Inside the Forgotten X Prize—the One That Can Save Your Life
On National DNA Day, PM's resident geek takes the first extensive look at the Archon X Prize in Genomics, the $10 million race for a cheap, disease-hunting gene sequencer that could land on your kitchen counter sooner than you think.
At $150,000 per box, George Church's Polonator device is the smallest and most affordable personal genetic sequencer on the market today. A competition to run through 100 genomes in 10 days for $10,000, however, could change that.
By Erik Sofge
Published on: April 25, 2008 CAMBRIDGE, Mass. — It's an odd-looking gadget—more like a free-standing safe than a self-contained DNA sequencer. This certainly doesn't look like the kind of machine that could prevent diseases and save thousands of lives. And at the moment, the Polonator G.007 isn't even sequencing anyone's DNA. Its belly loaded with dye and front panel opened wide, the arcane inner workings of the box are exposed—not that that's any less confusing, with fluid pumping through snaking, translucent lines. The handy labels on two of the internal containers—marked WATER and WASH—aren't helping much, either.
But that's the beauty of the Polonator, the world's smallest and cheapest available sequencing device, as it rests quietly in the Church Lab here at Harvard Medical School: To operate it, researchers load one cartridge with liquid reagents and two more with DNA, then shut the door. Wave a hand to activate its proximity sensor, and the sequencing run starts—pulsing LED lights, streaming data and a much clearer picture of lineage and inherited disease.
This is the closest you can get to gene sequencing for dummies. And it could also be the ticket to a $10 million purse for the Personal Genome Project (PGx) in one of the most important research competitions to date. Unlike the 100-mpg race for the Progressive Automotive X Prize or the YouTube moonshot of the Google Lunar X Prize, the unheralded Archon X Prize in Genomics has world-changing implications at stake within a decade—or sooner.
"In 10 years, these things will be small enough and cheap enough to have next to your toaster," says Jason Bobe, director of community for PGx. "We'll be sequencing everything—a plant from your garden or an Angus beef steak—to see if it's the real thing."
Bobe is (sort of) kidding, but the history of personal genomics has been one of incredibly rapid progress, thanks in large part to the man who runs this lab, Harvard genetics professor and Human Genome Project originator George Church. "The price has come down by a factor of 1000 in the past two years," he says. "But we have to make it cheaper. If we can reduce volumes by a hundredfold, we can come close to a $1000 genome."
In any discussion of personal genomics, it's easy to get buried by the numbers. For example, to win the Archon X Prize, a research team must sequence 100 individual genomes with an accuracy of more than 99 percent—within 10 days. Each sequence must include at least 98 percent of a genome and cost $10,000 or less. The first group to pull this off by fall 2013 wins $10 million (the same prize money as the AXP but only a third of what Google is offering). The key factors outlined in the rules and emphasized by early entrants are time, accuracy and cost. That's because the goal isn't to simply give a break to the institutions that already perform sequencing—it's to provide every person on the planet with the chance to have their own DNA sequenced, and potentially upend the medical industry.
"If you could sequence the genomes of 1000 patients with Parkinson's," says Marc Hodosh, senior director for the Archon X Prize, "and compare that to the rest of the population, you could recognize which genes are associated with it. Then, pharmaceutical companies could create targeted drugs, preventive pills." In some cases, such as an extreme predisposition to a type of cancer, doctors could possibly even perform a preemptive operation. An accurate genome could also help you avoid the onset of a given disease in less drastic ways, like staying away from certain drugs or eating specific foods.
Companies like 23andme already offer cheap DNA analysis, but they only offer fractional snips rather than full genomes. The X Prize Foundation is calling for at least 98 percent, with sequences that collect more data per genome than anyone has ever attempted, so controlling costs will be paramount. Church tries to use the least expensive reagents possible to bottom out at somewhere close to $10,000 per sequence, and future generations of the Polonator (the one here is his seventh, having sold two boxes for $150,000 each) could require fewer materials per sequencing run.
While he's excited about being one of seven accepted competitors for the X Prize (15 to 20 teams are expected to enter), Church insists that the real goal isn't a $10,000 genome. "There are 6.5 billion people who need their inherited genome done, as well as day-to-day changes," he says. "We need to really bring this down to $1000, or whatever's affordable, so you think nothing of going into a clinic and doing it again." Researchers are aiming for open-source enzymes and better access to equipment to reach that magic $1000 run. PGx spent years turning its cobbled-together, off-the-shelf sequencing gear—including a microscope rigged to two external PC towers—into a marketable, easy-to-use device (click here for complete plans).
Officials at the X Prize foundation agree that the era of practical personal genomics won't arrive until it gets cheaper, with hopes that a winning prototype could drop closer to $1000 after manufacturing and production. Hodosh likened the rapid increase in genome coverage and accuracy to the yearly upgrade cycle of personal computers, so you won't have to wait until 2013 for the first clues or hints of your genetic vulnerabilities. Call it insurance for your body—not a sure thing, but for a week's salary, it might be worth it.
The competition's final deadline, Hodosh admits, may be pushed back; a final deadline is already open-ended—when lives are at stake, research like this is a bit less sporty than, say, building a suborbital space jet. But when a team announces that it's ready for sequencing, the X Prize Foundation will offer one of two time slots during the year (in January or July), while other teams watch and wait like the rest of us. The first to wrestle those imposing numbers into shape—100 genomes, 10 days, $10,000 or less—wins the biggest number of them all. "For the smaller startups, it would be a real nice perk," Hodosh says. "But on the whole, there are teams that are going to spend more than $10 million. Most aren't doing it for the money. It's that Neil Armstrong moment, that Lindbergh moment, that everyone remembers, that paves the way for a new era."
But that's the beauty of the Polonator, the world's smallest and cheapest available sequencing device, as it rests quietly in the Church Lab here at Harvard Medical School: To operate it, researchers load one cartridge with liquid reagents and two more with DNA, then shut the door. Wave a hand to activate its proximity sensor, and the sequencing run starts—pulsing LED lights, streaming data and a much clearer picture of lineage and inherited disease.
This is the closest you can get to gene sequencing for dummies. And it could also be the ticket to a $10 million purse for the Personal Genome Project (PGx) in one of the most important research competitions to date. Unlike the 100-mpg race for the Progressive Automotive X Prize or the YouTube moonshot of the Google Lunar X Prize, the unheralded Archon X Prize in Genomics has world-changing implications at stake within a decade—or sooner.
"In 10 years, these things will be small enough and cheap enough to have next to your toaster," says Jason Bobe, director of community for PGx. "We'll be sequencing everything—a plant from your garden or an Angus beef steak—to see if it's the real thing."
Bobe is (sort of) kidding, but the history of personal genomics has been one of incredibly rapid progress, thanks in large part to the man who runs this lab, Harvard genetics professor and Human Genome Project originator George Church. "The price has come down by a factor of 1000 in the past two years," he says. "But we have to make it cheaper. If we can reduce volumes by a hundredfold, we can come close to a $1000 genome."
In any discussion of personal genomics, it's easy to get buried by the numbers. For example, to win the Archon X Prize, a research team must sequence 100 individual genomes with an accuracy of more than 99 percent—within 10 days. Each sequence must include at least 98 percent of a genome and cost $10,000 or less. The first group to pull this off by fall 2013 wins $10 million (the same prize money as the AXP but only a third of what Google is offering). The key factors outlined in the rules and emphasized by early entrants are time, accuracy and cost. That's because the goal isn't to simply give a break to the institutions that already perform sequencing—it's to provide every person on the planet with the chance to have their own DNA sequenced, and potentially upend the medical industry.
"If you could sequence the genomes of 1000 patients with Parkinson's," says Marc Hodosh, senior director for the Archon X Prize, "and compare that to the rest of the population, you could recognize which genes are associated with it. Then, pharmaceutical companies could create targeted drugs, preventive pills." In some cases, such as an extreme predisposition to a type of cancer, doctors could possibly even perform a preemptive operation. An accurate genome could also help you avoid the onset of a given disease in less drastic ways, like staying away from certain drugs or eating specific foods.
Companies like 23andme already offer cheap DNA analysis, but they only offer fractional snips rather than full genomes. The X Prize Foundation is calling for at least 98 percent, with sequences that collect more data per genome than anyone has ever attempted, so controlling costs will be paramount. Church tries to use the least expensive reagents possible to bottom out at somewhere close to $10,000 per sequence, and future generations of the Polonator (the one here is his seventh, having sold two boxes for $150,000 each) could require fewer materials per sequencing run.
While he's excited about being one of seven accepted competitors for the X Prize (15 to 20 teams are expected to enter), Church insists that the real goal isn't a $10,000 genome. "There are 6.5 billion people who need their inherited genome done, as well as day-to-day changes," he says. "We need to really bring this down to $1000, or whatever's affordable, so you think nothing of going into a clinic and doing it again." Researchers are aiming for open-source enzymes and better access to equipment to reach that magic $1000 run. PGx spent years turning its cobbled-together, off-the-shelf sequencing gear—including a microscope rigged to two external PC towers—into a marketable, easy-to-use device (click here for complete plans).
Officials at the X Prize foundation agree that the era of practical personal genomics won't arrive until it gets cheaper, with hopes that a winning prototype could drop closer to $1000 after manufacturing and production. Hodosh likened the rapid increase in genome coverage and accuracy to the yearly upgrade cycle of personal computers, so you won't have to wait until 2013 for the first clues or hints of your genetic vulnerabilities. Call it insurance for your body—not a sure thing, but for a week's salary, it might be worth it.
The competition's final deadline, Hodosh admits, may be pushed back; a final deadline is already open-ended—when lives are at stake, research like this is a bit less sporty than, say, building a suborbital space jet. But when a team announces that it's ready for sequencing, the X Prize Foundation will offer one of two time slots during the year (in January or July), while other teams watch and wait like the rest of us. The first to wrestle those imposing numbers into shape—100 genomes, 10 days, $10,000 or less—wins the biggest number of them all. "For the smaller startups, it would be a real nice perk," Hodosh says. "But on the whole, there are teams that are going to spend more than $10 million. Most aren't doing it for the money. It's that Neil Armstrong moment, that Lindbergh moment, that everyone remembers, that paves the way for a new era."
