SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
A first look at Illumina’s new NextSeq 500 AllSeq Vendor Forum 106 10-29-2017 11:27 PM
A heads up for all NextSeq 500 users! LizD Illumina/Solexa 10 02-08-2015 09:59 AM
no dual indices on NextSeq 500 (yet) SeqNerd Illumina/Solexa 9 10-20-2014 12:06 PM
100 Gb Data/Day – Nextseq 500 Sequencing Services Now Available on Genohub Genohub Vendor Forum 3 04-24-2014 09:28 AM
NextSeq 500 and HiSeq X Ten Services Coming Soon to Genohub.com Genohub Vendor Forum 11 04-22-2014 09:46 AM

Reply
 
Thread Tools
Old 11-02-2014, 07:50 PM   #1
newtoseq
Junior Member
 
Location: Canada

Join Date: Nov 2014
Posts: 2
Question Questions about whole-exome sequencing on NextSeq 500

Hi everyone,

My lab is looking into performing whole-exome sequencing on a small sample of human subjects on the NextSeq 500. I am responsible for researching the budget involved in such an endeavor and, as a newbie to this subject, would like to seek your advice on the number/type of sample prep/reagent kits to achieve our sequencing goals.

We would like to whole-exome sequence 4-8 (depending on total costs) human subjects at >100x coverage, pair-ended read using the Nextera Rapid Capture Exome Kit and, ideally, the High Output 300 cycle NextSeq Kit.

So, if we use 1 Nextera Rapid Capture Exome Kit (8rxn x 6plex), which according to documentation at 6plex can sequence 6 exome samples using NextSeq 500 High-Output kit, and 1 NextSeq Kit, High Output (300 cycle), can I whole-exome sequence up to 6 unique human subjects at >100x coverage with pair-ended read?

edit: As a follow up question, I'm assuming that 1 Nextera Rapid Capture Exome Kit (8rxn x 6plex) can support sequencing of up to 48 exome samples, by the 8 reaction x 6 plex criteria? I apologize for my ignorance, thank you very much for your help.

Thank you for your help.

Last edited by newtoseq; 11-02-2014 at 08:10 PM.
newtoseq is offline   Reply With Quote
Old 11-02-2014, 08:10 PM   #2
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,695
Default

Are you locked in to the NextSeq platform, or do you have the possibility of using something else?
Brian Bushnell is offline   Reply With Quote
Old 11-02-2014, 08:16 PM   #3
newtoseq
Junior Member
 
Location: Canada

Join Date: Nov 2014
Posts: 2
Default

Quote:
Originally Posted by Brian Bushnell View Post
Are you locked in to the NextSeq platform, or do you have the possibility of using something else?
Hi Brian, at this point, we are currently only looking at using the NextSeq 500. Thank you.
newtoseq is offline   Reply With Quote
Old 11-02-2014, 08:26 PM   #4
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,695
Default

I encourage you to look at this thread.

But that aside... I can't help you with the economics. In fact, I think human resequencing is one area where NextSeq might possibly be useful, though it highly depends on the price. Unless NextSeq is vastly cheaper than HiSeq per bp, it's a bad idea, since the error rate is currently so high. Particularly for exome capture, where the coverage is even more highly variable than usual for Illumina, forcing you to call variants at very low coverage.
Brian Bushnell 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 06:20 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO