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LaserGen Builds Prototype Sequencer; Plans to Sequence Bacterial Genome by Fall


By Julia Karow

Betting on the accuracy of its reversible terminator sequencing-by-synthesis chemistry, LaserGen is building a DNA sequencer that it hopes to commercialize within the next two years, initially targeting small and medium-sized laboratories.

Last week, the Houston-based Baylor College of Medicine spinout disclosed that it has teamed up with National Instruments, a provider of hardware and software for custom instrumentation, to build and validate a prototype sequencer that uses its "Lightning Terminator" chemistry.

Within the next several weeks, LaserGen expects to close a Series A funding round, allowing it to proceed with its validation work. By the fall, the company plans to submit a paper for publication showing that it can use its system to sequence a bacterial genome with high accuracy.

"This chemistry is going to be more accurate than any technology there is right now," said Mike Metzker, LaserGen's president and CEO and an associate professor in the department of molecular and human genetics at Baylor. "If you think about this technology moving into the clinic, I think accuracy is extremely important."

Like Illumina, LaserGen uses dye-labeled reversible terminators to sequence DNA in a stepwise fashion. But its Lightning Terminators, which have photocleavable dyes and terminating groups, have an unblocked 3'-OH group, so they can be incorporated by off-the-shelf DNA polymerases (IS 3/3/2009). Earlier this year, LaserGen described details about the selectivity and termination of its reagents in a paper in Nucleic Acids Research.

Since January, the company has secured three patents on its technology and is expecting a fourth, "major" patent to issue soon. It continues to file for additional patents, Metzker said.

LaserGen has been working with National Instruments since March to build its first breadboard prototype, which it plans to use to sequence the Escherichia coli genome in the coming weeks. The goal is to submit a paper on that genome to a peer-reviewed journal by the end of September, Metzker, said, "illustrating all the sequencing metrics involved in genome analysis," such as accuracy and coverage. In parallel, the company plans to submit at least two technical papers for publication, showing improvements in the cleavage time for the Lightning Terminators, which reduces the overall cycle time.

Following the "important milestone" of the bacterial genome sequencing project, the partners plan to build a second, more advanced prototype that they want to place at a genome center for independent validation. The name of the center is currently undisclosed as the company is finalizing the paperwork, but it is likely to be Baylor's Human Genome Sequencing Center, where Metzker is a faculty member. The goal is to deploy a second prototype instrument at another external site by mid-2012, and to commercialize the system within two years.

According to LaserGen's current plans, the prototype system will complete a run in about 25 hours and generate more than a gigabase of data, comprising unpaired reads of at least 50 base pairs. The company has not yet released a price estimate for its commercial system or consumables.

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The sample prep currently involves standard emulsion PCR, but the company is looking to simplify this and is in discussions with several groups about licensing technologies that would streamline the sample-prep process.

After bacterial genomes, LaserGen researchers plan to sequence targeted regions of mammalian genomes, followed by exome sequencing. Later on, the company wants to add paired ends and enable applications other than DNA sequencing, such as RNA-seq and methyl-seq.

"We are targeting intermediate throughput goals for now," Metzker said. "We are not really pushing for resequencing human genomes in a run. Eventually, we will get there, but I think we can still gain a lot of nice applications just out of those experiments."

A medium-throughput instrument "has a huge potential for small and medium-sized laboratories," he said. "That's really the market we want to target first."

National Instruments bring its expertise in hardware and software for systems controls, data acquisition, and analysis to the collaboration. "Our objective is to build a general-purpose platform and tools, and we work with domain experts, such as LaserGen, to define the tools that are right for that industry," said John Hanks, the company's vice president of life science.

Specifically, National Instruments will work on improving the systems controls that coordinate the different parts of LaserGen's instrument, and on speeding up data processing using field programmable gate arrays. It is also working on imaging algorithms for detection and location analysis, he said.

While other researchers have used National Instruments' tools before to build prototype DNA sequencers, this is the first time the company is focusing on this application, Hanks said. He added that the goal is to present the results of the collaboration at the Advances in Genome Biology and Technology conference in early 2012.

The market for medium-throughput so-called desktop sequencers is already crowded, of course, with Roche/454's GS Junior and Life Technologies' Ion Torrent PGM already available and Illumina's MiSeq waiting in the wings.

Besides LaserGen, other smaller players are also working on new sequencing-by-synthesis platforms, such as Intelligent Bio-Systems, which is developing a low-cost sequencer for clinical applications (IS 3/29/2011).

But Metzker believes that the accuracy of LaserGen's reversible terminators, combined with the system's anticipated high speed and low cost, could give it an edge.

Metzker did not disclose the expected size of the pending Series A funding round but said that commercializing the system will require a "much larger round" of financing and take approximately two years. Over that time frame, the company plans to expand its current staff of 10 to about 40 employees.

LaserGen is also already looking at other applications for its reversible terminators, for example in single-molecule sequencing, which it plans to pursue in partnership with others.

Have topics you'd like to see covered in In Sequence? Contact the editor at jkarow [at] genomeweb [.] com.
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