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Old 02-22-2008, 03:27 PM   #1
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Location: SF Bay Area, CA, USA

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Default Magnetically assembled ordered arrays will speed NGS on all platforms

A paper was just published in Analytical Chemistry describing a new technique that has the potential to significantly increase throughput of most of the current next gen sequencers.

Magnetic Assembly of High-Density DNA Arrays for Genomic Analyses
Kristopher D. Barbee and Xiaohua Huang*
Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412
Received for review October 23, 2007. Accepted December 5, 2007.
A method for rapidly assembling high-density DNA arrays with near-perfect order is described. Photolithography is used to generate a wafer-scale array of microwells in a layer of photoresist on a chemically functionalized glass coverslip. The array is enclosed within a microfluidic device, and a suspension of superparamagnetic microbeads conjugated to DNA molecules is introduced into the chamber. A permanent magnet is used to direct the rapid assembly of the beads into the wells, with each well containing a single bead. These beads are immobilized on the glass surface via affinity binding, and excess beads can be recycled or washed away. Nonspecifically bound beads are removed by dissolving the photoresist. The result is a high-density array of beads with virtually no background. This method can be used to produce protein arrays for chip-based assays and DNA arrays for genotyping or genome sequencing.
There is also an article on In Sequence about the UC San Diego researcher that has invented these magnetically assembled arrays.

Illumina GA, ABI SOLiD, and the Polonator all analyze unordered arrays of beads (or clusters), which has quite a few drawbacks related to imaging efficiency.

The idea here is to improve the organization by assembling beads into wells using a combination of magnets and microfluidics.

I haven't gotten a hold of the paper yet, I'm interested in how the density compares to 454 picotiter plates.
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Old 02-23-2008, 01:32 AM   #2
Location: Sydney, Australia

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Good spotting ECO.
I imagine this technology would also improve read bandwidth though removing exquisite DNA concentration requirements. The DNA and beads are initially present in excess then unbound beads washed away. No more concerns about too much DNA affecting read quality and too little DNA wasting bandwidth.

Things move pretty quick these days
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Old 02-23-2008, 10:53 AM   #3
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Good spotting, i get it!

I'm curious how far this is from a bead-deposition system that's compatible with ABI and Polonator flow cells.
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Old 02-25-2008, 04:12 AM   #4
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Hi guys.. The paper...
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