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X-Prize to Award $10M for Fast Sequencing

timothy posted more than 7 years ago | from the prizes-for-possibilities dept.

48

Shipud writes "The X-Prize foundation has announced the $10 million Archon X PRIZE for Genomics — for the first privately financed group to sequence 100 human genomes in 10 days. The motivation is to create an incentive for faster, cheaper genome seqeunceing, heralding the era of preventative personalized medicine. The winner will also receive an extra $1,000,000 for sequencing the genomes of 100 additional people; among them Larry King and Stephen Hawking. Apparently this is the largest medical prize in history."

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48 comments

Dupe (4, Informative)

Kazzahdrane (882423) | more than 7 years ago | (#16420903)

This was already covered by /. http://slashdot.org/article.pl?sid=06/10/04/151323 6 [slashdot.org] 9 days ago.

That means (1)

jeffmeden (135043) | more than 7 years ago | (#16422107)

Slashdot only has one day left to dupe this another 98 times if they hope to claim the prize...

TFA? Whats that?

Re:Dupe (1, Offtopic)

nyri (132206) | more than 7 years ago | (#16423439)

Good. Because last time the discussion was a disgrace. Let's hope this one will be better. I'm sorry for this off-topic rant but the state of slashdot is really bugging me.

I just read the last discussion. Two of the three score:5 comments were jokes. They weren't even very funny. First one was about Steve Ballmer and his chair throwing as if that thing isn't a cliche. The second one was obvious. It was about XXX-Price and "genetic material". You can figure the rest. It was pretty well writen. Hence, it was, at least, somewhat funny.

The one additional comment was about haves and have-nots. A decent comment that deserves a discussion. Well, where's the discussion. The whole story got 115 comments (and three score:5). This site is suposed to be "news for nerds, stuff that matters". At the moment the most commented article on the front page is a FUD posting about Vista's supposedly über-draconian EULA [slashdot.org]. One of the first score:5 comments [slashdot.org] goes as follows:
I just read through the entire EULA because I just couldn't believe they had included "Home Basic users can't copy ISOs to their hard drives". Turns out I was right. As far as I can tell there is no restriction to ISO's per-se, instead the original author was attempting to infer a lack of a right of some versions to store a copy of the software [meaning, a copy of the vista DVD] on "network storage" based on the fact that this right is permitted for Ultimate. However, just because they grant a right to some versions doesn't mean you don't have that right when it isn't explicitly granted - for instance even if they only enumerated the right to backup copies for Ultimate you'd still have that right for all others, existing law generally grants it.

The translation to "can't copy [any] iso's" happened in the last step, by the comment submitter, and is as far s I can tell just a complete fabrication.

Some part of me wonders why a website full of people who swear to their grave that they'll never run a piece of software is so intent on discrediting it that they make up shit. Carry on though boys, have fun.


Does people continue reading the comments, the story and posting more comments? Hell, yeah!! And does anyone bother to come and discuss about one of the most intresting new themes in our society, namely the coming of an age where every person's genetic makeup can and will be analyzed. It seems not.

Re:Dupe (1)

dsanfte (443781) | more than 7 years ago | (#16428861)

The IT types are not scientists. Most of them work tech support, some work in data centers, many are consultants. Comparatively few work as engineers in software or hardware. Fewer work at the bleeding edge of their fields.

Slashdot's target audience is, as a whole, uneducated with respect to molecular biology, genetics, and soforth. Most are pretty good with mathematics, but throw some advanced genetics at them and they will get lost in a hurry. It's just the way this site is.

Yeah (2, Funny)

joaommp (685612) | more than 7 years ago | (#16420971)

In China, they have the same competition. But then you win and they send the bill to your family.

Gattaca!!! (2)

javilon (99157) | more than 7 years ago | (#16421033)

Gattaca [wikipedia.org]

Re:Gattaca!!! (1)

DigiShaman (671371) | more than 7 years ago | (#16421999)

I was thinking the same thing the moment I read the headline. How long before such a device fits the size/profile of an inkjet printer? You just know potential employers and health insurance agencies will absolutely SWOON over such a product!

Do we have laws in place for genetic discrimination? If not, we should.

I don't know about the rest of Slashdot, but I don't recall the option of picking out my genetics prior to conception.

Re:Gattaca!!! (2, Insightful)

Teancum (67324) | more than 7 years ago | (#16424055)

There are laws against racial discrimination that could, with a good judge that is using his/her head, would also apply in this sort of situation as well in most cases. There certainly are racial characteristics that are mapped in DNA sequences. In fact, when DNA "profiling" is used for matching up parents with kids and in forensic evidence for like a police investigation, they specifically target those DNA sequences which are not related directly to specific racial profiles, but there isn't a law that says this absolutely must be the case.

The point here is that DNA sequencing researchers are very much aware of this issue, and the ethics and laws about this subject are not quite as unknown as you seem to apply. Still, if there were a database of genetic information, it would certainly be considered private medical information and could only be disclosed along similar kinds of laws as well.

Only $1,000,000 More? (1)

theshibboleth (968645) | more than 7 years ago | (#16421151)

So for your first 100 people you get $10 M. That's $100 K per person. Then you only get $10 K after that--and for sequencing the genes of people who have the greatest capacity to pay? Doesn't really seem to be worth the effort after the first hundred. I mean, isn't it worth at least $10,000 to those extra 100 people who would have their genes sequenced and possibly have great medical benefits because of that.

Re:Only $1,000,000 More? (1)

Xiroth (917768) | more than 7 years ago | (#16421393)

A million bucks is a million bucks. If they've already got it going, presumably it'd be worth it.

Re:Only $1,000,000 More? (1)

sillybilly (668960) | more than 7 years ago | (#16425759)

The real goal here is to be able to genetically analyze people, and not what the article claims, to help them. Like any tool, it can be used for good and for bad. Like any new technology, such as aviation, or nuclear, it will probably be first tested out by the military or at least tested out in all its negative connotations before it is put to work for public good. Such people-analyzing technology will allow a new form of racism, or at least some form of historical revenge-taking. How would you like to know that your genetic makeup is 26% of a genetic class #AA5FE most prevalent in lower Poland, Checz Republic, Northern Ireland and Southern Iran, then 32% is class #BY98Z most prevalent in southern Sweden, 5% class #CCXFE most prevalent in ancient Greece(from archeological bone-marrow extracts) but practically extinct (therefore you'll be heavily studied and bread with similar people containing this ancient Greek recessive gene to study the ancient Greeks better, especially by people who have an axe to grind with the ancient greeks), 2% class #FE3X2 of a gene most prevalent in North Korea and South America, etc. Imagine if you possessed a gene that's most prevalent in North Korea, Iran, Iraq, Libya (wait, Libya no longer belongs to this axis of evil group), imagine if such a gene was found that's most prevalent in the countries that happen to fall into the current axis-of-evil vogue category. Aha! We found the evil gene, now let's go find people that have it in the USA, and send them to camps like the japanese were in WW2. There'll be people looking for the callousness gene, the atheist gene, the deist gene, the child-molester gene, the communist-gene, the capitalist-gene, and try to put people to death based on it, in the name of the good of society, just like witches were burned alive at the stake for being found guilty of mingling with the devil. For fire has a purifying power, it cleanses your soul of your sins, and being burned alive is like passing through a purgatory on this earth, therefore your soul has a higher chance of entering Heaven instead of Hell in the afterworld, so people who execute you at the town square like this do it out of brotherly love, in the name of saving your soul from eternal damnation, while the crowd cheers on.


Sometimes I just don't wanna know "who" exactly I am, or where I come from, or where the other guy next to me comes from. It's enough of a divide that he looks different, such as he's black, but now we're gonna fine tune the difference seeking amongst people, and turn man against man not because one looks black the other white, or because even if they look the same, one is serbian the other croatian, now we'll be able to turn people against each other and have them exterminate each other even when they look the same, speak the same language, hold the same culture, but hey!, they are genetically different! So go fight, compete, push your "kind" higher, push other "kinds" lower, as opposed to the old your nation higher, other nations lower, now you'll be able to do it even within nations better! There are native americans on reservations studying in schools, and here and there there is a blonde kid amongst them, even though his parents are both indian-looking, but carry some blonde recessive gene from all the past intermarriages. This blonde kid may think himself as indian, even though he might have a hard time dealing with his looks standing out in a crowd. But even indian looking people are told today they are not indian. They are told, look, here's your bloodline, your great great great gramma married a black guy, so that made your bloodline 1/2 native american, then 3 generations later your great great granpa married an italian, so that made it 1/4, and so on, 1/8, 1/16, 1/32, 1/64, 1/128th. The treaties signed by Abe Licoln giving this land to native americans do not apply to you, because the government has a policy to stop considering you indian once your genetic makeup falls below 1/64th native american, and 63/64th other. So it doesn't matter that you love native american culture and way of life, and you feel like you belong, we can tell you for certain that you're not native american. Sometimes you just don't wanna know you're "not native american by blood", when you used to live happily believing you were, but now it's gonna nonstop keep lingering in the back of your mind. Oh well, good old days, because this knowing your genetic makeup fully days will come, inevitably come, and come soon, but I wouldn't seek it so avidly, offering prizes, I'd hold onto these sweet days as long as I can.


Such technology will allow people to stick themselves into genetic classes, then naturally such genetic classes may end up competing, with one class prevailing and all the other gone, then the class will more fully be analyzed and divided into subclasses, and then box! the fight restarts, until in the end there will be only one subclass of one class left, and so severe inbreeding that the whole human population might be one disease away from the brink of extinction. You think it wouldn't happen?

Re:Only $1,000,000 More? (1)

rjhall (80887) | more than 7 years ago | (#16428291)

your name is very appropriate.

We've known of the existence of bloodgroups for years, but I'm fairly sure nobody's been discriminated against on the basis of being O- or A+.
In fact, nobody really cares.

except the japanese. seriously. (ketsu eki gata).

Re:Only $1,000,000 More? (0)

Anonymous Coward | more than 7 years ago | (#16432139)

Go take a first year English course.

The biggest prize... (1)

InDi0 (691823) | more than 7 years ago | (#16421177)

The biggest prize in medical history... Why is it the biggest? Cause for the last decades, new medicine means BIG business. I wonder how good that is. My view is kinda biased. My roommate's in biotech. Seeing first hand his ethics and beliefs as a scientist, I am really reluctant in handing my future to scientists like him...

ok but (3, Interesting)

FateStayNight (1000465) | more than 7 years ago | (#16421185)

Stephen Hawking I can understand but why is Larry King included. What makes him worthy of having his genomes sequenced.

Re:ok but (1)

Martin Blank (154261) | more than 7 years ago | (#16423583)

Maybe they're looking for extreme examples of the population. Hawking represents some of the best, while King represents... the other end of the spectrum.

Typical Larry King interview:

Larry: Bob, did you kill your wife as the prosecution claims?
Bob: (covered in blood, holding an axe still dripping from the night's first guest, whose head has been chopped into an unrecognizable blob) No, Larry, of course not. I could never hurt a fly.
Larry: There you have it, folks!

Now, if they'd been going for the extreme end, they'd have asked for Geraldo's genome, but you have to set the minimum standards somewhere.

Re:ok but (1)

Princeofcups (150855) | more than 7 years ago | (#16424517)

> Stephen Hawking I can understand but why is Larry King included. What makes him worthy of having his genomes sequenced.

I would assume to get lots of TV exposure.

jfs

Re:ok but (0)

Anonymous Coward | more than 7 years ago | (#16429771)

he's a rich jew... what do you expect.

DNA RAR (1)

Konster (252488) | more than 7 years ago | (#16421391)

Welcome to DNA RAR. We have developed an exclusive peptide encryption method using random RNA sequences as hash key while pinching out false exclusives, just for yucks.

DNA RAR allows all of your genetic material to be encoded within an encryption program that is both free source code and open source.

All of this fucking harcore science for DMCA.

Woo!

Rules details (4, Insightful)

nyri (132206) | more than 7 years ago | (#16421455)

Rules are available in here [xprize.org].

In short:

100 human genomes within 10 days or less with an accuracy of no more than 1 error in 10,000 base pairs, with sequences accurately covering at least 98% of the genome, and at a demonstrated cost of no more than $10,000 per genome.


An intresting detail:
During each X PRIZE competition test, a TEAM must use its device to sequence within 10 days 100 human dip-
loid genomes of 6 Gbp (6 giga base pairs, i.e., six billion pairs of DNA base molecules) each.


Note that Human Genome Project mapped and sequenced only some 3Gbp. And that was considered to be whole genome. Basically X-Price want winner to sequence all 46 cromosomes. This sounds quite difficult as the method have to be sure that is has sequenced both of the cromosomes (from a pair), not just the other one twice. And this must be valid all the 3Gbp. By bet? The working method just sequences emultiple chromosomes and determines the exact basepairs statically.

Re:Rules details (2, Interesting)

wikdwarlock (570969) | more than 7 years ago | (#16423361)

I think what's more interesting is that they want the sequences to be 98% accurate, but according to a national geographic report I found here [nationalgeographic.com] chimps and humans are only 4% different anyways. So they only want an accuracy of half the difference between people and chimps? What's the genetic similarity between Stephen Hawking and Larry King? Probably 99% or more.

Edification of Sequencing Data and Error Rates (1)

nodrogluap (165820) | more than 7 years ago | (#16424249)

With regards to this post, and the following post about 98 % coverage.

The quality (i.e. the error rate) must be 0.01%, which is the convention adopted as the Bermuda Standard back when large scale sequencing was becoming mainstream, and the first genomes (of bacteria) were being produced. The coverage must be 98%. Usually, the last 2% are virtually impossible to elucidate because they are so repetitive (e.g. around centromeres) that you cannot tell how many copies of the repeats there are. The repeat regions are much larger than the contiguous sequences of about ~1000 bases you get from the sequencing machine "reads", so unambiguously assembling the overlapping reads becomes impossible. Luckily, the most useful data is in the 98% percent that is easier to sequence.

With regards to the 6GB, the human genome project has sequenced much, much more than 3GB. What you end up with is an assembly of the sequence into 3GB based on the consensus of the genomic DNA used (they did not do just one individual). The differences between the individuals are also recorded, largely as Single Nucleotide Polymorphisms (SNPs). These SNPs form the majority of the differences between the 2 copies of chromosomes (23*2) we all have.

On a technical note, all of the new techniques that are being commercialized for very high throughput sequencing (e.g. 454) rely VERY heavily on computer power to assemble the results into meaningful, long sequences. If you though assembling the Human Genome Project would be a lot of work with its 1000 base reads, try assembling data from the new techniques, with their 100 or 25 base reads (depending on the technology you use). The less overlap you have between reads, the harder it is to resolve the assembly unambiguously...

Re:Rules details (1)

mlush (620447) | more than 7 years ago | (#16425397)

An intresting detail: During each X PRIZE competition test, a TEAM must use its device to sequence within 10 days 100 human dip- loid genomes of 6 Gbp (6 giga base pairs, i.e., six billion pairs of DNA base molecules) each.

Note that Human Genome Project mapped and sequenced only some 3Gbp. And that was considered to be whole genome. Basically X-Price want winner to sequence all 46 cromosomes. This sounds quite difficult as the method have to be sure that is has sequenced both of the cromosomes (from a pair), not just the other one twice. And this must be valid all the 3Gbp. By bet? The working method just sequences emultiple chromosomes and determines the exact basepairs statically.

Its not just 'difficult' I think thats going to delay a winner untill the inflation reduces the prize to pocket change. Its not that it doubles the amount of sequenceing that needs tobe done. To do this meaningfully you would need to sequence the maternal and paternal chromosomes Given that chromosomes differ by one base in 1000 you can't just mix them up and assign them stastically.

I suspect the best bet would be so sort out single chromosomes the use some sort of Whole Genome Amplification [wikipedia.org] to get sufficent DNA for sequencing. Sequencing single chromosomes has other advantages, it greatly simplifys the assemmbly process and brings the problem into the theoretical range of 454 sequencing [wikipedia.org]

The Future of Medicine (1)

skrew (111096) | more than 7 years ago | (#16421517)

In modern America, researchers search for cures to genetic disease in Soviet Russia, the party cures your genetic defect called life...by sending you to the gulag for "research"

Additional price? I call bullshit (1)

nyri (132206) | more than 7 years ago | (#16421523)

The winner will also receive an extra $1,000,000 for sequencing the genomes of 100 additional people; among them Larry King and Stephen Hawking.


I've been browsing the site now for some time and haven't found a single shread of evidence for this "extra price". I call bullshit. It's just a joke to mock the slashdot "editors".

Re:Additional price? I call bullshit (1)

eightball (88525) | more than 7 years ago | (#16422645)

I wondered about this before but I think I have it. In section 1.5, there is a limit of $10,000 cost per genome on average. In section 1.21, they state that they will pay a fee at actual cost per genome determined by the judge (nb this presumably may actually be less that $10,000). Hence, a maximum of $1,000,000.
It also seems that if you refuse the 'bonus', you may be penalize by twice that amount from the initial prize.

rules here [xprize.org]. Thanks nyri [slashdot.org]

My money (1)

espressojim (224775) | more than 7 years ago | (#16421577)

My cash is on CodonDevices. George Church has an incredible new sequencing technology, and he's making it open source. I know some of the peeps there writing software, and between the tech and the IT team, they'll be able to generate and handle the data - the big sequencing companies ought to be scared...

okay (1)

kdachev (471319) | more than 7 years ago | (#16421607)


Well, I usually hate to repeat myself but: ...here it is - I've decoded them! Gimme the money!!

And, now - give me the next 100. No probs! Next one, please.

Worthy, but (1)

B1ackDragon (543470) | more than 7 years ago | (#16421685)

Too bad the sequencing research these days is not so much focusing on fast sequencing (though that is of course still a major concern), as it is on accurate sequencing. One of the problems bio-folk are encountering is that the human genome is relatively easy to sequence: you can get all your DNA from one individual (so you only need to worry about getting two unique DNA sequences getting mixed up in the final result, one from the male and female parents) and there isn't as much repetition as compared to say, mosquito genomes. Further, when studying things like mosquitos, the shotgunning techniques currently need to use DNA from whole portions of a population, say 50 or more individuals (AFAIK), so your final result doesn't really represent any one member; a lot of useful information is lost this way.

Anyway, just my semi-educated two cents. I'm CS, so what do I know? Well, I'm told it's NP hard, so... good luck with getting that 10 Mil and still having an accurate result.

This is basically a joke... (2, Insightful)

JDevers (83155) | more than 7 years ago | (#16422507)

any true revolutions at a company or other entity that allows this level of an improvement over current sequencing tech will have so much VC money (or parent company cash) rolling in that $10 million won't even be worth the time for application. Then when the tech is validated and ready for use, they wouldn't have time to cash the check for $10 million while the billions are rolling in.

For those of you in other fields, imagine in the next jet propulsion X prize was $10 million to the first group to come up with a working drive capable of 20% of the speed of light within a day of ignition. Or how about a single computer CPU capable of processing 100 peta flops. Or a system capable of cracking a gallon of water but using only 100 joules of electricity.

Sure, some day these may all be possible, but right now they are pie in the sky at best.

The way this will really work.. (1)

Unequivocal (155957) | more than 7 years ago | (#16423977)

They'll try to make a super baby from the 100 people and it'll get the brains of Larry King and ALS from Hawking..

Reminds me of a George Bernard Shaw quote (mis-attributed sometimes to Einstein I think). When it was suggested to him by a beautiful woman that they could make super-babies together, he replied:

"But what if they had my looks and your brains?

What exactly does this mean? (0)

Anonymous Coward | more than 7 years ago | (#16425499)

Can someone explain what genome sequencing actually does? Does it "simply" give you a complete description of the base pairs of someone's DNA? Or is it a little more complicated than that, telling you where the individual genes begin and end? What information can you derive when you know the sequence of all the base pairs? How does genome sequencing differ from the mapping of the genome? As I understand it, the mapping of the human genome was completed a while back, but I have been able to find a decent answer about what that actually means, or what the significane of that is.

Wikipedia and a quick Google search ended up being worse than useless for getting any answers; the Wikipedia sequencing article is like any of the quantum mechanics articles in that it counterintuitively assumes the reader has a firm grasp of the underlying principles and concepts.

Re:What exactly does this mean? (1)

Shipud (685171) | more than 7 years ago | (#16430271)

Can someone explain what genome sequencing actually does? Does it "simply" give you a complete description of the base pairs of someone's DNA? Yes. Actually, even less than that. "Shotgun" sequencing give you a collection of random seqeunces of base pairs, ~1,000 BP long. You need quite a few of those to reassmeble the human genome, computationally. Or is it a little more complicated than that, telling you where the individual genes begin and end? What information can you derive when you know the sequence of all the base pairs? To determine that, you need to perfomr a computational analysis on the assembled (see above) genome. Gene prediction algorithms are relatively relaible, although there is room for improvement and error reduction. You can derive a lot of information, depending on how sophisticated the algorithms that your use are, and how much of an error margin you allow yourself: the beginning and end of genes, region that control gene transcription (that's copying DNA to RNA) and gene translation (that's RNA to protein), alternative splicing (differnt transcripts of the same gene). Once you have your translated protein sequences, you can do a lot more with that: predict their 3D atomic structure, look for similar proteins in other organisms, discover rates of evolution, detect hidden viruses in the genome, locate disease causing mutations....
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