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GE Researchers Will Use $900K NHGRI Grant to Develop Single-Molecule Next-Gen Sequencer

NEW YORK (GenomeWeb News) — When the National Human Genome Research Institute announced its grant awards this fall for 11 research groups working on innovative sequencing technologies, one big name stuck out: General Electric.
The company, whose GE Healthcare division has been selling Amersham Biosciences’ MegaBace sequencing technology since GE acquired Amersham in early 2004, has until now remained quiet about whether it is pursuing next-generation sequencing.
Its two-year, $900,000 award went to a group led by John Nelson in the molecular and cellular biology lab at GE Global Research, the company’s research organization, for a pilot study to test a single-molecule sequencing chemistry.
Nelson’s group, based in Niskayuna, NY, is part of biosciences, one of 10 laboratories within GE Research that span a variety of disciplines and develop technology for the GE businesses. The aim of the project is to test a new chemistry for next-generation sequencing-by-synthesis using existing enzymes and dye-tagged nucleotides.
A veteran of Amersham Pharmacia Biotech, Nelson is no stranger to the field. Having worked with DNA polymerases since his days as a graduate student at the University of Rochester in 1985, he helped develop several DNA sequencing and amplification kits while at Amersham. Two years ago, he and several other former Amersham researchers moved to GE Research in Niskayuna from GE Healthcare’s Piscataway, NJ, facility.

GE Healthcare “hope[s] to continue to be providers of sequencing technology.”

His group’s new project will bank on GE Healthcare’s experience and resources, including an enzyme library containing dozens of DNA polymerases, as well as nucleotides labeled at their terminal phosphate group. “We have been working with these nucleotides and enzymes for years,” Nelson said.
The idea is to combine these nucleotides with a DNA polymerase that has been selected for its incorporation efficiency. Whenever the polymerase adds a base, the scientists stop the reaction and trap the enzyme in a so-called closed complex, which allows them to image and detect the label before they resume the reaction. The label is then cleaved off before the next reaction cycle starts.
This chemistry is potentially more efficient than others, according to Nelson, allowing for longer reads. For example, the enzyme, while it has to handle modified nucleotides, does not have to work with unnatural DNA. “The DNA we make is completely unmodified, totally natural,” he said. “So we know the DNA polymerase is going to handle that DNA totally normally.”
This, he claimed, increases the efficiency of the reaction compared to other SBS chemistries in which the growing DNA strand is modified. In Solexa’s approach, for example, the reversible terminator nucleotides remain slightly modified even after they have been incorporated and their label removed, he said.
In contrast to 454 Life Sciences’ chemistry, he added, his group’s approach does not permit the polymerase to add several nucleotides in a row, thus preventing problems with homopolymer runs. Like Helicos BioSciences, the GE researchers plan to sequence single molecules without amplifying the template DNA.
The company has filed for a patent on the formation of the closed complex that pauses the enzyme. “How we do that is the part I cannot tell you,” Nelson said.

"In our grand scheme of things, we hope to be looking at hundreds of millions of templates at once.”

The aim of the two-year project, which may be increased and extended to five years if the researchers meet certain milestones, is to demonstrate that the chemistry works on a surface. “One of the reasons why our proposal was viewed as positively as it was by NIH was that we actually have a lot of preliminary data already, suggesting that the method works quite well,” Nelson said.
He initially hopes to be able to read at least 100,000 templates in parallel with a read length of 1,000 bases, resulting in 100 million bases per run. “In its final version, it’s [going to be] much bigger than that,” he said. “In our grand scheme of things, we hope to be looking at hundreds of millions of templates at once.”
Following the proof-of-principle of the sequencing chemistry, Nelson plans to develop the platform further by bringing in scientists and engineers from other disciplines at the Niskayuna facility, including optical engineers, microfluidics specialists, and bioinformaticists. “All of these people are right here on campus,” he said.
It might be too early to say how GE might commercialize the technology at the end of the five-year period, “but GE Healthcare is very interested in this project,” according to Nelson. “They hope to continue to be providers of sequencing technology.”
In principle, though, the chemistry could also be applied to other vendors’ sequencing platforms. “We can certainly see it as a single molecule sequencing system, but we also know that the chemistry lends itself to other people’s platforms,” Nelson said.
An official from GE Healthcare declined to comment for this article on possible commercialization strategies for the chemistry.    

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