SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Ion Torrent



Similar Threads
Thread Thread Starter Forum Replies Last Post
Barcoding vs anonymous pooling snapper Illumina/Solexa 15 01-16-2011 01:22 AM
Targeted sequencing ulz_peter 454 Pyrosequencing 1 05-04-2010 05:15 AM
Targeted Sequencing - How are you doing sample prep for your targeted sequencing prj? mike lee Sample Prep / Library Generation 0 01-26-2010 07:00 PM
Evaluation of next generation sequencing platforms for population targeted sequencing div1982 Literature Watch 0 04-23-2009 06:39 AM

Reply
 
Thread Tools
Old 02-05-2013, 12:36 PM   #1
ecrandall
Junior Member
 
Location: Santa Cruz

Join Date: Feb 2013
Posts: 1
Question Targeted sequencing of anonymous regions

We are trying to develop a panel of anonymous regions "randomly" sampled around the genome for population genetic purposes (so we would like to be able to run this panel on 100s of samples). These would be quite small - anywhere from 100 to maybe 1200bp long.

Thus far we have been investigating PCR-based amplicon sequencing using our own set of previously developed primers in a multiplex PCR reaction. While we have reasonable coverage in our test runs on just 48 loci (~100x on a 314), most of the reads are non-specific - blasting to the taxon of interest, but not the amplicons in our panel.

Our thoughts so far are that the multiplexing is amplifying too many non-specific regions and that it might be better to submit our regions of interest to a design process.

My first question is whether a PCR-based approach (such as ampliseq) or a hybridization/capture approach (such as targetseq) will work better for our particular application.

In addition, are there any particular kits that others have had success with? Beyond the ABI kits, we are especially interested in IDTs Xgen Lockdown (as it would allow us to build our panel slowly and sequentially), and possibly in Agilent's Haloplex.

Thanks for any advice you might have.
ecrandall is offline   Reply With Quote
Reply

Tags
amplicon sequencing, probe-based sequencing, sequence capture

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 10:54 AM.


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