SEQanswers

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



Similar Threads
Thread Thread Starter Forum Replies Last Post
NimbleGen SeqCap EZ Choice Library-preparation for the PGM ChrE Ion Torrent 6 05-29-2013 06:03 PM
NimbleGen SeqCap EZ exome V1 hangch The Pipeline 0 05-19-2013 09:49 PM
Exome Sequencing with nimblegen SeqCap EZ v3 airtime Sample Prep / Library Generation 5 10-26-2012 03:39 AM
Exome Sequencing with NimbleGen SeqCap EZ v2 Ulli Genomic Resequencing 4 04-25-2011 05:21 PM

Reply
 
Thread Tools
Old 05-23-2013, 12:55 PM   #1
mschnall
Junior Member
 
Location: Palo Alto

Join Date: May 2013
Posts: 2
Default Nimblegen MHC SeqCap EZ

Is anyone doing HLA sequencing with the Nimblgene SeqCap EZ Human MHC design? Or are you doing HLA with your own custom pull-down kit? If so, I would really like to talk to you. I'm at a startup building a sequencing sample prep/analysis technology that will (among other things) significantly increase the performance of HLA sequencing, and we are looking for potential collaborators in this area.
mschnall is offline   Reply With Quote
Old 05-24-2013, 01:27 PM   #2
DoubleA
Member
 
Location: Los Angeles

Join Date: Jul 2010
Posts: 16
Default

Hello mschnall,

Our lab has sequenced ~500 samples using NimbleGen's MHC design. For the most part, the sequencing worked quite well. Because of the high heterogeneity of several of the genes in this region (DQA1, DQB1, HLA-A, ect.), you will will have problems aligning reads to a single consensus sequence (hg19). Our bioinformatics core is currently helping us to resolve this problem.

DoubleA
DoubleA is offline   Reply With Quote
Old 05-27-2013, 12:59 PM   #3
mschnall
Junior Member
 
Location: Palo Alto

Join Date: May 2013
Posts: 2
Default

thanks a lot for the reply, doubleA. we are building a new technology that should help significantly with some of the alignment ambiguities as well as providing phasing information. if you think you might be interested in trying out our technology in the coming months, send me a private message and i can give you more details.
mschnall is offline   Reply With Quote
Reply

Tags
capture, hla, mhc, ngs, targeted

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 11:26 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO