SEQanswers

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



Similar Threads
Thread Thread Starter Forum Replies Last Post
Library Prep for Cancer NGS seq-ngs Illumina/Solexa 5 02-26-2015 01:01 PM
Biases in NGS Library Prep Genohub Sample Prep / Library Generation 0 01-23-2014 12:11 PM
GBS library prep rosatoc Sample Prep / Library Generation 0 05-10-2013 07:31 AM
The NEXTflex™ PCR-Free DNA Sequencing Kit Reduces Bias in NGS Library Prep Bioo Scientific Vendor Forum 10 12-20-2012 07:10 AM
Sample Prep for NGS Library addyblanch Sample Prep / Library Generation 2 08-30-2012 06:08 AM

Reply
 
Thread Tools
Old 01-12-2015, 07:51 PM   #1
BioGenomics
Member
 
Location: Belgium

Join Date: Apr 2009
Posts: 24
Default NGS library prep method for RRS/GBS/RADseq of degraded/ancient DNA?

Hi,

I am looking for the best NGS library prep method for RRS/GBS/RAD sequencing of degraded/low/template/ancient DNA ? Any good protocol available to genotype 5-10K SNPs in 100-200 inds reliably starting from already fragmented DNA ? Otherwise best SNP genotyping assay for such low qual DNA samples ?

Thanks

BG
BioGenomics is offline   Reply With Quote
Old 01-13-2015, 02:04 PM   #2
nucacidhunter
Jafar Jabbari
 
Location: Melbourne

Join Date: Jan 2013
Posts: 1,225
Default

Considering input DNA quantity and quality there are two options: 1- Illumina’s genotyping bead arrays. 2- For sequencing based approach preparing Illumina libraries using a low input kit followed by whole genome sequencing or a targeted capture approach (to reduce sequencing requirement). With current kits it is possible to perform capture with very low inputs (pg amount).
nucacidhunter is offline   Reply With Quote
Old 01-13-2015, 05:57 PM   #3
BioGenomics
Member
 
Location: Belgium

Join Date: Apr 2009
Posts: 24
Default

Thanks nucacidhunter. Well as I don't have an extensive list of SNPs for my species (some RAD data, but no good flanking regions... I might try a capture method as there is a draft genome (set of contigs/scaffold). What techniques would be cost-efficient ? I heard MyBaits would be good ? Thanks again
BioGenomics is offline   Reply With Quote
Old 01-13-2015, 06:41 PM   #4
nucacidhunter
Jafar Jabbari
 
Location: Melbourne

Join Date: Jan 2013
Posts: 1,225
Default

MyBaits are definitely cost effective and there are some published papers using their baits. For library prep I think ThruPlex DNA-seq could be good option if you have limited material. You may adapt the approach that has been described here: http://rubicongenomics.com/products/...x-dna-seq-kit/ to MyBaits capture protocol.
nucacidhunter is offline   Reply With Quote
Old 01-13-2015, 08:59 PM   #5
BioGenomics
Member
 
Location: Belgium

Join Date: Apr 2009
Posts: 24
Default

Looks promising indeed, how does this lib prep compare to the NEB Ultra DNA kit for instance ? Did you use it already ? Pricing ?
BioGenomics is offline   Reply With Quote
Old 01-13-2015, 11:38 PM   #6
nucacidhunter
Jafar Jabbari
 
Location: Melbourne

Join Date: Jan 2013
Posts: 1,225
Default

Quote:
Originally Posted by BioGenomics View Post
Looks promising indeed, how does this lib prep compare to the NEB Ultra DNA kit for instance ? Did you use it already ? Pricing ?
I have not used it, but reviewing manufacturer data, related patents and published literature indicates higher performance for this kit as claimed. Pricing is depend on kit size, as always with larger kits prices gets lower and it is pretty close to NEB kits price. I assume prices would be different depending on location.
nucacidhunter is offline   Reply With Quote
Old 01-14-2015, 08:46 PM   #7
nucacidhunter
Jafar Jabbari
 
Location: Melbourne

Join Date: Jan 2013
Posts: 1,225
Default

This paper also seems interesting for your application: http://journals.plos.org/plosone/art...l.pone.0096793
nucacidhunter is offline   Reply With Quote
Reply

Tags
ancient dna, gbs, illumina, neb, radseq

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 01:11 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO