Thanks to advances in chemistry and software, researchers can soon sequence a human genome for $1,000 in a day.
Back in July, Jonathan Rothberg, CEO of the Connecticut-based biotech company Ion Torrent, predicted that by 2013 his company would develop a chip that could sequence an entire human genome.
This week, the company surpassed that prediction with a new tabletop sequencer called the Ion Proton. The company introduced the device at the Consumer Electronics Show in Las Vegas on Tuesday, although the sequencer is only available to researchers at this point.
At $149,000, the new machine is about three times the price of the Personal Genome Machine, the sequencer that the company debuted about a year ago. But the DNA-reading chip inside it is 1,000 times more powerful, according to Rothberg, allowing the device to sequence an entire human genome in a day for $1,000—a price the biotech industry has been working toward for years because it would bring the cost down to the level of a medical test.
“The technology got better faster than we ever imagined,” Rothberg says. “We made a lot of progress on the chemistry and software, then developed a new series of chips from a new foundry.” The result is a technology progression that has moved faster than Moore’s law, which predicts that microchips will double in power roughly every two years.
Ion Torrent’s semiconductor-based approach for sequencing DNA is unique. Currently, optics-based sequencers, primarily from Illumina, a San Diego-based company, dominate the human genomics field. But, while the optics-based sequencers are generally considered more accurate, these machines cost upwards of $500,000, putting them out of reach for most clinicians. Meanwhile, at Ion Torrent’s price, “you can imagine one in every doctor’s office,” says Richard Gibbs, director of Baylor College of Medicine’s human genome sequencing center in Houston, which will be among the first research centers to receive a Proton sequencer.
The new Ion Torrent sequencer will also allow researchers to buy a chip that sequences only exons, the regions of the genome that encode proteins. Exons only account for about 5 percent of the human genome, according to the National Human Genome Research Institute, but they are where most disease-causing mutations occur, making so-called exome sequencing a faster and potentially cheaper option for many researchers. Although it’s the same price as the genome chip, the Ion Torrent exome chip can sequence two exomes at a time, bringing the per-sequence cost down to $500.
“Some researchers want to sequence single genes, others want to do exomes, and others—for example, cancer researchers—will want to sequence whole genomes, so all three are going to coexist,” says Rothberg. “It’s about finding the right tool for the problem.”
Whether Ion Torrent’s new technology will be enough to make it the dominant supplier of these tools remains to be seen. A day after the company debuted the Proton sequencer, Illumina also announced that it, too, had reached the $1,000 genome milestone.
“It’s a volatile field, and there’s no sentiment to keep researchers from switching to new technologies,” says Gibbs. Still, Ion Torrent clearly has the price advantage. For researchers who already have Illumina’s latest sequencer, the price to upgrade will be only $50,000, but the retail price will be $740,000, which will likely scare off most newcomers.