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BioNanomatrix Introduces Single-Molecule Analyzer to Researchers at ASHG

By Edward Winnick

NEW YORK (GenomeWeb News) – BioNanomtarix this week introduced its single-molecule genome analysis system to researchers attending the American Society of Human Genetics meeting in Washington, DC.

The firm is nearing a market launch, which it is planning for next year, of the system, called the nanoAnalyzer 1000.

The system is a silicon chip-based platform that uses thousands of nanochannels, in a massively parallel array format, to trap individual DNA fragments, image them, and then release them before the next DNA fragment flows into the channel. It uncoils and then linearizes DNA to be scanned, like a barcode, explained Edward Erickson, president and CEO of the Philadelphia-based firm.

The company — which was founded in 2003, with its core technology exclusively licensed from Princeton University — believes the system will provide high-resolution analyses of macromolecules, such as chromosomal DNA and proteins, and their interactions more rapidly, comprehensively, and cost effectively than currently available approaches.

"We don't slice and dice typically like a sequencer," Erickson told GenomeWeb Daily News in an interview. "We like, actually, longer fragments better," as those have the potential to reveal more genomic information than a user can obtain readily from current sequencing technologies.

"Unlike a sequencer, which considers long segments on the order of hundreds of base pairs, we [can use] long fragments measured in tends of thousands, if not hundreds of thousands or even greater than one megabase pair length fragments," he said.

The system is being developed for a variety of applications including genome assembly, structural variation analysis, and assessing DNA damage. But, Erickson pointed out, the firm's customer test sites are working with the company on defining "real applications that would be of value to them," though he didn't provide further details.

He said that structural variation is an "exploding field" right now, and the firm's technology enables researchers to look at genes and see if there are excess copy numbers, if something is missing, or has been translocated. In addition, he added that the technology has already shown that it can detect DNA damage, such as if a patient has been overexposed to radiation, or if there is accelerating damage which is unrepaired and is the result of some genetic disorder or just from aging or the effects of lifestyle.

Test versions of the nanoAnalyzer 1000 system have been placed with two customers thus far who are operating the machines with protocols that the firm has given them. BioNanomatrix also has other prototypes in house, but it will wait for data and feedback from those two customers before proceeding with a launch next year.

Erickson said that within the next few months the firm will start looking at the test data and application development status and then make a decision about whether it will proceed with an early-access program first before a full commercial launch.

He said the firm has done primary market research, and "we believe we can price this" similar to array platforms, even though it's not a microarray system per se, and the consumables will be comparably priced.

Asked whether the technology could be employed for diagnostics in the future, Erickson said, "There's plenty of real estate where we are. The big genome centers and core labs are sufficient in number with enough workflow that we can keep ourselves extremely busy for quite some time to come.

"What we envision is — since we're interested in structural variation and our customers are interested in structural variation — that that clearly is biomedical research," he said. "Where you identify specific targets or markers of interest it's natural to assume that some of those could potentially be used in diagnostics development," though the firm does not intend to become a diagnostics company. A more likely strategy would be to partner with established diagnostics firms.

In general, Erickson said that the firm is being very careful about its partnering strategy and the potential dilutive effects of giving away too much, too early.

In addition to its own work on the technology, BioNanomatrix has a collaboration with Complete Genomics to co-develop a sequencing workflow that could potentially enable the sequencing of a genome for only $100. That alliance, which received $8.8 million in funding from the National Institute of Standards and Technology in 2007, aims to combine BioNanomatrix's device with Complete Genomics' sequencing chemistry.

The advantage of this approach, according to the companies, is the combination of local sequence information with long-range information about its position in the genome.

Erickson said that the alliance with Complete Genomics is ongoing, but he declined to provide a further update or additional details.

BioNanomatrix has thus far raised about $22 million in total funding, of which around $12.5 million has come from venture capital investors, another $8 million from grant funding, and about a million and a half dollars of venture debt, said Erickson.

Though he said that the firm would consider additional investors to bring in funding, "the good news for us is … Battelle Ventures is our major investor and they've been a tremendous supporter of the company, and I don't see any change on that score."

Erickson joined the firm in 2007 as an independent director, and he was named non-executive chairman and then executive chairman last year. In December 2009, he became president and CEO and relinquished his role as chairman, a position now held by Tracy Warren, a general partner of Battelle Ventures.

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