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BioNanomatrix to Debut Single-Molecule Analysis System, Four Applications


By Justin Petrone

BioNanomatrix later this year will launch a single-molecule genome analysis system and four applications for use on the system, according to a company official.

The silicon chip-based platform, called the nanoAnalyzer 1000, relies on thousands of nanochannels in an array format to trap individual DNA fragments, uncoil and linearize the fragments, and then image them.

The Philadelphia-based firm introduced the system at the American Society of Human Genetics meeting in Washington in November, but will launch it sometime this year.

Gary Zweiger, vice president of business development at the company, told BioArray News recently that BioNanomatrix will position its technology for DNA sample quality control, DNA damage assessment, sequence assembly, and structural variation analysis.

According to Zweiger, there is "strong interest" in all four application areas. "We did market research and talked to potential customers and these were the applications they were most interested in," he said.

At the same time, structural variation analysis could be the largest market opportunity for the eight-year-old firm, and Zweiger sees BioNanomatrix targeting the same customers who have adopted high-density genotyping arrays and next-generation sequencing to assess variation.

"Structural variation analysis is a true unmet need," Zweiger said.

"Geneticists are dissatisfied with current solutions," he added. "There is a need to understand and assay duplications, deletions, translocations, conversions, and to do it better, faster, and cheaper than available methods."

Zweiger added that BioNanomatrix is "very interested" in what he referred to as the genome sequence market. "We see ourselves as complementary to the sequencing applications out there," he said.

Additionally, the firm has experienced a "strong pull" from scientists doing clinical diagnostics research. "People who want to understand the genomic structure of variation as a follow-on to all the SNP work that has been done," said Zweiger. "SNPs are important markers, but there is a realization now that structural variation is more important in understanding genetics."

BioNanomatrix's advantage, he contended, is that it is not a me-too technology. "It gives you access to imaging and analysis of long, intact pieces of DNA … with no amplification or bias introduced, with methylation sites intact as well, direct from the genome," he said.

Currently, the system requires nanogram-sized quantities of samples, but "ultimately picograms or less will be required and we are directly imaging those samples," Zweiger added.

According to the firm's website, the nanoAnalyzer assay involves samples of a few microliters, typically containing fewer than 15 nanograms of labeled DNA. Each chip accommodates up to three samples that can be run in succession, the firm maintains.

While researchers continue to invest in next-gen sequencing systems, Zweiger argued that BioNanomatrix's approach offers a "better way" to investigate structural variation than using sequencing-based applications.

"If you cut up the DNA, which is what sequencing shops do, you lose the structural variation," he said. "They try to recreate it using computational methodologies, but there is no better way to access that information than by having a direct image of it."

Zweiger likened the firm's approach to older technologies, such as karyotyping. "With karyotyping, you have a direct image of chromosomes in a cell," he said. "What we are doing is giving much greater resolution to that," he noted. "We are taking that three-dimensional structure, stretching it out in different channels, and getting access to image analysis of that."

BioNanomatrix was founded in 2003 based on technology developed at Princeton University. The core of the technology is the firm's nanoAnalyzer semiconductor chips that induce DNA fragments megabases in size to unwind and enter channels where they are confined and linearized.

BioNanomatrix has so far placed the instrument at a major genome center and a major academic research institute, both undisclosed, and has "nonexclusive collaborations with diagnostic companies, and, on the technology side, with international semiconductor companies," Zweiger said.

Zweiger declined to discuss the price of the system, but said that it will be "similar to array platforms" on the market. "It's a semiconductor chip so with volumes we should be able to rapidly decrease the cost," he said. "We definitely envision routine use for these consumables and reagent quantities are miniscule because you are looking at staining picograms of DNA."

The cost of the devices is therefore "entirely dependent on volume," Zweiger said. "Just as prices come down for cellphone components, the prices will come down for these chips."

Have topics you'd like to see covered in BioArray News? Contact the editor at jpetrone [at] genomeweb [.] com

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