By Kevin Davies
July 23, 2012 | Ion Torrent, the next-generation sequencing (NGS) platform from Life Technologies, is the first official entrant in the Archon Genomics X PRIZE competition, presented by Express Scripts, which is intended to catalyze the development of a clinical grade $1,000 genome technology.
The contest is provisionally slated to kick off on September 5, 2013 and last for 30 days. The $10 million purse will be awarded to the team that can sequence the genomes of 100 centenarians during that period for no more than $1,000 per genome, with a pristine accuracy of 1 error per 1 million bases and full phasing information.
|Jonathan Rothberg, Ion Torrent
“It would have cost $100 million and taken 33 years to meet this challenge when the competition was announced in 2006,” commented Ion Torrent founder and CEO Jonathan Rothberg. Rothberg says the Ion Proton instrument, which was unveiled earlier this year, “is designed to sequence a human genome for $1,000 in just a few hours. Semiconductor technology is transforming sequencing just as it has transformed every other industry it’s touched by driving research to ultimately improve health.”
Robert Weiss, vice chairman and president of the X PRIZE Foundation, welcomed Ion Torrent’s entry into the competition and hopes it will spur other sequencing companies to sign up by the May 2013 deadline. “We have been unwilling to compromise the criteria set for the Archon Genomics X PRIZE because the required levels of accuracy, speed and cost must be achieved to truly impact the field of genomics,” Weiss said.
“Ion Torrent’s registration and intention to compete is a dramatic statement about their commitment to delivering outstanding, ground breaking technology. They have thrown their hat in a ring that will hopefully soon include other companies vying for the prize and the chance to make history and revolutionize medicine.”
Grant Campany, senior director of the Archon Genomics X PRIZE, echoed Weiss’ statement. “I extend an open invitation to all the major sequencing companies and NGS start-ups to join Ion Torrent on September 5, 2013 and usher in a new era of medicine,” he says. The winner should be announced by the end of October 2013.
Last year, the X PRIZE organizers announced new rules for the competition to take into account the unforeseen advances in NGS technology, while still requiring high standards for medical-grade sequencing. The original rules when the contest was announced in October 2006 called for teams to sequence 100 miscellaneous genomes – Larry King and Stephen Hawking volunteered to participate – in just ten days for $10,000 or less. The ten-day time requirement would be a challenge even today, let alone six years ago.
With the new rules, teams must re-register for the competition. At least eight teams had previously registered for the competition, including Life Technologies and a few lesser known entities.
In the event that one team does not meet all three best-in-class criteria – accuracy, completeness, cost -- the competition will grant three separate purses, providing the entrants also meet minimum criteria across the board. Another subtle change was that, rather than hold the contest the moment a team declared it was ready to meet the contest guidelines, the organizers elected to set a firm date for the competition. The initial target was early 2013, but that has now been pushed back to September 2013.
The contest also announced sponsorship from Medco, the pharmacy benefits management company that has since been acquired by Express Scripts. This resulted in the decision to recruit 100 centenarians -- among them is the world’s oldest person, Besse Cooper, who turns 116 next month -- to be the subjects for the sequencing competition. Campany says the sequence data from the “100 over 100” will be made publicly available through a resource such as dbGaP.
In the run-up to the competition, the organizers are working with NGS specialists EdgeBio and other parties to develop a validation protocol. “The competition aims to define a medically actionable genome and provide an objective methodology to validate each team's performance against these criteria,” says Campany. “The validation protocol is our methodology to measure performance against our quality standards.”
The first draft of the protocol was created 18 months ago. Campany says EdgeBio presented the most compelling response to the Foundation’s request for proposals for a vendor to help provide the wet lab and bioinformatics support to fulfill the project.
EdgeBio CEO Justin Johnson says the validation approach involves identifying the appropriate partners, samples, standards, and open-source tools, including the creation of a scoring pipeline. Partners include the National Institute of Standards and Technology (NIST), Brad Chapman (Harvard), and Gabor Marth (Boston College).
EdgeBio will be performing in-depth sequencing on thousands of fosmid clones from two publicly available genome samples (NA 12878 and NA19239) using Illumina, SOLiD and Ion Torrent platforms. “We consider them the answer key,” says Johnson.
That will be the first of a three-phase program, which will develop and refine methods for sequence bias removal (each NGS platform has its own inherent bias) and software development.
Ed. Note: Further details about the AGXP validation protocol can be found at the following URL: https://edgebio.atlassian.net/wiki/display/AGXPPUB/01.+Introduction+and+Overview
A recent Bio-IT World webinar featured Campany, Johnson, and NIST’s Marc Salit discussing the validation protocol: http://www.bio-itworldsymposia.com/Bioitsymposia_Content.aspx?ekfrm=116674