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With New Techs Up for Grabs, ISB Studies Helicos

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The Institute for Systems Biology is “talking about testing” one of Helicos BioSciences’ gene-sequencing prototypes.

“We are ... doing some collaboration with ... Helicos, which is taking us further into downstream approaches to the analysis of single DNA molecules,” said ISB President Lee Hood at the 12th European Congress on Biotechnology, held at the University of Copenhagen this August.

“I think [new sequencing technologies] will have a profound impact on systems biology, because systems biology starts with complete genome sequences, and they’re difficult to obtain now with methods used in the past,” Hood said. “With some of the new methods coming out, [such as] parallel sequencing, we can see sequencing entire microbial genomes in a few hours.”

The Helicos technology relies on cyclic sequencing by synthesis, using 1.2 billion strands of DNA attached to a quartz slide to create a parallel process.

The collaboration keeps it all in the family for Hood. He has been on Helicos’ scientific advisory board since the company opened its doors in Cambridge, Mass., in 2003. He is also an alumnus of Caltech, where Steve Quake, Helicos’ founder, was a professor. (Quake is currently a professor of bioengineering at Stanford.)

Another Helicos partner is Eric Lander. Helicos expects to ship an instrument to Lander’s lab by the end of the year, and expects to have beta instruments out by next year with a commercial system available in 2007. Lander’s Broad Institute bought a platform from Helicos competitor 454 in March.

Hood’s disclosure comes at a time when companies, academic labs, and research institutes are jockeying for position to align themselves with one of the dozen or so companies that have sprung up in recent years to develop faster and less costly sequencing technologies.

— Kirell Lakhman

 

Nexia Holdings will acquire Axis Labs for 165,000 shares of its class C preferred stock. Axis is developing a reagent for DNA sequencing that would remove BigDye terminators in automated sequencing.

 

Solexa plans to launch its sequencing-by-synthesis instrument by the end of this year. In late summer, the company said it was entering alpha production to get the instrument to test labs run by the likes of Jane Rogers, Eric Lander, and Rick Wilson.

 

The Chimpanzee Sequencing and Analysis Consortium, comprised of members from the US, Germany, Italy, Israel, and Spain, completed the genome sequence of a chimp from the subspecies Pan troglodytes verus. The 3.5-fold coverage of the 3 billion bases is 96 percent similar to the human genome when indels are taken into account, the consortium reported.

 

Researchers from Germany and the US announced they sequenced the genome of Dehalococcoides sp. strain CBDB1, anaerobic bacteria that break down some of the most toxic chlorinated organic chemicals. The microbe’s genome was sequenced by researchers at the Max-Planck Institute of Molecular Genetics, Technical University in Berlin, and Cornell University.

 

Oregon State University scientists have sequenced the smallest genome to date — the ocean-dwelling bacterium Pelagibacter ubique, which has 1.3 million bases and the smallest known amount of junk DNA.

 

Datapoint

$32 million

NHGRI awarded more than $32 million in its second round of grants for new sequencing technologies. Here are the awardees, along with their projects and funding:

“$1,000 Genome” Grants:

Richard Fair, Duke University, $510,000 (2 years), Droplet-Based Digital Microfluidic Genome Sequencing

M. Reza Ghadiri, The Scripps Research Institute, and Hagan Bayley, Oxford University, $4.2 million (5 years), Single-Molecule DNA Sequencing with Engineered Nanopores

Jene Golovchenko, Harvard University, $5.2 million (3 years), Electronic Sequencing in Nanopores

Susan Hardin, VisiGen Biotechnologies, $4.2 million (3 years), Real-Time DNA Sequencing

Xiaohua Huang, University of California, $750,000 (3 years), Massively Parallel Cloning and Sequencing of DNA

Jingyue Ju, Columbia University, $970,000 (3 years), Modulating Nucleotide Size in DNA for Detection by Nanopore

Bud Mishra, New York University, $585,000 (2 years), Haplotype Sequencing Via Single Molecule Hybridization

Gregory Timp, University of Illinois at Urbana-Champaign, $2.1 million (3 years), Sequencing a DNA Molecule Using a Synthetic Nanopore

Stephen Turner, Nanofluidics, $6.6 million (3 years), Real-Time Multiplex Single-Molecule DNA Sequencing

 

“$100,000 Genome” Grants:

Gina Costa, Agencourt Personal Genomics, $1.2 million (2 years), Bead-Based Polony Sequencing

Vera Gorfinkel, The State University of New York at Stony Brook, $1.5 million (2 years), Ultra High Throughput DNA Sequencing System Based on Two-Dimensional Monolith Multi-Capillary Arrays and Nanoliter Reaction Volume

Greg Kellogg, Network Biosystems, $4.5 million (3 years), $100,000 Genome Using Integrated Microfluidic Capillary Electrophoresis

 

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