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Archon Genomics X Prize Revamps Rules Prior to 2013 Kick Off


 

 By Kevin Davies  

October 26, 2011 | The Archon Genomics X Prize, which offers a $10 million purse for a significant breakthrough in the whole genome sequencing of 100 genomes, has announced adjustments to its rules, criteria, and timing, as well as officially welcoming a major new sponsor – Medco Health Solutions.  

 In one major departure from the former guidelines, the competition has a set start and finish point: it will kick off on January 3, 2013, and end 30 days later. If there is no grand prize winner meeting the revised criteria, the purse will be split between category winners for accuracy, completeness and haplotype phasing.  

 Details of the new-look competition were presented at a press conference at the New York Academy of Medicine today, and are also the subject of a commentary by X PRIZE Foundation staffers Larry Kedes and Grant Campany in Nature Genetics released today. “Although most races can only have one winner, we believe that after this race, the competition will benefit and entire industry,” Kedes and Campany write.  

 According to the X PRIZE Foundation, the main goal of the $10-million genomics prize was “to drive breakthroughs in the future of predictive and personalized medicine to make significant advances in human genome sequencing.”  

 Launched in 2006 to great fanfare, the original competition rules stated that entrants had to sequence completely 100 human genomes in ten days or less at $10,000/genome to very high accuracy. The prize was initially funded by a Canadian diamond hunter named Stewart Blusson and his wife Marilyn. Blusson, who runs a company called Archon Minerals, co-discovered one of the world’s largest diamond mines in the northern territories of Canada two decades ago.   

 urther funding was supplied by genome sequencing pioneer J. Craig Venter, who in 2003, the same year as the official completion of the Human Genome Project, pledged to donate $500,000 from his foundation for a major breakthrough in next-generation sequencing. That was later rolled into the X Prize purse.  

 But over the next few years, only eight organizations registered to compete, including 454 Life Sciences, ZS Genetics, and an offshoot of George Church’s Personal Genome Project. Some observers suggested that the stringency of the rules – especially the 10-day timeframe and the requirement that the DNA sequences be phased – deterred several groups from entering.  

 Medco Mission   

 Ryan Phelan, the president and founder of DNA Direct by Medco, spoke to Bio-IT World about her company’s involvement in the prize.   

 “I hope this is the beginning of a new race for the human genome,” Phelan said from New York. “Getting a medical grade genome is essential in translating the human genome into clinical practice. Having worked with Medco, I know how difficult it is to effect personalized medicine from inside healthcare.”   

 “The race I’m intrigued watching is, once you have this medical grade sequence out there, will it be translated faster into healthcare than those individuals who will be doing their own DNA sequencing, such as BGI or other independent labs? I think we’ll have parallel tracks here, but it ups the ante in an interesting way.”  

 Phelan says many people don’t fully grasp how Medco, under CEO Dave Snow, has been “driving innovation around personalized medicine for at least five years… Dave has always had the understanding that in order to make medications safer and more efficacious, we have to look to a bigger view of medicine and what are the driving forces, like pharmacogenomics. Medco was one of the first, and is still one of the only, Fortune 500 companies, to really embrace personalized medicine to this degree.”  

 Medco’s management felt that the field of genome sequencing and interpretation was moving very quickly. “Our sense was that we could help move the needle in this area. How could we not help usher in this new era of personalized medicine?”  

 Medco’s team supported the idea to sequence the genomes of centenarians. “What will centenarian genes tell us that’s different?” said Phelan. “We’ve had so much focus in medicine on disease, and looking for rare mendelian diseases. I think now we get to look forward to what is the science of health.  Hopefully we’ll see a big explosion in the bioinformatics, getting this information then how do we interpret it? That’s the biggest white space.”  

 Phelan is anxious to get the competition started, but recognizes it will take time to consent the centenarian volunteers. She declined to reveal how much Medco was funding the competition, other than to say it was a “big commitment” on Medco’s behalf.  

 Making the Grade  

 In the announcement made today at the New York Academy of Medicine, the X Prize Foundation announced several key changes to the structure of the competition.  

 First, the details of the competition have been revised – relaxed in some cases, tightened in others. Teams will be judged on accuracy, cost, speed and completeness of genome sequencing. The organizers believe that “the competition’s audacious target criteria for accuracy and completeness of sequencing could define for the first time a ‘medical grade’ genome.”    

 Teams are now given 30 days to sequence the genomes of the 100 subjects, but the cost has been cut to $1,000 or less per genome, a reflection that mainstream NGS platforms are already well under the original $10,000 X PRIZE threshold. The genomes must be sequenced to an overall accuracy of 99.9999%, or no more than one error per million base pairs.   

 Details of the validation protocol that will be set up prior to the competition kick-off are published in the Nature Genetics commentary by Kedes and Campany.  

 Second, the pharmacy benefits manager Medco Health Solutions, has joined as the competition’s presenting sponsor. The prize will now be known as the Archon Genomics X PRIZE presented by Medco.  

 Medco Research Institute president Felix Frueh said that the partnership further signifies Medco's commitment to improving health care, in part through more effective genetic testing. “We believe that the Archon Genomics X PRIZE presented by Medco is the game changer that's needed to reach that final mile and transform the full promise of genomic research into practical clinical care."  

 Third, the 100 genomes to be sequenced will be those of volunteering centenarians, rather than an eclectic group of celebrities, scientists and other volunteers discussed in the original guidelines. These centenarians, or the ‘Medco 100 Over 100,’ are in the words of the X PRIZE press release, “donating their genome to this competition in order to further medical science.”   

 “Our goal is to assemble an ethnically diverse group of ‘genomic pioneers’ who are at least 105 years of age,” said Campany, senior director of the genomics X prize. “Such individuals who have evaded all of the common diseases associated with aging are effectively supercontrols whose genomes deserve to be scrutinized in contrast to the genotypes of the many disease cohorts currently under investigation,” commented the editors of Nature Genetics.  

The sequencing results will be compiled into a public database (such as dbGaP), raising the notion that the resulting data might help elucidate the presence of so-called ‘wellness’ genes. It should be noted, however, that several other initiatives to parse the genomes of centenarians are already underway. For example, Complete Genomics and Scripps Health announced earlier this month that they will collaborate on a project to sequence the genomes of 1,000 ‘wellderly’ individuals.  

Nevertheless, the organizers and administrators of the new-look X PRIZE are excited about the prospects of revealing best practices in genome sequencing, annotation and interpretation.  

 “While many new technologies have been developed over the last decade and many human genomes have been sequenced, there is still no technology that can produce a highly accurate, reproducible human genome usable for diagnostics and medical treatment,” said Venter, who co-chairs the competition. “We believe this competition will be the impetus to truly usher in the era of personalized medicine.”  

 “Sequencing the genomes from 100 centenarians… is an exciting prospect that will advance medical research,” said Robert Weiss, vice chairman and president of the X PRIZE Foundation. “The results will likely be the most accurately and completely sequenced set of human genomes ever assembled, empowering scientists around the world to conduct powerful bioinformatics research that can help unlock the secrets of healthy aging.”  

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    While this will tell us more about longevity, it's likely to be more complex than just the genes - however, at the very least it could drive down the cost of whole genome sequencing. We've written about it at Genome Engineering www.genome-engineering.com/archon-genomics-x-prize.html

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