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Quantapore Working Towards Commercialization of Optical Nanopore Sequencing Tech

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NEW YORK (GenomeWeb) – Quantapore is working towards commercializing its optical nanopore sequencing technology, which it has been developing over the past few years and which it plans to demonstrate on a small genome in the near future.

Earlier this summer, the Menlo Park, California-based company raised $15.6 million in a Series 3 funding round that was led by Northern Light Venture Capital, following a Series B round in 2014. It is in the process of growing its current staff of about 10 and moving into a larger space.

Like Oxford Nanopore Technologies, Quantapore uses a nanopore-based sequencing approach, but instead of measuring changes in the electric current through the pore, it records an optical signal from fluorophores attached to the DNA that get activated when the DNA exits the pore.

The company, which uses a combination of protein and solid-state nanopores, has not disclosed details about its technology yet, but, according to CEO Martin Huber, the optical readout offers a number of advantages over an electrical readout.

For example, the approach can be scaled to hundreds of thousands of nanopores, he said, because it does not require a sensor for every nanopore but can use a single CMOS (complementary metal-oxide semiconductor) sensor chip to record signals from all of the pores. In addition, the DNA does not need to be slowed down by a motor protein.

Still, the DNA needs to be labeled prior to sequencing, and the four bases are distinguished by the use of different tags, or by the absence of a label. "We have a very simple sample prep that only takes half an hour to get the DNA ready for sequencing," Huber said.

Over the past few years, Quantapore has been developing its nanopore chips and building alpha instruments for in-house use. "We're planning to sequence our first small genome in the foreseeable future," Huber said, which could be either a viral or a bacterial genome.

Following that, the firm plans to present the data publicly and to provide more details about the technology. "We want to have some solid data, and we're working on that right now," he said.

After the demonstration project, the plan is to start collaborations with early adopters and to place beta instruments in their labs in order to get outside validation and to "iron out any kinks that might still be in the system," Huber said.

The main selling points for the system will be its low consumables costs and high scalability, which translates to flexibility and the possibility of high throughput. "How many nanopores you put on the chip basically defines your throughput," he said, "so there will be a wide range of applications that can be performed on one sequencing system." The first commercial version will likely have up to about 100,000 nanopores, he said, but that will not be the limit.

In addition, the system will generate comparatively long reads, on the order of kilobases, which Huber said he believes will have high accuracy.

Prior to launch, and in collaboration with its early adopters, Quantapore plans to define a set of initial applications for the system, to which it will add later on. "We don't want to limit ourselves or define certain applications that we will be focusing on – we have a fairly flexible system," Huber said.

Pricing for the sequencer, which will initially be for research use only, has not been determined yet and will depend on how the market evolves in the next 12 to 18 months, he said, but it will be "disruptive."

During beta testing, the company also plans to implement some of the documentation that will allow it to apply for FDA clearance for clinical use later on, Huber said, "so that we don't have to go back and do everything again."

On the intellectual property side, Quantapore has amassed a portfolio of patent applications, a handful of which have been granted, and the firm believes that it does not step on the IP of others. "We've created our own little niche with our optical readout," Huber said. "That's what differentiates us from Oxford Nanopore and any other existing prior art in the nanopore field. We're very confident that we have freedom to operate."

The most recent funding round will take the firm through precommercial development, including manufacturing beta instruments and starting the early-adopter program. However, for a commercial launch, additional funding will be needed, Huber said.

In the meantime, Quantapore still has challenges to overcome. "It's not trivial to build a sequencing technology, especially if it's not just a modification of an existing technology," Huber said, and if it is a single-molecule technology. "That's why you don't have a launch of a new sequencing technology every other week."

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