SEQanswers

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



Similar Threads
Thread Thread Starter Forum Replies Last Post
Sequencing WGA ChIP DNA fedora Illumina/Solexa 5 01-20-2011 03:17 AM
RT-PCR vs Next Gen Sequencing NicoBxl Bioinformatics 4 11-04-2010 09:09 AM
LIMS for Next gen sequencing aperera Illumina/Solexa 4 10-08-2010 08:31 AM
Next Gen Sequencing Training Course maojn7488 Bioinformatics 12 09-29-2009 06:00 AM
next-gen sequencing in diagnostics brjordan General 0 04-07-2009 05:08 AM

Reply
 
Thread Tools
Old 01-21-2009, 04:40 PM   #1
Suzanne
Registered Vendor
 
Location: Southern California

Join Date: Nov 2007
Posts: 10
Default WGA pre-Next Gen Sequencing

Hi all,
Is anyone using Phi29 amplified genomic DNA for next gen? I am specifically interested in using it before 454 for metagenomic analysis but anyone with experience or opinions with other systems would be helpful.
The newsbot listed a WGA paper but it wasn't analyzed with a next gen instrument so even though it worked great on a bead array, I'd like to know if it has been validated on sequencing platforms.

Thanks,
Suzanne
Suzanne is offline   Reply With Quote
Old 01-21-2009, 11:57 PM   #2
mgenome
Junior Member
 
Location: Korea

Join Date: Sep 2008
Posts: 4
Default

In the following paper, the authors used the MDA method (phi29 DNA polymerase) and 454 sequencing for viral metagenomics study.
http://biology.plosjournals.org/perl...l.pbio.0040368
PLoS Biology - The Marine Viromes of Four Oceanic Regions

But, MDA may make (maybe significant) quantitative bias on the composition of each member.

For MDA bias, you can referr to a paper reporting selective amplification of ssDNA viruses using MDA.
http://aem.asm.org/cgi/content/abstract/AEM.01275-08v1
In this paper, circular DNA can be amplified very effectively and alter the composition of the amplified DNA.

Last edited by mgenome; 01-22-2009 at 12:30 AM.
mgenome is offline   Reply With Quote
Old 01-22-2009, 02:27 PM   #3
Suzanne
Registered Vendor
 
Location: Southern California

Join Date: Nov 2007
Posts: 10
Default

Thanks!!
This is a great help.
Suzanne
Suzanne is offline   Reply With Quote
Old 03-04-2009, 07:24 AM   #4
EPICENTRE
Registered Vendor
 
Location: Madison

Join Date: Mar 2009
Posts: 5
Default

There was another application by the FBI that looked at various ligation conditions prior to WGA.
http://www.promega.com/geneticidproc...ions/Nunez.pdf
EPICENTRE is offline   Reply With Quote
Old 03-19-2009, 07:51 AM   #5
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,287
Default

Here is another paper for answering this question:

Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing.
ECO is offline   Reply With Quote
Old 03-19-2009, 09:04 PM   #6
Suzanne
Registered Vendor
 
Location: Southern California

Join Date: Nov 2007
Posts: 10
Default

Thanks E- This reference is perfect.

S
Suzanne 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 01:15 PM.


Powered by vBulletin® Version 3.8.6
Copyright ©2000 - 2014, Jelsoft Enterprises Ltd.