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Although Genia, Nabsys, and Oxford Nanopore each use nanopores in their gene sequencers, their tactics vary.
While some companies make their nanopores from inorganic materials, Genia’s nanopore is a genetically engineered protein. Here’s the short version of the way Genia’s sequencer works: In each well of a Genia microchip, a single nanopore is placed into an interior wall that separates the well into two compartments. The nanopore creates the only channel for electrical current between the two chambers. In the upper chamber of the well, biological molecules process the DNA strand being studied, releasing small chemical byproducts into the nanopore, altering the flow of current. In the lower chamber, sensors record those changes in current—and analysis of the data reveals the sequence of the DNA strand.
To understand the method in more detail, picture hundreds or thousands of separate wells on each Genia microchip. Each well is about the size of a living cell, and each has layers like a hamburger. At its base are components you might find in a mobile device, including electrical sensors. Spread over that lower compartment like a slice of cheese is a thin fatty seal called a lipid bilayer, which is very much like the wall or membrane of a living cell. It prevents any electrical current from passing from the upper compartment down to the sensors. But a single nanopore is placed into the lipid layer in each well, opening a channel for electrical current. The nanopore protein is very similar to the naturally occurring transmembrane proteins that regulate the passage of ions and other molecules through the cell wall.
In the upper chamber of the well, connected to the top of the nanopore, is a polymerase enzyme that can assemble copies of a DNA strand, just as enzymes do in nature. The piece of DNA being analyzed in each well serves as a template for the new copy that is made when a sequencing run begins. The raw materials for the new copy are added to the upper chamber of the well—a mixture of the four different types of nucleotides from which the DNA code is spelled out.
In Genia’s machine, each of the four types of added nucleotides bears one of four characteristic tags. As the polymerase enzyme joins each single nucleotide to the DNA copy, the nucleotide’s tag is clipped off and drops into the nanopore. The electrodes below the nanopore detect the unique changes in electrical current that are caused by each of the four different tags. Thus, the DNA sequence of the copy strand is revealed.
“It’s like creating an artificial cell and putting electrodes inside,” Roever says.
Teams at Columbia developed the nucleotide tag system used by Genia, and George Church’s lab at Harvard created the nanopore channel connected to the polymerase enzyme that copies DNA strands.
Researchers can choose to prepare the DNA samples in different ways before they are placed in the Genia sequencer, Roever says. A scientist could isolate specific segments of the genome for analysis, purifying material from a single type of human cell. Or the instrument could be used to sequence DNA from a mixed sample that might contain different bacterial strains. In any case, software would be needed to sort out the results. Like other gene sequencers, Genia’s device has limits on the length of the individual DNA strands that can be analyzed. But the Genia instrument may be able to handle “read lengths” of several thousand nucleotide bases, rather than a few hundred, Roever says.
The major players in the commercial sequencing arena have been backing Genia and other startups that may develop the sequencers of the future. Genia received an investment of about $10 million from Life Technologies in 2011, and is now raising a Series B round, Roever says.
Illumina invested $18 million in Oxford Nanopore in 2009. Like Genia, the UK company uses a polymerase enzyme to copy the single DNA strand being sequenced in an individual well. But it feeds the DNA copy itself through the nanopore, rather than the snipped-off nucleotide tags used in Genia’s system.
Academic researchers have been test-driving the alpha version of Genia’s sequencer, which contains a few hundred wells. Sometime next year, the company will share its beta prototype containing more than 100,000 wells with a broader collection of academic labs, Roever says. Researchers will be the initial market when Genia releases its first commercial gene sequencer, a desktop model with a million wells, he says.
But the big turning point will come when sequencing goes mobile, Roever says. Genia hopes to develop a handheld model as “a decentralized, universal diagnostic tool” found in doctors’ offices and clinics. A Web interface would connect physicians with a choice of specialized diagnostic applications in the cloud, available through a market similar to Apple’s iTunes store. These apps could interpret a whole genome sequence, for example; look for particular genes that point to hereditary disease risks; identify infectious diseases; or detect the genetic mutations in cancerous cells.
Genia, which has 25 employees, is taking one step at a time. Although the company would consider an acquisition offer, its business plan calls for growth as an independent company. To rival Apple’s trajectory in the tech world, a sequencing company would have to assemble the best hardware, the best operating system, and the best apps, Roever says.