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Contest to sequence centenarians kicks off
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投稿者 MR 日時 2012 年 7 月 25 日 13:37:21: cT5Wxjlo3Xe3.
 

Contest to sequence centenarians kicks off

First entrant pins hopes on semiconductor technology.


Monya Baker
23 July 2012

A poster used to recruit DNA donors.
X PRIZE FOUNDATION
 
The first competitor has swaggered up to the starting line for a contest that aims to push the limits of genome-sequencing technology. The X Prize Foundation of Playa Vista, California, is offering a US$10-million prize to the first team to accurately sequence the genomes of 100 people aged 100 or older, for $1,000 or less apiece and within 30 days. Ion Torrent, part of Life Technologies of Carlsbad, California, believes that its semiconductor-based technology gives it a shot, and on 23 July it announced that it will compete.

The Archon Genomics X Prize competition, to be held in September 2013, is intended to spur technology, boost accuracy and drive down costs ― currently $3,000–5,000 per genome. Peter Diamandis, the X Prize Foundation’s chief executive, says that the contest will help to establish a standard for a “medical grade” genome, with the high accuracy needed to diagnose or treat a patient. Eventually, says Michael Snyder, a geneticist at Stanford University in California, “I do see a world where you’ll have a funny-looking mole and they’ll pull that off and want to sequence its genome.”

The contest will also test the claims that sequencing companies have made. “I call it the truth serum for the genome-sequencing field,” says genome maven Craig Venter, co-chairman of the competition.

Entries can be made until May next year, and organizers hope that the competition will be keener than in past events. An earlier incarnation of the competition, launched in 2006, drew several registrants, but none came close to winning.

This time, the X prize Foundation has relaxed the time frame, allowing competitors 30 days ― rather than the 10 specified by the 2006 contest ― and focused on centenarians, who might carry gene variants promoting longevity. The winning team will be the first to sequence all 100 genomes to 98% completion, with less than one error per million base pairs, and to determine which variants appear on which of the paired chromosomes. In case there is no outright winner, lesser ‘best in class’ awards are on offer. “It would surprise me if one team gets all of the criteria,” says Kevin Davies, editor-in-chief of Bio-IT World and author of the book The $1000 Genome (Free, 2010).

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Ion Torrent believes that its edge will come from its technology, which measures a tiny change in pH each time a specific base is added to a growing DNA strand. Most sequencing technologies rely on light emitted as bases are incorporated, which requires higher built-in costs for optical equipment.

Davies regards Oxford Nanopore Technologies in Oxford, UK, as a potential rival. Earlier this year, the company said that it would soon be able to sequence a human genome in 15 minutes. Its technology threads a DNA strand through a nanometre-scale hole and senses each base as it passes through. But the company would not say whether it intends to enter the competition. Spokespeople at the sequencing-services companies BGI in Shenzhen, China, and Complete Genomics in Mountain View, California, said that the firms had not yet decided whether to enter.

Clifford Reid, chief executive of Complete Genomics, worries that it will be difficult for the judges to assess the accuracy of the newly sequenced genomes. “The technologies participating in the competition are the only technologies for judging the competition,” he says, adding that he is hopeful that contest organizers can come up with “a clever solution that makes everyone happy”.

Although the contest will reward technological prowess, Venter says the key challenge is not amassing sequence, but understanding what it means for biology and medicine. “The trivial part of the equation to solve is the sequencing technology,” he says. “It’s necessary, but not sufficient.”

Nature 487, 417 (26 July 2012) doi:10.1038/487417a
Related stories and links
From nature.com
Nanopore genome sequencer makes its debut
17 February 2012
Functional genomics: The changes that count
08 February 2012
The new date, new format, new goals and new sponsor of the Archon Genomics X PRIZE Competition
27 October 2011
Blogpost: The $1,000 genome: are we there yet?
From elsewhere
Archon Genomics X Prize
http://www.nature.com/news/contest-to-sequence-centenarians-kicks-off-1.11053  

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