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X Prize Foundation Encourages DNA Decoding
Carl Bialik from the WSJ writes "The X Prize Foundation, the group behind the $10 million prize for human space flight, 'plans to offer a $5 million to $20 million prize to the first team that completely decodes the DNA of 100 or more people in a matter of weeks, according to foundation officials and others involved,' the Wall Street Journal reports. 'Such speedy gene sequencing would represent a technology breakthrough for medical research. It could launch an era of "personal" genomics in which ordinary people can learn their complete DNA code for less than the cost of a wide-screen television.' But don't set aside that TV purchase just yet: Foundation officials don't expect the prize money to be claimed for five to 10 years."
Wouldn't it take more than the prize money to accomplish this task? If so, does this really give people incentive or am I missing something?
Thanks!
While there's no disputing that speedy, accurate genome sequencing will have a significant positive impact, being the pessimist I am, I can't help but dwell on the possible downsides:
Brave new world, indeed.
____
~ |rip/\/\aster /\/\onkey
check again ;)
Folks, make sure you obtain a large polythene sheet before "decoding" peoples DNA.
I tried it once and apart from a blood stained carpet, I'm serving 12 years for my trouble.
liqbase
I'm sure that the same companies who fire employees who dare to smoke on their own time would NEVER dream of sequencing the genes of employees and fire any who have a 2% change of heart desease. Oh no. That will never happen. And if it did, I'm sure that congress, who does not receive enormous donations from the companies, will pass laws that will protect us.
What about this screams, "good idea?!"
The usual problem with science reporting, particularly in biology. The article says "... the first team that completely decodes the DNA of 100 or more people ..." No; the prize winner will sequence the DNA. That is a looong way from "decoding" the human genome, or even the genomes of any particular 100 people. Sequence information is valuable, but it's not "decoded" in any meaningful sense of the word. Imagine looking at an enormous program written in a language you've just started learning, and full of function and variable names like "do_stuff()" and "x1".
The correlation between ignorance of statistics and using "correlation is not causation" as an argument is close to 1.
Personal genome or widescreen TV for some big-screen fragging?
:-)
DNA shmeeNA. BOOM! Headshot!
This is a $10 million prize for a several billion dollar technology. It'll be nice for sparking interest in the field, but it shouldn't make any more Celera Genomics-types. "The plan for a genomics X Prize fell into place last year after Google Inc. co-founder Larry Page joined the foundation's board and then recruited Dr. Venter to become a director." (Dr. Venter is the Vietnam vet who started Celera Genomics [comes from "Celerity"]) Well, that just took the idea from "unrealistic" to "unnerving." I see Google has decideed to keep its mission statement about "[organizing] the world's information and [making] it universally accessible and useful," despite having trashed it's "don't be evil motto." That's nice.
a= array('T','C','G',A');
for (j=0;$j100;$j++)
{
for (i=0;$i$num_genes_in_human;i++)
{
print a[rnd*4];
}
}
claim_prize();
What will they find first in the DNA? A Monsanto trade secret, or the DeCSS code?
my pet machine
ordinary people can learn their complete DNA code for less than the cost of a wide-screen television.
Coincidentally, once these ordinary people get their code sequenced, they find out that they have highly-evolved genetic tendencies for couch potato-ness, eating crunchy foods and better wide-angle vision.
He who knows best knows how little he knows. - Thomas Jefferson
Cheap and accurate gene sequencing in the hands of insurance companies could make it difficult for a person with a genetic predisposition to disease to obtain health or life insurance.
;) But seriously, if people want designer children they don't need to screen their mates, but rather take the genes and then alter them through whatever seems to produce the best kids. Chances are that most people post 2020 won't be mating with humans anyways (see Real Dolls with AI or true virtual reality) and population control will take care of it self.
Chances are with this level of technology, health concerns will start to be a moot point. Predisposed to being over weight or having cancer... Well why not just use gene therapy to fix that.
Cheap and accurate gene sequencing in the hands of corporations encourages said corporations to discriminate in their hiring practices on the basis of genetic predispositions to everything from coronary disease to psychological problems.
Gattica overhyping. Chances are you are more likley to get replaced by cheap foreign labor in the 2010s or non-organic workers (see robots or thinking computers) in the post 2020 era.
Cheap and accurate gene sequencing in the hands of people searching for a spouse could lead to rigorous screenings of prospective mates for evidence of genetic 'undesirability'.
Why even bother. Most people mate because they drink too much alcohol and forget protection
Cheap and accurate gene sequencing in the hands of governments could lead to governments investigating citizens on the basis of 'questionable genetic heritage'.
Well... They do that anyways without the technology by investigating people based on family relations. Chances are you should be more concerned whether these actions are preformed without a warrant/court order.
"I am the king of the Romans, and am superior to rules of grammar!"
-Sigismund, Holy Roman Emperor (1368-1437)
Is the prize for sequencing or for sequencing and assembling?
Some companies like 454 have got the technology to quickly sequence large genomes but assembling them is a completely different problem. And anyway we understand (roughly) about (roughly) 30% of the genes of any species that has been completely sequenced (mostly bacteria). I wish there was a prize for technics to annotate genomes accurately.
I'll do it for cheesy poofs.
So if it won't be claimed for five to ten years, nobody gets the money?
It says that the people must do it within a matter of weeks, and if it can't be done for 5-10 years, it can't be claimed.
while having my Wheaties, I poured the toasty goodies into a cereal bowl and out fell a cellophane wrapped prize. Wahoo, it was a secret DNA decoder ring... Yes, come to papa you lovely $10 million!
I just couldn't resist!
I lost my sig...
DNA decoding uses nano-technology and supercomputer, both of which are on Moore's law curve. This means costs decrease an order of magnitude every five years. So if it costs a million bucks to decode a mammal's genome today, it will cost $100 in 2025.
..because DNA doesn't come with an EULA. This kind of reverse-engineering is allowed!
the first draft of the human haplotype map (HapMap) is already done: http://www.hapmap.org/ for a short commentary see N Engl J Med. 2005 Oct 27;353(17):1766-8.
I know very little about the specifics of DNA sequencing, but everything I've read says that the genes that make individual humans different are less than 1% of the total.
So... you don't sequence the known quantity and just sequence the 1% that is different.
Venter's scientific enemies (like Lander and Sulston) have tried to convince the public that Venter aims to be the Bill Gates of biology. That isn't, and never was, true. You need to understand the history of Craig. He started out at NIH and then started the non-profit institute TIGR (where I work today) when the NIH was too shortsighted to support sequencing in the early 1990's. He joined Celera when it was clear the public effort wasn't using modern methods and would take forever to complete. Take a look at the public database Genbank. Do you know what person has the record for largest total contribution by nucleotide? Craig -- and even before the recent Celera genome deposit. For all their talk, neither Lander nor Sulston comes close. Do you know what Craig is doing now? He's running the J. Craig Venter Science Foundation, another non-profit institute similar to TIGR. (his ex-wife Claire Fraser is the current head of TIGR).
Venter can be a jerk sometimes (and is egotistical; who else would name their science foundation after themselves?) but look at the facts -- he gives data to the public, and is hardly the only scientist who has worked in both the private and public sectors.
It could launch an era of "personal" genomics in which ordinary people can learn their complete DNA code for less than the cost of a wide-screen television.
Fine, but why would I want to know my DNA sequence. It's fun to know off course, but usefull?
Sure, and if you have a fast disassembler, all software bugs can be immediatly fixed. Right?
The Tao of math: The numbers you can count are not the real numbers.
. . .when reading about the X-Prize Foundation rewarding all this work in DNA sequencing was:
"I guess they're doing that so it will be easier to identify and differentiate the remains of the tourists who get blown up while flying in experimental spacecraft."
Just part of a morning of disturbing thoughts. . .
This sig is a test. If this had been an actual sig, you would be reading something quite a bit wittier than this now.
supercomputer$> diff myDNA chimpanzeeDNA
supercomputer$>
D'Oh!
I wonder how many genetically perfect people there are? Would there be enough genetically perfect people for companies to hire, so that they could ignore the imperfect ones?
Chances are with this level of technology, health concerns will start to be a moot point. Predisposed to being over weight or having cancer... Well why not just use gene therapy to fix that.
There are only a few successes of gene therapy. Getting the minute details of human physiology is hard. The results from mouse metabolism studies do not always carry over to humans. Researchers are make some progress on understanding the basis of obesity (i.e., leptin, ghrelin, etc.) that lies beyond the obvious "overeating makes you fat". Stay tuned.
To-do List: Receive telemarketing call during a tornado warning. Check.
I saw it done on CSI!
I think this challenge is pointless. The race for speeding up genome sequencing has been going on for several years and this price will not change anything. It will not bring in new players and the ones that are already there are working fiercely on the problem anyway. Just this summer there were two different papers in Nature, I think, that introduced nano-scale sequencing techniques with a speedup of 100x compared to "traditional" techniques. The foundation should spend its prize money on some other noble goal where the rewards are not already so high.
Reality or nothing.
You know... that was a great post, because, yes, what you said is so true, i can see it coming 10 miles away.
Although you are right, my optimistic self cannot help but point the followings :
Cheap and accurate gene sequencing would help detect babies with genetic disorder before their birth, possibly allowing the correction of the defective genes prior to the baby's birth.
Cheap and accurate gene sequencing would most certainly be helpful curing uncurable diseases such as AIDS or Cancer
Cheap and accurate gene sequencing would allow a human with missing limbs to have new limbs created for him/her.
well, ive pointed out the three most obvious and i havent read article completely.
The point of my post is to illustrate that there isnt such a thing as a bad-only situation (or good-only). Any breakthrough will bring its share of pros and cons.
Did that ever stop us from advancing ? of course not! Especially in the medicine area. I mean, sure DNA sequencing isnt all that good, but put it this way. What if Pasteur had never created the vaccine ? lots of people would have died of course. But if he hadnt created the vaccine, our body wouldnt have learned to protect against those viruses and if the body hadnt learned to protect itself, the viruses wouldn't have mutated in even more virulent forms of viruses. Does that make us think that the vaccine is a bad thing ?
I think not.
If you look like your passport photo, you're too ill to travel. - Will Kommen
In the ten years it takes to develop "turbo-sequencing", we will have find that very little of the sequence will now NOT be copyrighted by some corporation. So any possible research "cures for what ail ya" will be slowed down by having to take the time to bribe the copyright owner.
"Love heals scars love left." -- Henry Rollins
Is there really a prize for this? I can show anyone how to sequence their entire DNA structure in a matter of minutes with some basic electronics. And NO I'm not talking about DNA matching for evidence, I'm talking about full blown DNA sequencing of a single strand. It's very easy. I don't understand how something like this could be overlooked... How do I claim the prize?
The assembling of sequences obtained from so called shotgun sequencing are hard to assemble, because you don't know where each piece of sequence belongs. (shotgun sequencing chops th DNA in random chuncks, isolates single chunks and sequences these) But once you know where a chunk belongs, and that is pretty easy if you have more than 1000 bases, you can just put it on the map. There will be viariation in the sequence as people do not have 100% the same sequence, but this is very small compared to the similarities.
This also shows that shotgun sequencing in this case is not the best approach, as you will waste resources with chuncks that overlap eachother (in the first sequencing this overlap will give you a welcome verification).
This would be my conservative approach: (I am not active in this field anymore): Determine candidate primer sites on the whole human genome some 1000 (or whatever the maximum readable sequencelengt is nowadays) A primer in this case is a short piece of single strand DNA that you use to make lots of copies of with PCR. You can use 1 of those primers to read the sequence per fragment.
There are ~3 billion basepairs in the human genome. If even if you could read say 3kbp in one run, you'd still had to do 1 million runs. That is certainly doable if you throw enough money at it, but not doalble for say 10K. The price of the raw reagents is just too high (many methods have been patented making it even more expensive)
So that leaves open two alternatives (or more?) Only sequence what you can connect to a phenotype (ie. some inherited disease). That is where to problem lies now, not the capacity to determine a DNA sequence.
Or get develop techniques that do not require large amounts of reagents per sequence determined. I think this would require nano technology, as you need to connect proteins to silicon. Maybe you could glue RNA or DNA polymerase to a chip and have the chip register what kind of base gets incorporated in the new strand. Put a lot of these mini detectors on a chip, add a few (mili)grams of raw bases and your sequence will be read.
But then again, right now we have nothing to actually interpret that data.
This space is intentionally staring blankly at you
The concept of being able to archiave my DNA is just so amazing that I am perfectly willing to wait 20 years before I can afford it. Not even having children offers this level of hereditary legacy. One day there may even be a library where everyone can submit their DNA for archive. It's very exciting.
--The universe will not be altered by forum threads, even those which are very wry. --Tycho Brahe (Penny Arcade)
I bet this could be accomplished with a reasonable cost using technologies like those provided by NimbleGen. They make custom DNA microarrays within weeks. They could pump out enough chips for 100 people's worth of DNA. This prize sounds like a good way to pump interest into DNA related sciences, and could spark new development.
patent != copyright, go to the bottom of the class.
How we know is more important than what we know.