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ISB Uses Helicos Data for Prostate Cancer Gene-Expression Study

NEW YORK (GenomeWeb News) - Helicos BioSciences has been sending Jared Roach of the Institute for Systems Biology cDNA sequencing data  as part of the groups' early-access partnership, Roach told GenomeWeb News last week.

As part of the alliance, which is the first of its kind for Helicos, Roach and colleagues use the data for transcript enumeration, a method to study gene expression, in a prostate cancer project, Roach said. Details of the project are still confidential, but he said "early results are promising."

Roach has used MPSS and Affymetrix microarrays in the past to study gene expression 

and said he will be comparing results from Helicos' single molecule sequencing technology with other methods for quantifying gene expression, which may or may not include these.

He said he is working with Helicos to develop strategies to minimize the variability of sample preparation and to develop sequencing protocols. Also, he has been developing software at ISB to analyze transcript enumeration data statistically, including data from Helicos' platform.

Roach said this is the only one with Helicos that ISB has announced. He said he plans to publish the results of the project in a scientific journal.

Helicos said it has attracted "a lot of interest" from other institutions that want to collaborate and is currently signing up more early-access partners, according to John Boyce, the firm's senior director of marketing. Boyce told GenomeWeb News that Helicos has now decided on which applications its instrument will focus, though he declined to disclose them. The company remains on track to beta-test and launch the instrument in 2007, he said.

DeltaDot Launches Label-Free Desktop Sequencer

DeltaDot launched its label-free desktop capillary electrophoresis DNA sequencer at the Human Genome Meeting in Helsinki earlier this month.

The company said its low-throughput single-capillary instrument, called Merlin, will enable researchers to sequence DNA quickly in their own labs at lower running costs. It also has applications in forensics, where it can analyze short tandem repeats.

Merlin, which lists for $140,000, provides short reads of 200-300 base pairs, DeltaDot said. It uses standard dideoxy terminator chemistry and 512 UV detectors in a photodiode array to measure the length of the terminated DNA molecules, thus eliminating the need for labels. Because the technology does not require fluorescent dye terminators, it can save money on reagents, according to CEO Tony Baxter.

 
He said that quantifying reagent costs per run was difficult, but cited that sequencing core facilities typically spend several thousand dollars a day on dye terminator reagents.

Main competitors include Beckman's P/ACE MDQ capillary electrophoresis system and ABI's Prism 310 Genetic Analyzer, which are not label-free, according to DeltaDot Chief Commercial Officer Frank Smith.

The company said it plans to market the instrument both to molecular biology researchers and for forensic applications. For example, researchers wanting to validate a SNP or verify the sequence of a clone can use Merlin to obtain the sequence in their own labs in hours rather than sending the samples to a core facility, Smith said. However, "the real killer application, as we see it, is in the forensics area with STRs," he said.

DeltaDot, which is collaborating with an undisclosed UK-based forensic science service provider, will be competing in this area with ABI, which has said in the past that forensics represents a significant part of its business for ,lower-throughput sequencers.

Baxter said DeltaDot has so far received four orders for Merlin and hopes to sell up to 50 units in within the next 12 months.

The London-based company, founded in 2000, is a spin-out from

Imperial College in London, from which it has licensed the label free intrinsic imaging technology. In March DeltaDot raised £6 million ($10.4 million) in venture capital to help it manufacture and market the technology and to develop it for protein analysis applications.

Norwegian Startup Developing 'Design Polymers' for Harvard's Nanopore Sequencer
Preben Lexow, founder of now-defunct DNA sequencing company Complete Genomics in Norway -- not to be confused with the recent Callida Genomics spinout of the same name of the same name
-- has resurfaced at Oslo-based LingVitae, a company he founded, GenomeWeb News has learned.

LingVitae, which has been around at least since 2004, has been collaborating with Amit Meller at

Harvard University as part of a 2004 "$1,000 genome" NHGRI grant entitled "Ultra fast nanopore readout platform for designed DNAs."

According to the grant abstract, LingVitae has been developing a method to convert target DNA into easily readable code units, so-called "Design Polymers." Meller's group is working on a rapid readout system for the design polymers using a nanopore-based approach.

Lexow has one issued US patent, No. 6,723,513, entitled "Sequencing method using magnifying tags," as well as one additional published patent application of the same title.

LingVitae is still setting up shop and will provide more information on its activities in a month or so, Lexow told GenomeWeb News last week.


Julia Karow covers the next-generation genome-sequencing market for GenomeWeb News. E-mail her at [email protected].
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