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ABI Sheds Light on Agencourt’s Sequencing Tech

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Applied Biosystems in early October disclosed details of its Agencourt Personal Genomics next-generation sequencing platform to the scientific community at a meeting in Cambridge, Mass.

By next summer, ABI expects that the technology, called “Supported Oligonucleotide Ligation and Detection,” or SOLiD, will generate up to 500 million bases of sequence data per run “but we can see the platform getting north of 10 gigabases” per run in the future, says Kevin McKernan, senior director of scientific operations at ABI’s high-throughput discovery unit in Beverly, Mass.

ABI reiterated plans to place early access systems by mid-2007 followed by a full release with “fully supported workflows,” according to Kevin Corcoran, the company’s vice president and general manager of genetic analysis.

The audience was all ears when Gina Costa, director of R&D projects in Beverly, explained how the technology works, how it has developed it over the last eight months, and how it has performed in a cancer resequencing project.

ABI’s Agencourt technology differs from its rivals mainly in that it uses reversible terminating ligation rather than sequencing by synthesis to read the DNA, though it bears some similarities to its competitors.

Like 454’s Genome Sequencer 20, the technology uses emulsion PCR to amplify the sample. And like Solexa’s 1G Genome Analyzer, it performs the sequencing reactions on a glass slide array. At the moment, the method reads two bases per step and generates 20-base reads, but 25-base reads are “just around the corner,” according to McKernan. The commercial instrument, expected to launch next year, will run two arrays in parallel with two separate flow cells, microscopes, and cameras included.

— Julia Karow

 

SHORT READS

The X Prize Foundation announced its $10 million Archon X Prize for Genomics, which will go to the first team to create a technology that can map 100 human genomes in 10 days. Teams that enrolled in the competition are VisiGen, 454, and a group comprising the Westheimer Institute for Science and Technology, the Foundation for Applied Molecular Evolution, and Firebird Biomolecular Sciences, led by Steve Benner.

 

NIH selected lung, brain, and ovarian cancers as the ones to map for its Cancer Genome Atlas project. Genome sequencing centers will work with biospecimens from Brigham and Women’s Hospital, the MD Anderson Cancer Center, and the Children’s Hospital of Ohio State University.

 

NHGRI awarded BioNanomatrix a $397,750 research grant to develop its nanoscale whole genome imaging platform, a system that allows nanoscale single molecule identification and analysis of the entire genome.

 

For the first time, scientists analyzed a complete genome sequence of a tree, the poplar or Populus trichocarpa, which they claim could help develop biofuels. The study identified more than 45,000 protein-coding genes.

 

Solexa raised $75 million by securing a commitment to sell that much in common stock Azimuth Opportunity. The cash will be used to develop and commercialize its Genome Analysis System as well as for general uses.

 

DATAPOINT

$13 million

The National Human Genome Research Institute announced the latest round of funding for next-generation sequencing technology development. In all, the institute distributed more than $13 million for 11 investigators.

 

$1,000 Genome

J. Michael Ramsey, University of North Carolina, $3.8 million (4 years),Nanoscale Fluidic Technologies for Rapidly Sequencing Single DNA Molecules

Amit Meller, Boston University, $2.2 million (3 years), High-Throughput DNA Sequencing Using Design Polymers and Nanopore Arrays

Timothy Harris, Helicos Biosciences, $2 million (3 years), High-Accuracy Single Molecule DNA Sequencing by Synthesis

Dmitri Vezenov, Lehigh University $905,000 (3 years), Force Spectroscopy Platform for Label Free Genome Sequencing

John Nelson, General Electric Global Research, $900,000 (2 years), Closed Complex Single Molecule Sequencing

Peiming Zhang, Arizona State University, $895,000 (3 years), Fabrication of Universal DNA Nanoarrays for Sequencing by Hybridization

Carlos Mastrangelo, Case Western Reserve University, $815,000 (3 years), Large-Scale Nanopore Arrays for DNA Sequencing

Jens Gundlach, University of Washington, $605,000 (2 years), Engineering MspA for Nanopore Sequencing

Xiaohua Huang, University of California, San Diego, $275,000 (1 year), Genome Sequencing by Ligation Using Nano-Arrays of Single DNA Molecules

 

$100,000 Genome

Michael Metzker, Baylor College of Medicine, $500,000 (1 year), Ultrafast SBS (Sequencing by Synthesis) Method for Large-Scale Human Resequencing

Steven Jeffrey Gordon, Intelligent Bio-Systems, $425,000 (1 year), High-Throughput DNA Sequencing by Synthesis Platform

 

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