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With New Management, Nabsys Shifts Focus to Cancer Structural Variation Analysis

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This article was originally published Nov. 3.

NEW YORK (GenomeWeb) – Following the recent appointments of a new CEO and CSO, Nabsys is shifting its strategy toward developing a platform for clinical applications, in particular structural variation analysis of cancer genomes.

In clinical cancer analysis, "there are a lot of opportunities for technologies today, including our own, and right now, we are testing that landscape" with the goal of defining clinical opportunities for the company's probe-based electronic genome mapping technology, said Tony Shuber, who joined Nabsys as CSO last month.

Shuber brings experience in the oncology area, joining Nabsys from Ignyta, a developer of targeted cancer drugs and biomarkers, where he was CTO. Prior to that, he was the co-founder and CTO of Predictive Biosciences, which developed a bladder cancer diagnostic test but went out of business last year, and he is a scientific co-founder of Exact Sciences, which has a colorectal cancer molecular screening test that was recently approved by the US Food and Drug Administration.

Late this summer, Nabsys also appointed a new president and CEO, Steve Lombardi, who was tasked with the commercialization of the firm's technology. He replaced former CEO and Co-founder Barrett Bready, who remains a company director. Lombardi joined Nabsys from Real Time Genomics, where he was also president and CEO. Before that, he held the same roles at now-defunct single-molecule sequencing firm Helicos BioSciences, and prior to that, he was a senior vice president for Affymetrix and a vice president of genetic analysis at Applied Biosystems.

Earlier this year at the Advances in Genome Biology and Technology conference, Nabsys presented an update on its technology development and commercial plans, which have now shifted.

At the time, the company showed that it could use its nanodetector platform to generate genome maps for baker's yeast, bacterial artificial chromosomes, phage genomes, and bacterial genomes, and was able to distinguish several closely related bacterial strains.

One of the first applications of the technology was going to be the de novo assembly of microbial genomes, in conjunction with data from short-read sequencing platforms. The plan at the time was to start a beta-testing program this summer and to ship commercial instruments during the second half of this year. The first system, NPS8000, was going to have eight independent modules, each with a single nanodetector.

Those plans have changed now with the new focus on cancer applications and human whole-genome structural variation analysis, originally a longer-term goal. "I really don't like to talk about commercialization," Shuber told In Sequence, saying that the company is currently in the development phase, which is about "learning what the technology can and can't do and making sure we understand where it's most appropriate in answering clinical questions." Commercialization plans will only be revealed after the technology has been validated for potential clinical applications, he said.

Shuber and other company officials provided no updates on where the technology has gone since February, but he said that it "has definitely progressed to the point where my coming on board is not premature."

"I would not have come here if I didn't believe the technology was far enough along where we have to start thinking today about what clinical questions in cancer there are that we can answer," he said, adding that the company is already considering collaborations.

The long-term goal is to provide whole-genome structural variation mapping of cancer genomes, but along the way, there might be targeted mapping applications to address specific clinical questions, he said.

In terms of proof of concept for human whole-genome mapping, "it can't be any longer than a year," he said. "As that's being developed, I'm looking at the opportunities and we're aligning the progress [Nabsys' technology development team is] making on whole-genome structural variation analysis with the list of opportunities in oncology that I'm generating."

While whole-genome mapping would require a larger number of detectors, he said, targeted structural variation analyses might not. As of February, Nabsys was already working on a new generation of chips with more than one nanodetector.

Nabsys' mapping technology will largely serve as a complement to whole-genome sequencing, Shuber said, providing structural information that is difficult or impossible to gain with short-read sequencing.

The company will need to compete in this space with other technologies specializing in long-range structural genome analysis, such as Pacific Biosciences' long-read sequencing platform, or BioNano Genomics' genome mapping technology.

One possible advantage of Nabsys' technology over some other platforms is that even a single sample can be analyzed at relatively low cost, which is important if individual clinical test results need to be returned quickly. "The cost of doing an analysis needs to be low, even if one analyzes just one sample, and not require economies of scale by analyzing hundreds of samples simultaneously," which is required by many next-gen sequencing platforms, Shuber explained. He did not say how much an analysis on the Nabsys platform will cost, but back in February, the company cited $300 per experiment, including a chip and consumables.

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