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Old 08-20-2013, 09:42 AM   #1
NanYu
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Default best way to re-sequence a few Mb of genomic sequences

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
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Old 08-20-2013, 09:57 AM   #2
Heisman
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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.
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Old 08-20-2013, 07:18 PM   #3
SNPsaurus
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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.
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Old 12-07-2014, 05:05 PM   #4
Ganesh Ujwal
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You could fragment the genome and clone it then probe your clones to find the fragment(s) that contain the sequence of interest.
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