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Nanopore Sequencing Firm Armonica Technologies Progresses Towards Single-Base Detection


NEW YORK – Armonica Technologies, a University of New Mexico spinout, has been making progress in developing a Raman spectroscopy-based DNA sequencing method that features nanochannels and proprietary "nanoantennas" that boost resolution.

The company said it has identified spectral fingerprints for the four natural DNA bases as well as nine epigenetically modified bases and has separately demonstrated single-molecule measurements of a surrogate molecule.

"We have a ways to go yet to prove feasibility" of sequencing DNA molecules, Armonica Cofounder, VP, and Chief Scientific Officer Steven Breuck said, "but the whole thing is coming together."

Earlier this month, the firm announced a $349,200 Small Business Innovation Research grant from the National Human Genome Research Institute to optimize its nanostructures for single-base sensitivity and spatial resolution,

Now, the company will use the money to put it all together and create a data package showing its ability to generate spectra for bases and detect and distinguish single molecules, which it hopes to use to raise the funds necessary to build and validate a sequencing instrument.

Esch was clear that the company did not yet have a full-blown sequencer yet. Though the firm claims it has been able to detect all the bases and many of their modifications, it has yet to determine its read error rate. Given the state of its technology, he said it was too early to discuss cost. However, he did say that Armonica will be testing 1 kb reads in its next phase, with ambitions to go up to at least 400 kb. He claimed that in their current state, the nanopore chips contain about 20,000 channels that can each provide about 30 measurements per second, suggesting 600 kb per second throughput.

"We're getting into the realm where we have unprecedented performance," Esch said." If someone gave us $20 million tomorrow, we'd have a working product in two years."

Since 2017, Armonica has been developing technology that makes use of Raman scattering, where some photons interacting with molecules undergo a change in energy. Those unique energy changes show up as telltale spectral lines, offering a way to identify the molecule. To boost sensitivity, Armonica uses surface-enhanced Raman scattering, which adds special features at the molecule-light interface to boost spatial resolution. "They're super small so they have a small interaction zone, they can address just a single nucleotide," Esch explained.

Armonica's "nanoantennas," as Esch calls them, are the key to moving forward. In 2017, Armonica Brueck, a professor emeritus in electrical and computer engineering at UNM, told GenomeWeb that it was an open question whether they could lead to single-molecule detection.

That question has been settled, Breuck said. "We have shown in other experiments we can take single molecule and it pass through the pores. We have to marry those now and put the pore at the [nanoantenna] and move it through with enough time in between bases that we can take spectra," he said.

Now the firm is seeking up to $8 million in the next few years to mature the technology. In addition to the existing SBIR funding, Esch said Armonica is in the process of raising approximately $2 million now, mostly from people already involved with the company but also from some outside investors, to put together the data package that he hopes will help raise $6 million in the next round.

That's on top of the $3.3 million the company has raised so far, including $1.3 million in convertible debt over the last year and a half, he said. The company now has 10 employees, most of them involved in R&D at its Albuquerque location. Esch and a handful of other staffers work out of an office in Carlsbad, California. The company is "growing a little bit," he noted.

With no amplification or labelling needed and a clear signal on modified bases, Armonica's technology, in theory, represents a more direct way of sequencing than current sequencing-by-synthesis technologies. "If you ask people what they want, they'll say it is to be able to grab some DNA and just measure it as you got it from its native environment," Esch said. He claimed that Armonica has been approached by acquisitions departments from other companies but declined to name them.

If it is successful in creating a long-read sequencer, Armonica would join Pacific Biosciences and Oxford Nanopore Technologies (ONT) in that niche of the sequencing market. PacBio's HiFi sequencing protocol has already reached 99.9 percent accuracy and ONT's devices and base calling algorithms continue to get better.

It is one of a slate of startups working on new sequencing technology including Taiwan-based Personal Genomics, Element Biosciences, iNanoBio, and others.  

Both ONT's and PacBio's technologies can also detect DNA methylation directly, but Armonica claims it has already detected multiple modified bases, including 5-methylcytosine, 5-hydroxymethylcytosine, and hydroxymethyluridine triphosphate. 

Armonica plans on making a research-use-only sequencer to start, but has set its sights on cancer panel testing as a way to enter the market as well as guide development. "You have to have something to drive specs," Esch said. "It's hard to make a machine that works for everything." Specifically, Esch said the company will try to provide long reads with epigenetic information to guide therapy selection. "It's a way to have something you could do in a CLIA lab and make money and prove you can make money and do something that’s meaningful from a clinical standpoint," he said. "We're ultrafocused on the tech now, but a product intro path would be along those lines."

"You never know what's going to fail along the way," Esch said, but he's hopeful the company can progress along a product development path that he's seen in some of his earlier roles, as CEO of DNA Electronics and NanoMr. "It's a critical mass kind of thing," he said. "You can have too much money, too, but to do it efficiently, you need a certain amount to get all the critical components done in parallel."