NM startup on cusp of DNA sequencing breakthrough

BY KEVIN ROBINSON-AVILA / JOURNAL STAFF WRITER
PUBLISHED: SUNDAY, OCTOBER 2ND, 2022 AT 9:02PM 

Copyright © 2022 Albuquerque Journal
Source: https://www.abqjournal.com/2537204/startup-nearing-dna-breakthrough.html

UNM created these nano-scale tunnels to stretch out strands of DNA for scanning under optical readers as they flow through the channels. Researchers form the nanochannels by stacking individual silicon carbide particles.

Technology to rapidly read long strands of DNA with accurate, molecular-level precision has eluded researchers for decades.

But an Albuquerque startup is close to achieving that breakthrough in genomic sequencing, now backed by $2 million in funding from the National Institutes of Health.

Armonica Technologies Inc. says it can accurately identify single molecules among millions of particles attached to strands of DNA as they shoot through measuring devices, based on new methods developed at the University of New Mexico. The technology could potentially open the floodgates to “personalized medicine,” allowing for much faster medical diagnostics and more effective treatments for things like cancer.

The company, which launched in 2017, has raised nearly $8 million to date to advance its technology, which has already proven effective in laboratory testing through UNM’s Center for High Technology Materials, or CHTM. But it must still develop standardized methods for manufacturing market-ready systems that work with the speed and accuracy required for medical diagnostics, something the new NIH grant will help Armonica develop, said company CEO Victor Esch.

“We’re currently working to implement manageable fabrication technology at CHTM,” Esch told the Journal. “It doesn’t yet scale well for standard manufacturing. It’s still not very reproducible, so we’re working to transition it into mainstream fabrication technology.”

The NIH grant, approved in August, reflects significant enthusiasm about Armonica’s technology, said Waneta Tuttle of Tramway Venture Partners, which invested in the company.

“The NIH peer review panel expressed real excitement in the technology’s potential,” Tuttle told the Journal. “It’s a real vote of confidence.”

Santa Fe-based Cottonwood Technologies Fund and Sun Mountain Capital have also invested in Armonica. So did Hamamatsu Ventures USA, a subsidiary of global company Hamamatsu Photonics K.K., which is a world leader in photonics, or light-based, technologies.

Hamamatsu was attracted to Armonica’s photonics-based innovation, which applies laser technology to identify the individual molecules in DNA strands using advanced analytics tools that illuminate the molecules under study to better capture and measure their characteristics.

“We basically fabricate ‘nano-antennas,’ or enhancement structures, which are super-tiny antennas that resonate with optical light to probe individual molecules,” Esch said.

A full DNA genome encompasses more than three billion nucleotides, or base parts, which constitute the individual building blocks of DNA. Researchers chop up those full genomes into smaller parts, or strands, of DNA to capture and identify the individual molecules in bite-sized chunks as they pass through laser-reading devices.

But with current technology, researchers have struggled to accurately detect and identify all the individual nucleotides in each DNA strand, something Armonica’s technology now enables.

In addition, Armonica has developed nano-scale channels, or nanopores, to push DNA strands through laser readers. Those microscopic holes force the DNA strands to stretch out and slow down as they move through reading devices, permitting the lasers to accurately process them. And that, in turn, allows Armonica to use larger strands of DNA in the laser readers, permitting it to record a lot more nucleotides in a single sample, while also speeding the process of measuring all the chopped up strands of DNA that lead to sequencing a full genome.

That process acceleration could potentially reduce the time for full genomic sequencing from days or weeks today to perhaps minutes, according to Armonica. And, with accurate readings at the individual molecular level, Armonica’s technology can provide a lot more critical information for medical diagnostics that’s often missed with current sequencing systems.

Researchers, for example, often miss “structural variants,” or individual nucleotides, that attach to DNA and change their function or characteristics, turning things on and off, Esch said.

“Many diseases like cancer are the function of structural variants,” he said. “It’s critical to capture and measure those variants in medical diagnostics.”

Accurately detecting and identifying those variants, known as “epigenetics,” could advance medical breakthroughs in many fields, such as studying the aging process.

“Longevity studies today look at how epigenetics influences the way the body ages,” Esch said. “It could lead to therapies that modify things that are causing the body to slowly break down.”

Hamamatsu senior associate Robert Warren said Armonica’s next-generation sequencing capability could significantly advance medical diagnostics.

“It can help to understand DNA at a much deeper level,” Warren told the Journal. “It can provide a full picture of what’s going on with each molecule.”

It may still take five to 10 years to fully develop Armonica’s technology and bring it to market, said Richard Oberreiter, managing director of Hamamatsu Ventures USA.

“Transformative technology takes time and money,” Oberreiter told the Journal. “… But these types of technological advances can lead to breakthroughs in personalized medicine and treating disease.”