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Genia Aims to Build the iPhone of Gene Sequencing

Xconomy San Francisco — 

Stefan Roever, CEO of the bleeding-edge gene sequencing company Genia Technologies, first made his name as a software entrepreneur. When he talks about the future growth of Mountain View, CA-based Genia, he envisions a dynasty similar to the one founded by the tech giant Apple of Cupertino, CA.

Roever’s ideal dynasty, like Apple’s, would be based on a novel device, a high-grade operating system, and a vast constellation of apps.

A business empire could be founded by the company that develops a cheap, highly accurate gene sequencer about the size of a sci-fi medic’s tricorder in an old Star Trek episode, Roever says. For about $100 a test, it would decode a human genome—or quickly sequence the genes of a germ plaguing a patient who gives a blood sample to a clinic nurse. The sequence would be uploaded into a universe of cloud-based diagnostic applications that could identify the microbe by the time the patient gets in to see the doctor.

Genia is trying to build that first-in-class, best-in-class device. It’s one of the companies in a race to transform gene sequencing from a costly activity in research labs to a routine part of clinical medicine. The company, founded in 2009, will share in a recently awarded $5.25 million NIH grant with scientists from Harvard Medical School and Columbia University who have already developed much of the technology that makes Genia’s gene sequencing device a contender in that race.

“I think the winner here is going to be the company that can make a cheap enough, accurate enough ecosystem where anyone can have access to it,” Roever says. The NIH grant will help Genia fine-tune its prototype sequencing system, in which DNA strands are rapidly analyzed by integrated circuits on semiconductor chips.

Stefan Roever, CEO of Genia Technologies

Stefan Roever, CEO of Genia Technologies

“It’s a convergence of IT and DNA,” Roever says.

Genia’s instrument is an alternative to current gene sequencing methods that involve costly, time-consuming steps, such as producing many copies of the genetic material under study to ensure accuracy. In another series of steps used by older commercial sequencers, the four different “letters” of the DNA code are labeled with four different fluorescent tags, one type of tag at a time. These tags can be distinguished from each other by the light sensors used in most gene sequencing machines on the market.

The device developed by Genia, now about the size of a desktop printer, can sequence a single DNA strand, eliminating the need to make multiple copies. Genia routes each single piece of DNA to an individual well on a microchip containing many wells. Electrodes in each well identify the sequence of “letters,” or nucleotides, in the strand by detecting changes in an electrical current, rather than using light sensors.

“Our view is that the market is, in the longer term, moving toward single molecule, electrical detection,” Roever says.

Similar shifts in sequencing technology are being pursued by other companies such as Oxford Nanopore of Oxford, UK and Providence, RI-based Nabsys. Like Genia, these companies are moving gene sequencing into a high-tech world that blends computer technology with synthetic biology in the same nanoscale device.

The first semiconductor-based gene sequencer was introduced into the market in 2010 by Carlsbad, CA-based Life Technologies (NASDAQ: [[ticker:LIFE]]), which acquired the technology when it bought Ion Torrent Systems of South San Francisco and Guilford, CT.  The inexpensive, benchtop Ion Proton systems now compete with rapid sequencing machines made by industry leaders such as San Diego-based Illumina (NASDAQ: ILMN). But the Ion system still requires multiple copies of the DNA strands being analyzed, and multiple, separate steps to identify each of the four nucleotides that make up the DNA alphabet.

To read single strands of DNA, Genia and other startups use a key element called a nanopore—a tiny channel through which an electrical current can flow and be measured by an electrode in a microchip. When a biomolecule enters the nanopore, it alters the current flow in a pattern characteristic of that molecule.

The potential of nanopore-based sequencing got a big vote of confidence recently when NIH’s National Human Genome Research Institute awarded a total of $17 million in funding under its so-called “$1,000 Genome” grant program to eight separate research groups, including Genia’s collaboration. Of those grant recipients, five are tinkering with nanopores. The largest grant of $5.25 million went to the inventors of the core technology used in Genia’s instruments—Jingyue Ju of the Columbia University school of engineering, and synthetic biology leader George Church of Harvard.

The NIH is trying to help companies bring the cost of sequencing an individual human genome down to $1,000. The current commercial price is still at least $4,000 to $5,000. Price is still an obstacle for physicians who would like to have patients’ genetic data to help them reach a diagnosis or choose the best medicines.

The current cost of thousands of dollars is a triumph, however, when you consider that the Human Genome Project achieved the first sequencing of a human genome only 10 years ago, through the combined efforts of an international consortium of research labs at a cost of $1 billion. By 2009, the price was $100,000. Next-generation sequencing companies such as Illumina and Life Technologies have brought that cost into the four-digit range. Now several of the recipients of the NIH’s $17 million grant round, including Genia, are aiming for the $100 genome.

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.

“The winning players are the ones that put it all together,” he says.