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NHGRI: Why One Sequencer Is Never Enough

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When it comes to next-generation sequencing instruments, Jeff Schloss doesn’t think there will be one winner, and that’s a good thing.

“These different technologies with different capabilities are going to be useful for different kinds of studies,” says Schloss, program director for technology development at the National Human Genome Research Institute.

While sequencing centers want instruments that are speedier, cheaper, and accurate, they also see a need for instruments with various read lengths and different abilities.

Most centers say they need a read length of 500 to 700 base pairs for de novo sequencing of mammalian genomes, but opinions vary on the read length needed to resequence the human genome. “It becomes a statistical argument — what proportion of the genome can you uniquely assign at some read length,” Schloss explains.

To Schloss, however, a market exists for sequencers that can generate varied reads. “If one can deliver very, very cheap 25- to 100-base reads that are of sufficient quality, people will figure out ways to use those for lots of different things,” he says. Likewise, if researchers focusing on nanopore strategies can achieve single-read lengths of 10,000 or 100,000 bases, researchers will also put these instruments to good use, perhaps in ways people haven’t thought of today. Long reads, for example, could be useful in analyzing soil samples that contain hundreds of organisms.

Schloss points out that many in the field are focused on sequencing individual human genomes to understand disease susceptibilities and potential adverse drug reactions, but this is only a piece of the pie. “There are all different kinds of reasons for collecting genomic information ... whether it is understanding the biota, or looking for infectious diseases that are spreading in a hospital setting or a shopping mall, or for biowarfare detection,” says Schloss.

— Kate O’Rourke



NSF and the USDA have allocated nearly $15 million for the 2006 Microbial Genome Sequencing Program, inviting proposals for high-throughput sequencing of the genomes of microorganisms such as viruses, bacteria, archaea, fungi, oomycetes, protists, and agriculturally important nematodes. It also invites proposals to develop and implement strategies, tools, and technologies to make currently available genome sequences more valuable to the user community. Proposals are due March 2, 2006.

Applied Biosystems has acquired an undisclosed stake in VisiGen Biotechnologies, a Houston-based company developing next-generation sequencing technology. VisiGen’s approach involves engineering both polymerase and nucleotide triphosphates to act together as direct molecular sensors of DNA base identity in real time.

NSF, USDA, and DOE have allocated nearly $30 million to sequence the maize genome. Four research institutions will complete the project: Washington University, the University of Arizona, Iowa State University, and Cold Spring Harbor Laboratory.

An international research team led by scientists at the Broad Institute of MIT and Harvard has completed a high-quality genome sequence of the domestic dog, together with a catalog of 2.5 million specific genetic differences across several dog breeds.

PATENT WATCH

US Patent No. 6,969,488. System and apparatus for sequential processing of analytes. Inventors: John Bridgham, Kevin Corcoran, George Golda, Sydney Brenner, Michael Pallas. Assignee: Solexa. Issued: November 29, 2005.

The patent covers an apparatus and system for simultaneously analyzing a plurality of analytes anchored to microparticles. The invention relates generally to systems and apparatus for carrying out large-scale parallel reactions on solid phase supports and, more particularly, to systems and apparatus for monitoring and carrying out reactions on arrays of microparticles.


US Patent No. 6,972,339. Compounds and methods for fluorescent labeling. Inventors: Eugeny Lukhtanov, Alexei Vorobiev, Michael Reed, Nicolaas Vermeulen. Assignee: Epoch Biosciences. Issued: December 6, 2005.

This covers a method for preparing a fluorescent dye-labeled biological agent, the method comprising contacting an unlabeled biological agent with a fluorescent dye-fused lactone derivative under conditions sufficient to covalently attach the fluorescent dye to said biological agent and form a fluorescent dye-labeled biological agent. The lactone dyes can be used to prepare phosphoramidite reagents suitable for labeling biological agents or materials in, for example, automated synthesizers.


Datapoint
$61 million
In November, Solexa announced a private stock deal expected to net the company $61 million. The company expects to recognize revenue from its sequencing machine in the first half of this year.
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