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Old 03-18-2008, 11:19 AM   #1
ECO
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Default Nimblegen officially describes "SeqCap" genome decomplexing service



As we've talked about in the past, Nimblegen has developed a seqeunce enrichment technology for next gen sequencing sample prep.

Looks like they are ready to talk officially about it as they've put up a webpage describing "SeqCap" technology here:

http://www.nimblegen.com/products/seqcap/

Interesting points from their FAQ below:

Quote:
When will this technology be available as a product through Roche NimbleGen?

Sequence Capture technology is not available as a formal product from Roche NimbleGen today, but researchers can order our custom arrays and follow the published protocols in Direct selection of human genomic loci by microarray hybridization (Nat Methods. 2007 Nov;4(11):903-5). View Abstract Download Free Reprint
Roche NimbleGen plans to launch our first Sequence Capture product as a service in the first quarter of 2008. Customers will be able to send DNA samples to Roche NimbleGen, specify regions of interest, and Roche NimbleGen will capture those regions and ship enriched DNA back to the customer. The DNA will be in a form that is ready for downstream 454 sequencing.
Later on in 2008, Roche NimbleGen will launch a kit including all necessary reagents enabling researchers to perform their own sequence capture experiments.
Please understand, however, that these protocols are not optimized, validated commercial products, and as such, Roche NimbleGen technical support staff may not be able to provide the level of technical support that accompanies a launched product. We continue to focus on developing more robust methods.

What regions can be captured by this technology?


These can be any regions in the genome, either contiguous, such as disease associated regions, or discontiguous, such as exons of a candidate gene panel. Please note that, in our technology development efforts, we currently only design probes against unique parts of the genome, although some repetitive regions can be captured by the array and sequenced with long reads from 454 technology if they flank unique regions. The total size of captured regions per array can vary from a few hundred kilobases to a few megabases using existing 385K feature arrays. With HD2 high density arrays (2.1 million features) and optimized protocols, a single array will be able to capture much more of the genome.
For more information on the current technology status, please see: Direct selection of human genomic loci by microarray hybridization (Nat Methods. 2007 Nov;4(11):903-5). View Abstract Download Free Reprint


What is the cost for using this technology?


Commercial pricing has not been established at this time. For most studies that require resequencing of large regions of the genome, this technology will clearly offer significant benefits in terms of cost and time, particularly when compared with multiplex and/or long-range PCR.


Will this technology be compatible with all next-generation sequencing platforms?


The initial Roche NimbleGen products and services will be optimized for the 454 platform. But the system is fundamentally “open”, and certain early access customers are already working on modified protocols to enable use of Roche NimbleGen Sequence Capture arrays and reagents with other sequencing platforms. Roche NimbleGen plans to offer validated, optimized support for other platforms in the future.


Is this technology available for species other than human?


Yes. Although the initial publications have all been human studies, technically this method should work with any species where a sequenced genome is available. Further optimization might be needed for certain species and pilot tests are recommended.

Can I work with Roche NimbleGen as a collaborator or an early-access customer?


We are currently working with a very limited number of collaborators and early access partners to further optimize the technology. Due to resource constraints, we are not taking on any additional early-access customers at this time. However, if you have ideas that can improve the technology or address new applications, we encourage you to contact us so that we can try to work with you when resources become available.

How can I get access to Sequence Capture technology now?


Most researchers will benefit by waiting for the launch of our official product, which will be fully supported by Roche NimbleGen, and will have enhanced performance (more even coverage, direct compatibility with 454 sequencing, etc.) If you wish to experiment with sequence capture technology prior to availability of optimized and validated products and services, you can simply order arrays from Roche NimbleGen and the reagents described in published papers and follow the protocols included in these publications.
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Old 06-18-2008, 11:50 PM   #2
imera
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NimbleGen is now offering a full service Sequence Capture (5 samples for $5000). However, it only applies to human and mouse samples...
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Old 10-08-2008, 11:41 AM   #3
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Raindance? How will that compare to Nimblegen capture?
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