a known part of the chromosome (we know the reference genome sequence) of ~1Mb to find the possible mutations (SNP or INDEL) that caused a certain phenotype. What is the best platform to do it?

I don't like the idea of just extract the whole genome and re-sequence everything. But is there a sample preparation technology that allows me to amplify/sequencing only part of the chromosome?

Thanks!
Nan

[Heisman]

Look into earray with agilent - custom capture. Won't be very cost-efficient for only one sample but if you have a decent amount it's one thing to look into for sure.

[SNPsaurus]

For sequencing a few samples, custom pulldowns are often more expensive than doing whole genome shotguns. If you have lots of samples, then it makes sense.

For a few samples, the most inexpensive platform I've seen is mybaits mycroarray. My academic lab did a really cheap approach of biotinylating BAC or fosmid DNA covering a region. Also a not-high on-target rate, but any purification will give you good coverage for 10 million reads. See http://scholar.google.com/citations?...J:b0M2c_1WBrUC for that.

[Ganesh Ujwal]

You could fragment the genome and clone it then probe your clones to find the fragment(s) that contain the sequence of interest.