SEQanswers

Go Back   SEQanswers > Applications Forums > Sample Prep / Library Generation



Similar Threads
Thread Thread Starter Forum Replies Last Post
exome capture kit from Illumina lingfung.tang Sample Prep / Library Generation 1 01-27-2012 04:33 AM
Exome capture validation arvi8689 Genomic Resequencing 2 01-18-2012 02:45 AM
TCGA : capture vs. exome question? Richard Finney Genomic Resequencing 1 09-24-2011 10:50 PM
Illumina TruSeq exome capture Geneus Sample Prep / Library Generation 0 02-17-2011 08:50 AM
Whole Exome Capture Bruce E Illumina/Solexa 2 02-25-2010 07:29 AM

Reply
 
Thread Tools
Old 10-04-2010, 06:31 AM   #1
upenn_ngs
Member
 
Location: philadelphia

Join Date: Sep 2009
Posts: 70
Default Barcode before exome capture

We are interested in barcoding samples and pooling them before hybridization with exome capture (in order to reduce cost per person).

Has anyone met success with this approach? If so, how many individuals were pooled per capture, and what was the blocking strategy?
upenn_ngs is offline   Reply With Quote
Old 10-14-2010, 09:21 AM   #2
upenn_ngs
Member
 
Location: philadelphia

Join Date: Sep 2009
Posts: 70
Default

Just used a blocking scheme that appears to work, using short oligos to block sequence before and after the barcode (at 50uM). Three individuals in "one" agilent capture, now off to Hong Kong for sequencing at BGI, crazy world.
upenn_ngs is offline   Reply With Quote
Old 10-14-2010, 06:17 PM   #3
Fabrice ODEFREY
Member
 
Location: Melbourne

Join Date: May 2010
Posts: 21
Default

let us know how it goes we would be interested here to do the same in the future for the same reasons...thanks!
Fabrice ODEFREY is offline   Reply With Quote
Old 10-21-2010, 07:32 AM   #4
NextGenSeq
Senior Member
 
Location: USA

Join Date: Apr 2009
Posts: 482
Default

Quote:
Originally Posted by upenn_ngs View Post
Just used a blocking scheme that appears to work, using short oligos to block sequence before and after the barcode (at 50uM). Three individuals in "one" agilent capture, now off to Hong Kong for sequencing at BGI, crazy world.
Yeah, crazy that Illumina sends all their HiSeq instruments to China, thereby screwing over all their current GAIIX customers.

Thankfully that will backfire on them since the data from BGI is garbage.
NextGenSeq is offline   Reply With Quote
Old 10-21-2010, 08:09 AM   #5
HGENETIC
still a novice
 
Location: Cardiff

Join Date: Jul 2010
Posts: 34
Default

Quote:
Originally Posted by NextGenSeq View Post
Yeah, crazy that Illumina sends all their HiSeq instruments to China, thereby screwing over all their current GAIIX customers.

Thankfully that will backfire on them since the data from BGI is garbage.
Is this a known problem with BGI and in what way is the data garbage? Not sent anything there but some other collaborators have so it would be interesting to know what sort of output they are giving in case my PI fancies sending some of our data there in the future.
HGENETIC is offline   Reply With Quote
Old 11-01-2010, 03:27 PM   #6
spenserbsmith
Junior Member
 
Location: USA, CA

Join Date: Sep 2010
Posts: 7
Default

Quote:
Originally Posted by HGENETIC View Post
Is this a known problem with BGI and in what way is the data garbage? Not sent anything there but some other collaborators have so it would be interesting to know what sort of output they are giving in case my PI fancies sending some of our data there in the future.
I was in a seminar a couple weeks ago with Jun Wang, the director of BGI, and their data is not garbage. They had like 4 covers of nature and science this year and 19 other praised publications. All peer-reviewed. I don't think that's quite parallel with BGI making garbage data. I think they just have insane throughput, and in such a situation, some errors occur. I don't think that warrants it being "garbage."

But, if you have more informed experience I'd be willing/wanting to hear it, NextGenSeq.
spenserbsmith is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:21 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO