UNM technology accelerates genomic sequencing - Albuquerque Journal

UNM technology accelerates genomic sequencing

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 up individual silicon carbide particles. Source: The University of New Mexico

Today, DNA sequencing is a tortuous process that often takes days and sometimes weeks to read a full human genome, but University of New Mexico researchers may have found a way to cut that down to minutes.

Investors are now lining up behind UNM’s breakthrough, which they say could accelerate the healthcare industry’s use of “precision medicine” based on each individual’s unique DNA structure.

New Mexico-based Cottonwood Technology, Tramway Venture Partners and Sun Mountain Capital are jointly pumping an initial $1.5 million investment into Armonica Technologies Inc., a new startup that’s working to take UNM’s discovery to market.

“Most industry efforts in DNA sequencing today are incremental, next-generation steps to speed things, but this technology is way beyond that,” said Tramway Ventures managing partner Waneta Tuttle. “This could have a dramatic impact to enable the rapid study of (genomes) at lower cost. It’s truly breakthrough technology.”

Distinguished professor emeritus Steven Brueck is leading a team of researchers to fully prove the technology’s viability at UNM’s Center for High Technology Materials. Brueck’s group already demonstrated the ability to push much larger strands of DNA through optical readers than is possible with state-of-the-art industry methods today, potentially paving the way to process a full human genome in minutes.

The team is now working to show that laser readers can accurately scan all of the DNA’s individual characteristics as it passes through the device, something the new venture investment may help accomplish.

A new technique

It’s a daunting challenge, because a full human genome includes about three billion base pairs, or parts, that are matched up in a myriad of ways. Taken together, they form the individual codes that define everything from a person’s hair and eye color to disease susceptibility.

To read, or sequence, the full genome, researchers break the DNA into tiny strands of just 200 to 300 base pairs, which are then pushed individually through an optical scanner.

Afterwards, researchers reassemble all the individual readings to create a complete picture of the full genome. That requires highly advanced computational analysis, which is time-consuming and expensive.

“Current technology breaks the genome into millions of little pieces to read them individually,” Brueck said. “It then tries to put them back together again … Our goal is to sequence much larger sections of DNA, starting with 50,000 bases, meaning much less effort to put it all back together.”

The central problem is that genomic strands are incredibly finicky. They fold and clump up, making it difficult to stretch them out for processing through an optical reader. And when they do go through, it’s at breakneck speed, making it difficult to scan accurately for sequencing.

Brueck’s group has created a new, “optical nanopore sequencing” technique that pushes DNA strands through nano-scale channels, or microscopic holes about one-billionth of a meter. The channels force the strands to stretch out and slow their movement down, allowing the laser readers to process them.

Brueck’s team is also lining up multiple channels side by side, potentially allowing many DNA strands that together contain up to a million base pairs to be processed simultaneously.

Researchers elsewhere have tried pushing large DNA strands through simple nanopores, or one-dimensional holes, that are etched into silica, or glass. But it’s hard to guide the clumped-up strands through them, and the etched material is difficult and expensive to fabricate.

UNM, in contrast, creates three-dimensional nanochannels by stacking silicon carbide particles on top of each other, forming an enclosed tunnel. That’s cost-effective, because those particles are commercially available and inexpensive, Brueck said.

Unique approach

With the new venture investment, Brueck’s team will work on building additional capacity into optical scanners to accurately read the individual strands of DNA. The money will pay for more high-tech equipment and additional researchers for the project.

But the team’s achievements to date have already generated excitement.

“UNM’s technology could provide tremendous acceleration for genomic sequencing,” said Armonica Technologies President and CEO Scott Goldman. “It could be truly transformative, enabling researchers to analyze an entire genome in a fraction of the time it takes today.”

Cottonwood Technology managing director David Blivin said UNM’s unique approach could change the standard for DNA sequencing.

Both Cottonwood and Tramway have received money from the New Mexico government’s new Catalyst Fund, which aims to boost financing for local startups. Gov. Susana Martinez said that’s now helping to grow and diversify New Mexico’s economy.

“This is an example of a homegrown startup that is going to stay right here in New Mexico and help grow our high-tech sector,” Martinez said in a prepared statement. “I’m proud to help companies like Armonica get off the ground and thrive.”

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