SEQanswers

Go Back   SEQanswers > Literature Watch



Similar Threads
Thread Thread Starter Forum Replies Last Post
PubMed: Targeted next-generation sequencing for routine clinical screening of mutatio Newsbot! Literature Watch 0 09-14-2011 03:00 AM
PubMed: Targeted next-generation sequencing: microdroplet PCR approach for variant de Newsbot! Literature Watch 0 08-25-2011 11:10 AM
PubMed: Next generation massively parallel sequencing of targeted exomes to identify Newsbot! Literature Watch 0 01-29-2011 11:50 AM
PubMed: Genomic-scale capture and sequencing of endogenous DNA from feces. Newsbot! Literature Watch 0 11-09-2010 03:50 AM
PubMed: Targeted capture and massively parallel sequencing of 12 human exomes. Newsbot! Literature Watch 0 08-18-2009 06:01 AM

Reply
 
Thread Tools
Old 11-02-2008, 04:34 AM   #1
Newsbot!
RSS Posting Maniac
 

Join Date: Feb 2008
Posts: 1,443
Default PubMed: Targeted next-generation sequencing by specific capture of multiple genomic l

Syndicated from PubMed RSS Feeds

Targeted next-generation sequencing by specific capture of multiple genomic loci using low-volume microfluidic DNA arrays.

Anal Bioanal Chem. 2008 Oct 29;

Authors: Bau S, Schracke N, Kränzle M, Wu H, Stähler PF, Hoheisel JD, Beier M, Summerer D.

We report a flexible method for selective capture of sequence fragments from complex, eukaryotic genome libraries for next-generation sequencing based on hybridization to DNA microarrays. Using microfluidic array architecture and integrated hardware, the process is amenable to complete automation and does not introduce amplification steps into the standard library preparation workflow, thereby avoiding bias of sequence distribution and fragment lengths. We captured a discontiguous human genomic target region of 185 kb using a tiling design with 50mer probes. Analysis by high-throughput sequencing using an Illumina/Solexa 1G Genome Analyzer revealed 2150-fold enrichment with mean per base coverage between 4.6 and 107.5-fold for the individual target regions. This method represents a flexible and cost-effective approach for large-scale resequencing of complex genomes.

PMID: 18958448 [PubMed - as supplied by publisher]



More...
Newsbot! is offline   Reply With Quote
Old 11-02-2008, 08:23 AM   #2
seqer
Member
 
Location: Palo Alto, CA

Join Date: Feb 2008
Posts: 16
Default

7% specificity? This does not sound impressive... This further highlights the problems of microarray-based enrichment methods, particularly for smaller size of non-contiguous regions.
seqer is offline   Reply With Quote
Old 12-02-2008, 09:11 AM   #3
mrothe
Junior Member
 
Location: London, UK

Join Date: Jun 2008
Posts: 2
Default

At least its a start. When you look at the first Nimblegen papers they are also not better. I think the microarray based enrichement is the way of choice for targeted resequencing.

Regards
mrothe is offline   Reply With Quote
Old 12-02-2008, 07:11 PM   #4
seqer
Member
 
Location: Palo Alto, CA

Join Date: Feb 2008
Posts: 16
Default

Although Nimblegen papers are not great, but their metrics are better than this (e.g., ~50% specificity). Also, I don't see the reason why microarray based enrichment is the choice. Different methods have pros and cons, but to me, the solid phase capturing has fainter future.
seqer 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 05:32 AM.


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