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Nabsys Using DNA Mapping Tech in 'Collaborative Mode'; Eyes Cancer Structural Variant Panels


NEW YORK (GenomeWeb) – Following Nabsys' announcement last week that it is working with Ariana Pharmaceutical to identify structural variations related to breast and prostate cancer and their impact on clinical outcomes, executives from the company provided additional details about the collaboration and its commercialization strategy.

Nabsys CEO Steve Lombardi and CSO Tony Shuber, both of whom joined the company just last year, spoke with GenomeWeb at last week's JP Morgan conference in San Francisco.

Lombardi said that the company's semiconductor-based DNA mapping technology works and is currently being used in "a collaborative mode." The firm is now focused on scaling the technology so that it reaches a viable price-to-performance ratio, he said.

Shuber said that the goal of the collaboration with Ariana is to establish the clinical validity of identifying structural variants and also to show that Nabsys' technology can identify those variants at a lower cost than next-generation sequencing.

Ariana will use existing databases that have been developed through the Cancer Genome Atlas to identify "signatures associated with clinical outcome" that would inform therapy, Shuber said. In parallel, Nabsys will demonstrate that its technology can detect those structural variants.

Lombardi added that the company's first order of business is to "prove the clinical value of the known structural variants out there and then enable a whole new generation of them to be discovered."

Providence, R.I.-based Nabsys last year hired new management and shifted its focus to oncology. Previously, it had been developing its technology to map bacterial genomes with plans to incrementally increase resolution and throughput to move into larger genomes.

The firm is still targeting a $150,000 list price for its system, which will initially enable mapping of multiple genomes per day. With "turns of the crank" it will eventually enable tens of genomes to be mapped per day at a couple hundred dollars per genome, Lombardi said.

Lombardi noted that currently, researchers typically use NGS to first do whole-genome sequencing to identify diseases-associated SNPs and then build disease-specific panels targeting those SNPs. He anticipates that with Nabsys' system researchers similarly will first build whole-genome maps of cancer genomes to identify all structural variants and then build structural variant panels.

He said that the company plans to sell reagents that will enable researchers to do whole-genome mapping and design their own structural variant panels. In addition, he said that Nabsys would likely also market pre-designed panels that target structural variants in cancer.

Previously, Nabsys' system was going to have eight independent modules, each with a single nanodetector. Last week, Lombardi said that the instrument will be composed of multiple chips, each with multiple nanodetectors, although he declined to specify exact numbers.

The core technology behind Nabsys' platform remains the same, Lombardi said. Essentially, the company uses sequence-specific probes that it hybridizes to DNA fragments, which are run through a solid-state semiconductor nanodetector at a speed of more than a million bases per second. Electronic signals from the probes passing by the nanodetector are recorded and translated into positional maps.

The goal is to be able to cover structural variants at 20x to 30x, Lombardi said. Currently, the company routinely generates reads of 200 kilobases and above. Lombardi said that the theoretical limit of the technology is around 1 megabase per second per nanodetector.

"We're not there now, but we have a good understanding of how to get there. What we're looking to do in the next six months is to finance the company to commercialize our first product, continue the [clinical] collaborations, and work on [developing] high-density chip technology," Lombardi said.

The main development efforts between now and commercialization will be related to chip engineering, Lombardi said, noting that "the current architecture of the chip limits the size of the DNA fragment that can get in and be detected."

A much longer-term goal for the company is to develop a diagnostic platform based on its nanodetector technology. "We want to develop the instrument for the applied research side of cancer and in the process, understand what a diagnostic instrument would require and then redevelop the technology in the context of a clinical regulatory environment," Lombardi said.

Lombardi said the advantages of the Nabsys system are that it is single-molecule; it can identify structural variations much more cheaply than sequencing; and it can identify structural variations that sequencing cannot.

Nonetheless, when it does launch its system, the firm will likely compete with BioNano Genomics, which markets a genome mapping system called Irys, as well as with Pacific Biosciences, which has been ramping up the throughput and read lengths of its system to enable sequencing of larger, more complex genomes, like human. In addition, it may also compete with Oxford Nanopore's MinIon.