Genome sequencing X Prize

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Genome sequencing X Prize

Postby dignan » Thu Oct 05, 2006 3:34 pm

I love the idea of prizes for specific scientific achievements. I really think if somebody came up with a good, attainable goal for MS research, it would probably speed things up. Anybody got a spare $10 mil sitting around?



Genome sequencing X Prize announced - Competition on to sequence 100 human genomes in 10 days: how tough can it be?

October 5, 2006 - Nature - Two years to the day after the first private craft carrying a person to the edge of space clinched the Ansari X Prize spaceflight competition, the X Prize Foundation has announced its next contest: sequencing 100 human genomes in 10 days.

The winner of the Archon X Prize for Genomics will get $10 million and a headstart at cornering the human genome sequencing market. Contest organizers hope that the competition will spur the development of personalized medicine — drug treatments tailored to an individual's genetic makeup.

Completing the challenge will lack the panache of a dramatic spacecraft launch and landing in the Mojave Desert, but contest organizers have spiced things up by requiring the winner to sequence an additional 100 genomes from select celebrities, millionaires and people suffering from a range of diseases. That list so far includes astrophysicist Stephen Hawking, Google co-founder Larry Page, American talk show host Larry King, and the most recent space tourist, Anousheh Ansari, whose family put up the money for the spaceflight prize.

Experts say meeting the foundation's demands will present a daunting challenge. "It's not going to violate any laws of physics to get there, but it is quite a stretch," said Francis Collins, director of the US National Human Genome Research Institute in Bethesda, Maryland, and former leader of the Human Genome Project. It took years to stitch together the 'finished' human genome sequence that was completed in 2003; at present it takes at least months to sequence a genome from scratch.

"I would be surprised if anyone does it within five years," says Leroy Hood, founder of the Institute for Systems Biology in Seattle, Washington, and a member of the genomics X prize scientific advisory board.

Competition is expected to be fierce: there are many more potential contenders than in the spaceflight race. And while success may seem far off today, observers expect sequencing capabilities to accelerate over time: the race will probably have a sprint to the finish.

For the past two years, the US National Institutes of Health (NIH) has funded programmes aimed at developing "revolutionary genome sequencing technologies" that would enable a human genome to be spelled out for $1,000 a pop. Several projects funded by this initiative have focused on driving down costs by using nanotechnology to reduce the amount of reagents used and shrink the size of the reaction platform.

It's not going to violate any laws of physics to get there, but it is quite a stretch.

Xiaohua Huang, a bioengineer at the University of California, San Diego, is an early contender who is following this approach. He is developing a system that will allow him to simultaneously sequence 1.6 billion fragments of DNA tightly packed together on a single 4-centimetre square chip. Because such technology is cheaper it is also likely to be faster.

Huang says it's still a long journey until his technology will be ready for practical use. But when asked if he intends to enter the X prize, he says: "Of course. Why not?"

The judges will have to be on the lookout for cheats. George Church, director of the Lipper Center for Computational Genetics at Harvard Medical School in Boston, Masschusetts, and another member of the X prize scientific advisory board, notes that at present it wouldn't be hard to fake a result. The sequence variation between individuals is so low, he says, that a team could simply download the already known human sequence and get a computer to insert a few changes in spots known to vary among individuals. Repeat 100 times and voilà: $10 million.

Church says that standards for sequence accuracy will be set high enough to stop such attempts. Such details haven't yet been written into the rulebook: the X Prize Foundation says that it expects final guidelines to be approved within the next six months. It will also need to make clear exactly how complete each genome needs to be, with defined margins for errors or omissions.

Hood estimates that companies will invest in excess of $20 million to develop their technologies, with some possibly shelling out well over $100 million.

"I don't think the prize money really justifies the effort," says Michael Metzker, a molecular geneticist at Baylor College of Medicine in Houston, Texas, and chief executive officer of LaserGen, a small Houston-based start-up company that is developing new sequencing methods (and aims to join the competition). The real prize, says Metzker, will be grabbing a firm hold on the sequencing market. "There are a lot of players currently jockeying for space in the field," he says. "The first to do it really gains credibility."

http://www.nature.com/news/2006/061002/ ... 002-9.html
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dignan
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