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Old 08-20-2013, 09:42 AM   #1
Location: USA

Join Date: Apr 2011
Posts: 21
Default best way to re-sequence a few Mb of genomic sequences

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?

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Old 08-20-2013, 09:57 AM   #2
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Location: St. Louis

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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
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Location: Eugene, OR

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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 for that.
Providing nextRAD genotyping and PacBio sequencing services.
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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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partial chromsome, re-sequencing

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