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BioNanomatrix Opens San Diego Office; Moves into Product Development


By Julia Karow

This article has been updated to note that the instrument's list price could be outside the projected range.

BioNanomatrix has relocated its headquarters to new digs in San Diego as it moves toward commercializing its single-molecule imaging platform for whole-genome analysis.

The firm closed a $23.3 million Series B round of equity financing in March and said at the time that it was planning to expand to the West Coast (IS 3/22/11). Its technology analyzes single molecules of fluorescently labeled DNA flowing through nanochannels, using a CCD camera.

A few weeks ago, the company moved into new office and lab space in San Diego's University Science Center. "Now that we have built a prototype field-testable system, we need to begin to commercialize applications on the platform, and we are going to need to be recruiting people who have experience in product development, especially in this industry," said Erik Holmlin, who became BioNanomatrix's president and CEO earlier this year and who lives in San Diego.

The company will maintain its original location in Philadelphia, where the majority of its 35 full-time employees are currently still located, but over the next few weeks, 10 to 15 staff members will relocate to San Diego. Over time, the West Coast facility will become the firm's main site, Holmlin said.

In order to focus on developing its platform into a commercial product, the NanoAnalyzer 1000, BioNanomatrix plans to hire another 15 people, he said, including in the areas of engineering, chemistry, reagent development, informatics, and computer science. The company recently hired Todd Dickinson, the former director of product development for Illumina's DNA sequencing business, as vice president of product development; and Xing Yang, a co-founder of Epic Sciences, as vice president of system integration (see Paired Ends, this issue).

Late last year, the company started shipping prototype systems to a total of four early field test sites, and is now "collecting feedback" from these sites that will inform its further commercialization and application development. Though the company cannot disclose the sites, they include a "world-renowned" genome center, a "well-known" service provider, and two academic sites, one focusing on clinical translational research, the other on bioinformatics, Holmlin said.

He said the test sites are expected to publish results "in due course," probably next year. The company as well as the test sites may also present data on posters earlier than that, he added, probably later this year.

The chips used by the current prototype system are divided into three devices, each with 4,000 channels that are 100 nanometers wide and have a total length of 6 feet. The system is currently able to scan between at least 50 and 500 megabases of DNA per device in five minutes, depending on the loading concentration.

A new generation of chips will have smaller dimensions, allowing for "better stretching and resolution," said Han Cao, the company's founder and CSO.

For the remainder of the year, BioNanomatrix will focus on fine-tuning the system, protocols, and data analysis routines, Holmlin said. Late this year or early next year, it plans to launch a beta program, including up to half a dozen sites that will overlap with the current test sites, followed shortly afterward by the commercial launch of the system in 2012.

The list price of the benchtop system has not yet been determined, but it will likely be somewhere between the price of a MiSeq and a HiSeq system from Illumina, Holmlin said, though that could still change. The list prices of those systems are about $125,000 and $690,000, respectively.

The first two applications the firm is planning to develop for its platform are long-range genome analysis for de novo genome sequence assembly and structural variation analysis.

According to Cao, users will be able to complement short reads from high-throughput sequencing platforms with physical maps from the BioNanomatrix platform in order to improve genome assemblies. "It has really become an urgent need to reduce the number of contigs, and to increase the length of contigs and scaffolds," he said.

Researchers are also looking into other technologies to provide long-range information for genome assemblies, for example optical maps from OpGen and long sequence reads from Pacific Biosciences.

BioNanomatrix's NanoAnalyzer could also provide haplotype or phasing information, which Cao said is critical for clinical applications of sequencing, for example in cancer.

While the company is working on several applications in parallel, it plans to introduce the sequence assembly application first, followed by structural variation analysis.

It is also working on a variety of genome types at the moment. "We believe that the success of our platform will be tied to the ability to address a broad range of genomes," Holmlin said.

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