I'd love to hear some comments from people about how this is affecting experiments in their labs.
Completely obsoleting huge PCR-driven resequencing studies?
Anyone talked to Nimblegen to get an idea of availability? At GME2007 a 454 rep told me they will be launching the exon platform soon (6 mo.?), but perhaps on the higher density chip so they can get it all on one.
Anyway, if you're reading this, don't be shy...
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
This is a sticky topic.
X
X
-
Nimblegen arrays for targeted genome enrichment
Two papers were recently published in Nature Methods detailing an astonishing new technique which combines the flexibility of on-demand array technology with the power of next gen sequencing instrumentation.
These papers demonstrate the specific capture and sequencing of specific genomic regions, using a programmable microarray platform (from Nimblegen)
Direct selection of human genomic loci by microarray hybridization (Albert, et al)
and
Microarray-based genomic selection for high-throughput resequencing (Okou, et al)
Both studies capture defined regions of the genome (either ~6,700 exons or up to a 5Mb contiguous region) using Nimblegen arrays, and present 454 sequencing data of the enriched regions. ~65-75% on target reads were reported, with median single base coverage of 5-7 fold. The Albert study validated their technique against four samples from the HapMap collection, and were able to identify 79-94% of known variants in the target regions.
A third paper in the same issue of Nature Methods from the Church lab ("Multiplex amplification of large sets of human exons", Porreca et al) demonstrates another technique for capture. Rather than capturing the targets using hybridization directly on the array, this study uses a programmable array to synthesize "molecular inversion" capture probes that are cleaved from the array and used to fish out small regions of interest (~60-191 bp exon fragments). Enriched fractions were then sequenced with the Solexa Genome Analyzer.
The results reported in this study were less than impressive, with only 28% on target hits. There was also a significant problem with calling heterozygous polymorphisms, however the authors hope this can be optimized at the reaction level. This technique, which relies on a dual hybridization event surrounding the region of interest followed by gap-filling/ligation, is much more complicated and seems that it will require intense optimization to approach the success had with direct capture.
In any event, this enrichment technology will make a significant impact on any study examining a defined subset of the genome, such as candidate region sequencing workflows. What once was a laborious process of PCR primer design, optimization, amplification, and normalization, has become a simple one-pot hybridization event.Tags: None
- Stuck
Latest Articles
Collapse
-
by seqadmin
Metagenomics has improved the way researchers study microorganisms across diverse environments. Historically, studying microorganisms relied on culturing them in the lab, a method that limits the investigation of many species since most are unculturable1. Metagenomics overcomes these issues by allowing the study of microorganisms regardless of their ability to be cultured or the environments they inhabit. Over time, the field has evolved, especially with the advent...-
Channel: Articles
09-23-2024, 06:35 AM -
-
by seqadmin
During the COVID-19 pandemic, scientists observed that while some individuals experienced severe illness when infected with SARS-CoV-2, others were barely affected. These disparities left researchers and clinicians wondering what causes the wide variations in response to viral infections and what role genetics plays.
Jean-Laurent Casanova, M.D., Ph.D., Professor at Rockefeller University, is a leading expert in this crossover between genetics and infectious...-
Channel: Articles
09-09-2024, 10:59 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 10-02-2024, 04:51 AM
|
0 responses
13 views
0 likes
|
Last Post
by seqadmin
10-02-2024, 04:51 AM
|
||
Started by seqadmin, 10-01-2024, 07:10 AM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
10-01-2024, 07:10 AM
|
||
Started by seqadmin, 09-30-2024, 08:33 AM
|
0 responses
25 views
0 likes
|
Last Post
by seqadmin
09-30-2024, 08:33 AM
|
||
Started by seqadmin, 09-26-2024, 12:57 PM
|
0 responses
18 views
0 likes
|
Last Post
by seqadmin
09-26-2024, 12:57 PM
|
Leave a comment: