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The 1000 Genomes Project

kdawson posted more than 6 years ago | from the reaching-for-statistical-significance dept.

Biotech 95

jd writes "An international consortium of specialists in genetics has announced the 1000 Genomes Project, in which at least 1,000 people from around the world will have their genomes fully sequenced as part of an effort to discover the relationship between genetics and disease. At present, over 100 regions of DNA are known to be related to illnesses, but the maps that exist are vague and are drawn from an extremely small population pool. According to the article, this results in the need for slow, expensive, and laborious studies to pinpoint causes, especially for rarer conditions. This project aims to find conditions that might only appear once in every 2,000 people (though how they intend to do that with half that number is unclear). The researchers hope to massively speed up the diagnosis of genetically linked illnesses and to improve the reliability of such diagnoses."

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Chinese (2, Informative)

Anonymous Coward | more than 6 years ago | (#22150352)

I wonder why there's so much funding coming from China for this project.
You can see the list of all participants (including funders) here [1000genomes.org] .

Re:Chinese (2, Informative)

Ajehals (947354) | more than 6 years ago | (#22151216)

The three countries with groups funding this are The US, China, and the UK, (although there is no indication of the proportion of funding being supplied by which), in each case the funding is being provided by organisations that exist to further science, in some cases specifically genome research. If you look at the other elements of the study you will see that pattern repeated, so I guess it is a case of (in the words of Jim Hacker) "great nations working together to answer the great questions of our age...".

Why you singled out China is surprising, especially given the rate of growth their economy is showing and the sheer number of graduates in the sciences that China produces each year (educated at home and abroad), unless of course you are suggesting that there is some ulterior motive that we should be ascribing to China.

I think it is great to see funding coming from multiple nations, working together, especially given how this kind of research should benefit all of us in the long run, it shows that countries that can afford it are still putting money into research (something that you wouldn't believe if you read some of the science related news in the media). Although I must say I am beginning to get concerned with the level of hostility and suspicion being levelled at certain members of the international community, it is reminiscent of the the suspicions between east and west during the cold war, I had hoped that now that is over we could start to see real global co-operation ans opposed to confrontation and competition (although competition may well be beneificial).

Re:Chinese (1)

The Spoonman (634311) | more than 6 years ago | (#22153352)

Why you singled out China is surprising, especially given the rate of growth their economy is showing and the sheer number of graduates in the sciences that China produces each year

Agreed, folks in the US seem to think they hold a monopoly on scientific acumen, when in fact, our hold isn't "slipping", it's passed into "slipped". Other nations have been rocketing past us in terms of not only scientific growth, but social and financial as well. The people in the US are told on a daily basis that they live in "the greatest country in the world", and believe it totally. At our current pace, it's only going to be a few more years before mothers in China will be saying "there's kids starving in the US, do you want me to send your dinner to them?!"

Oh, wait, that's right, in the land of plenty, there's already kids starving every day. My bad, sorry. Got caught up in the provincialism. China, little help?

Re:Chinese (1)

Gospodin (547743) | more than 6 years ago | (#22165784)

Listen, John Edwards, I know the campaign isn't working out too well for you, but you're not going to save it by posting on Slashdot.

Re:Chinese (1)

CrazedWalrus (901897) | more than 6 years ago | (#22160662)

I had hoped that now that is over we could start to see real global co-operation ans opposed to confrontation and competition


You must be new here.

Selection (5, Insightful)

mastershake_phd (1050150) | more than 6 years ago | (#22150358)

This project aims to find conditions that might only appear once in every 2,000 people (though how they intend to do that with half that number is unclear).
 
Well, they could sequence the DNA of people known to have rare diseases.

Re:Selection (0, Troll)

jd (1658) | more than 6 years ago | (#22150406)

That rules out discovering what causes some people to become lawyers.

Instead (1)

Smordnys s'regrepsA (1160895) | more than 6 years ago | (#22150496)

They'll probably pick *prime* examples out of the areas, trying to find the genetic norm for the population, then weed out what may be "normal" in the problem regions. In other words, it looks like they're searching to redefine the ranges of "normal"

of course, IANA Genetic Researcher

Re:Selection (2, Informative)

Arthur Grumbine (1086397) | more than 6 years ago | (#22150520)

Unfortunately, I think their sensitivity to peoples' privacy will prevent them from doing just what you suggested.

From TFA:

These people will be anonymous and will not have any medical information collected on them, because the project is developing a basic resource to provide information on genetic variation. The catalog that is developed will be used by researchers in many future studies of people with particular diseases.

Re:Selection (1)

budgenator (254554) | more than 6 years ago | (#22151680)

I don't know why everyone is so sensitive about Scientists and Medical Professional have access to your medical information, the real problem is usually the high school educated billing clerk in the basement of the hospital or your insurance company. If a hospital told the average six-pack Joe that they'd rebate half his co-pay if he let them send in his medical info and DNA for research and longitudinal study he'd jump at it.

RTFA (3, Insightful)

RML (135014) | more than 6 years ago | (#22150752)

There are other projects that sequence the DNA of people known to have rare diseases such as cystic fibrosis, and there are projects that sequence the DNA of people with common diseases like heart disease, but we don't know much about the variants in the middle that are neither very common nor very rare. This is an attempt to fill in that gap in our knowledge.

Rare Conditons (4, Informative)

MassiveForces (991813) | more than 6 years ago | (#22150776)

Finding diseases that eventuate in 1 in 2000 people with a genomic study of 1000 people is entirely possible... with one thousand people you have two thousand sets of genes. Since most genetic diseases are caused by two of the same recessive alleles (usually resulting from broken genes) in a single haplotype there would be lots of carriers; those with a single disease allele that could be spotted as a major deletion relative to the genomic reference sequence.

Re:Selection (1)

sorak (246725) | more than 6 years ago | (#22152592)

IANA Scientist, but the article seems to portray it as if they are simply trying to make a catalog of what normal variations exist.

But, there is one part that still does confuse me. From TFA:

These people will be anonymous and will not have any medical information collected on them, because the project is developing a basic resource to provide information on genetic variation.

Wouldn't it make much more sense to have a detailed listing of their medical history? For example, if one of those people has Alzheimer's disease (or any disease with a possible genetic connection), then that would be an interesting little footnote to have in the documentation.

Re:Selection (1)

Toonol (1057698) | more than 6 years ago | (#22154608)

Using 1,000 samples, won't you get about half of the conditions that occur once in every 2,000 people? For that matter, won't you get 0.1% of those that occur once in a million? There are a lot of conditions out there.

No niggers, please (-1, Troll)

Anonymous Coward | more than 6 years ago | (#22150390)

Let's keep this project "pristine," if you know what I mean.

Ron Paul

Re:No niggers, please (0)

Anonymous Coward | more than 6 years ago | (#22150412)

i didn't think Republicans believed in genetics..

Re:No niggers, please (0)

Anonymous Coward | more than 6 years ago | (#22151364)

Genetics?

Hell, most of them believe in eugenics!

Re:No niggers, please (0)

Anonymous Coward | more than 6 years ago | (#22151686)

yeah, but they can't actually pronounce it.

1 in 2000 people (5, Informative)

rsidd (6328) | more than 6 years ago | (#22150392)

This project aims to find conditions that might only appear once in every 2,000 people (though how they intend to do that with half that number is unclear)

Let's try to make it clearer, then.

The probability that a given condition appears in an individual is 1 in 2000, or 0.0005. The probability that it does not appear in that individual is 0.9995. The probability that it does not appear in any of 1000 individuals is 0.9995^1000 = 0.6 approximately; and the probability that at least one of the 1000 individuals has it is 0.4. Not bad at all. (If you used 2000 people, the probability that at least one of them would have it would improve to about 0.6.)

Suppose you aren't interested in just one conditions, but in lots of conditions -- say, ten of them. The probability that at least one individual would have at least one of those conditions is 1 - 0.9995^(1000*10) = 0.993 == ie, practically certain.

They really ought to teach basic probability theory in schools...

Re:1 in 2000 people (5, Insightful)

nacturation (646836) | more than 6 years ago | (#22150562)

This project aims to find conditions that might only appear once in every 2,000 people (though how they intend to do that with half that number is unclear)

Let's try to make it clearer, then.

The probability that a given condition appears in an individual is 1 in 2000, or 0.0005. The probability that it does not appear in that individual is 0.9995. The probability that it does not appear in any of 1000 individuals is 0.9995^1000 = 0.6 approximately; and the probability that at least one of the 1000 individuals has it is 0.4. Not bad at all. (If you used 2000 people, the probability that at least one of them would have it would improve to about 0.6.)

Suppose you aren't interested in just one conditions, but in lots of conditions -- say, ten of them. The probability that at least one individual would have at least one of those conditions is 1 - 0.9995^(1000*10) = 0.993 == ie, practically certain.

They really ought to teach basic probability theory in schools...

Your post is like that scene in Indiana Jones with the guy making some really impressive sword moves, looking all menacing... while Indy just pulls out his revolver and shoots him. You could get a whole room full of geeks cranking numbers and arguing over how many people they would need to find in order to exceed a particular probability that any one participant has Lou Gehrig's disease, while a simpler person would leave the room, come back the next day, and say "Hey guys, meet my neighbor Bob... he has Lou Gehrig's."
 

Re:1 in 2000 people (1)

giorgist (1208992) | more than 6 years ago | (#22150750)

Or in other words, to avoid Indiana Joannes references, ... gather a whole heap of people with interesting conditions and sequence them. G

Re:1 in 2000 people (2, Funny)

jd (1658) | more than 6 years ago | (#22150818)

Or, in other words, Indy's companions are always arguing and therefore geeks.

Re:1 in 2000 people (1)

secretwhistle (1116881) | more than 6 years ago | (#22150862)

Or, in other words, Indy's companions thought archaeology was a genteel profession and are dismayed to find guns and swords entering the picture frequently.

Re:1 in 2000 people (2, Funny)

El Yanqui (1111145) | more than 6 years ago | (#22151644)

They really ought to teach basic gun and sword fighting in school.

Re:1 in 2000 people (1)

Threni (635302) | more than 6 years ago | (#22151732)

> Your post is like that scene in Indiana Jones with the guy making some really impressive sword moves, looking all menacing... while Indy just pulls
> out his revolver and shoots him. You could get a whole room full of geeks cranking numbers and arguing over how many people they would need to find
> in order to exceed a particular probability that any one participant has Lou Gehrig's disease, while a simpler person would leave the room, come
> back the next day, and say "Hey guys, meet my neighbor Bob... he has Lou Gehrig's."

Not really - Indiana Jones' response to the sword wielding guy is devestating, whereas disturbing Bob's coffee proves nothing.

Sad, but true. (1)

occidentaltourist (948527) | more than 6 years ago | (#22153048)

The simpler person would completely miss the point. Indy's shot would miss, and he would be slain -- by his undiagnosed malignant brain tumor, and not by the man with the sword, who was engaged in mind-focusing techniques in preparation for performing surgery.

Re:1 in 2000 people (1)

Methuselah2 (1173677) | more than 6 years ago | (#22153184)

Way to go, Indy!

But two things in the original post triggered a bell:
"...over 100 regions of DNA are known to be related to illnesses, but the maps that exist are vague and are drawn from an extremely small population pool. According to the article, this results in the need for slow, expensive, and laborious studies to pinpoint causes..."

1. "Related to illness" doesn't mean causes illness. If successful, the temptation will be to say, "Oh, you've got a predisposition" to the illness, and stop there, instead of seeking further info, like, "Do you drink more than 10 cups of coffee a day, and do you exercise regularly?" While the potential is good for help in screening, the potential to "save money" by simply looking at a gene may prove too tempting in a for-profit health care industry, resulting in potentially less advice, other than to change their DNA, to those predisposed to the illness.
2. The quote implies that gene sequencing 2,000 people, and then viewing the DNA of patients will be faster and less expensive. I'm not entirely sure that will be the case. (And, if, "change your DNA" is the only suggestion, I suspect changing one's DNA might be a tad more expensive too!)

Re:1 in 2000 people (2, Insightful)

Ignis Flatus (689403) | more than 6 years ago | (#22150586)

they really ought to teach basic genetics in schools.

you neglect the fact that each person has two sets of genes, one inherited from their mother, the other from their father. that brings the total number of genes to 2000 sets. and it's also likely they're interested in many more than ten conditions. so you should think more in terms of a probability density function of conditions found versus their rarity.

Re:1 in 2000 people (2, Informative)

Cassius Corodes (1084513) | more than 6 years ago | (#22150610)

I thought this too (two sets of genes) - but its useless if they find a gene for a rare disease in a person if its not expressed (and hence not detected by the researchers). Hence having two sets of genes does nothing but complicate things further (as they now have to find which particular gene out of the two is the one causing the problem).

Furthermore another issue is that the genome is one huge causality network - for all but the most simplest disorders you'll need to have a cascade of genes to get a particular outcome - which increases further the number of people they need to detect disorders.

Re:1 in 2000 people (1)

Ignis Flatus (689403) | more than 6 years ago | (#22150716)

well, that's what computers are for, sifting haystacks. and surely they're interested in far more than just rare diseases. most all of us end up taking a handful of pills by the time we're 65. cardiovascular disease, cancers, and dementia are where the money's at.

Re:1 in 2000 people (1)

cheater512 (783349) | more than 6 years ago | (#22150802)

Google could get in on this.

Knowing them they would attack the problem at right angles to how its normally tackled.
Just like how they made their translation service by feeding stacks of data in to a probability engine to get a extremely accurate translator, they could throw in tons of genetic data and out will pop the answers with pretty good accuracy.

These sorts of problems are ideal for brute force techniques like that.
Only problem is you need one of Google's datacenters to do it properly.

Re:1 in 2000 people (2, Interesting)

jd (1658) | more than 6 years ago | (#22150830)

I'm not convinced it's coincidental that Google's research space was announced shortly before this project. I suspect Google is/was thinking along very similar lines. BLAST may be adequate for many things, but GoogleBLAST would be about what it would take to crunch any significant collection of entire human genomes.

Re:1 in 2000 people (1)

foobsr (693224) | more than 6 years ago | (#22151100)

one huge causality network ... you'll need to have a cascade of genes to get a particular outcome

And if you, on top, follow the idea that physical conditions (starting at the molecular level, INGBER [childrenshospital.org] ) are a major determinant of gene expression you might eventually come to your own conclusions regarding the value of simply linking 'the genome' to conditions of ill health.

CC.

Re:1 in 2000 people (1)

budgenator (254554) | more than 6 years ago | (#22151776)

You do realize that genomic data is extremely noisy; they take the DNA and break it into pieces that start with a known sequence of base pairs and end with a known base. Then the problem is to reassemble the broken pieces into the most likely way that is not the only way. It's like putting together a jigsaw puzzle that has pieces missing, extra pieces present, wrong pieces that go together and no picture on any of the pieces.

The first pilot will involve sequencing the genomes of two nuclear families (both parents and an adult child) at deep coverage that averages 20 passes of each genome. This will provide a comprehensive dataset from six people that will help the project figure out how to identify variants using the new sequencing platforms, and serve as a basis for comparison for other parts of the effort.

That means the are going to sequence the the genomes of 6 people 20 times each to be sure they get it right.

Re:1 in 2000 people (1)

kabocox (199019) | more than 6 years ago | (#22152720)

they really ought to teach basic genetics in schools.

Um, they did back when I went to high school. What they really need to do is do a better job of teaching stat math so terms like 1/X won't confuse those that made it through high school educated people when the sample size is smaller than X.

In college, you learn most stats, polls, and surveys are just plan lies to push you in the desired direction.

Not quite... (2, Insightful)

hung_himself (774451) | more than 6 years ago | (#22150698)

It's sort of right. Usually the phenotype will be recessive - so two bad copies need exist for the condition to be seen but only one bad copy needs to exist for it to be a useful sequence. For example, although the frequency of cystic fibrosis in Caucasians is 1/400, but the allele frequency is 1/20. So you need to look at the square root which gives you much higher probability of a hit. (BTW, the frequency in Asians is I believe on the order of 1/500,000 so CF could be cured simply by outbreeding - and no - that never worked for me as a pickup line...)

Note, that you don't necessarily need to have a visible phenotype for the sequence to be useful. You might have a marker already from previous studies to allow you to identify a single bad copy.

Re:1 in 2000 people (1)

ewanb (18483) | more than 6 years ago | (#22150702)

Also, don't forget that each person has two haplotypes, one from each parent, so
when one sequences a person, one captures the variation on two human genomes at once.

Of course, this all relies on the coverage you sequence at, and one option for
the 1,000 genomes project is doing this at low (2x?) coverage, using pretty sophisticated
methods to combine statistical power between sample datasets.

The "1,000" though is more a round number that is in the right range. it might well be
1346 people or something like that (often some multiple of 96, as 96, or 4*96, 384
is the standard size of a molecular biology "tray" put into a robotic system).

We're going to have alot of fun at http://www.ensembl.org/ [ensembl.org] with this...
 

Re:1 in 2000 people (1)

jd (1658) | more than 6 years ago | (#22150800)

Yes, but only some fraction of those will have both the genetic propensity and the symptoms of the condition. Some other fraction will have just the genetic propensity. Yet another fraction will have identical symptoms from an unrelated cause. If the overlap that has both is unknown, you have problems. If family history data indicates that it is likely to be one in ten, then the 0.993 drops to 0.0993. Of the fraction that have a genetic propensity, there may be N different possible genetic causes that have the same observable symptoms even though the mechanisms and pathways may be entirely different. So, rather than looking at 10 diseases, you are actually looking at 10 x N diseases. Even if you find someone who has both genetic cause and observable effect, I can't see any obvious way of either knowing this to actually be the case for that individual, as this experiment can have no control group, or any way of knowing which of the 10 x N diseases the person has, which is critical if this is to be useful in diagnosis.

Re:1 in 2000 people (0)

Anonymous Coward | more than 6 years ago | (#22151316)

The original post states "This project aims to find conditions that might only appear once in every 2,000 people (though how they intend to do that with half that number is unclear)."

My guess is that each person having two parents plays a role in this as well. Also, the probability is they will detect some genetic diseases, not all of them.

Re:1 in 2000 people (0)

Anonymous Coward | more than 6 years ago | (#22152554)

Yes, and it would be good to teach some English grammar as well. After all, they didn't claim to be able to find ALL people with diseases which occur once in 2000 people. In fact, they didn't even claim to ONLY be searching for diseases which occur once in 2000 people.

 

Re:1 in 2000 people (1)

DrKyle (818035) | more than 6 years ago | (#22153154)

If we assume the populations are at Hardy Weinberg equilibrium (which they will not be for all diseases as there is some negative selection on afflicted individuals) then we use the formula p^2 + 2pq + q^2 = 1. If q^2 = 1 in 2000 then p is 0.9776 and q is 0.0223. This means that the rate of carriers of the disease is 0.9776 * 0.0223 * 2 which is 0.043. If we multiply it out to see what are the chances of taking 1000 people and none of them being a carrier it is (1-0.043)^1000 which gives us the extremely low probability of 3.84 x 10^-20 or 0.0000000000000000000384, so for most diseases this is sufficient even if you don't take people known to have the disease.

Biology geek solves your problem for you. (2, Informative)

NIckGorton (974753) | more than 6 years ago | (#22155132)

They really ought to teach basic probability theory in schools...
Or maybe basic biology maybe? The Hardy-Weinberg equation plus a little basic algebra solves the problem:

p + q = 1

p^2 + 2pq + q^2 = 1

P and q are the frequency of a specific gene (assuming there are only two variants, but lets KISS.) Each organism has two copies of a given gene. They can be pp, pq, or qq. So the number of p genes and q genes must equal 100%. And the number of people who are pp, qp, or qq must equal 100%, hence the two equations.

In the case of a simple autosomal recessive gene, the disease exists when an individual is qq. So qq = 1/2000 = 0.0005. So q (the prevalence of the allele) is 0.02. So you would expect that 1/50 people has the q gene (almost all of them as heterozygotes who have one p and one q gene.) If a gene exists in 1/50 people and you sample 1000, the odds that you wouldn't find it is pretty remote.

There fixed it for you. No need to thank me.

Re:Biology geek solves your problem for you. (1)

rsidd (6328) | more than 6 years ago | (#22164922)

Many replies in one, here; and a day late so I guess nobody will read it.

If a gene exists in 1/50 people and you sample 1000, the odds that you wouldn't find it is pretty remote.

But you'd only care if you see the disease. That's the point you and other geneticists above are missing. Otherwise you'd never know whether the gene is linked with a disease in its variant form, or is harmless.

For the story to be convincing, in your sample population, you need to show that one person has the disease AND that person has the qq version AND nobody else has the qq version AND about one in 50 people have the qp version. This, also, is why you don't just go directly for the guy who has Lou Gehrig's disease: you need to compare with lots of "normal" people.

Re:1 in 2000 people (0)

Anonymous Coward | more than 6 years ago | (#22158524)

For recessive disorders, which many genetic disorders are, the disorder gene needs to be present on both chromosomes for the person to have the disorder. If 1 in 2000 show the disorder, f(aa) = .0005. From this Hardy-Weinberg principles [wikipedia.org] can be used to give approximations of the gene pool. If f(aa) is .0005, q (the frequency of the recessive gene in the gene pool) is roughly .0224, thus p (the frequency of the dominant, non-disordered gene in the gene pool) is roughly .9776. The probability that an individual is a carrier, f(Aa), is 2pq or about .044. Thus, if I remember high-school biology correctly, out of your 1000 genomes, about 44 people will be carriers of the disorder and have the gene on one of their chromosomes. Plenty of people to work with.

Conditions that might only exist in 2,000 people? (-1, Troll)

Anonymous Coward | more than 6 years ago | (#22150402)

Rule out big lips, foul odor and general filthiness because a lot more than 2000 niggers exhibit these conditions.

Dr. Ron Paul, MD

they consider homosexuality to be a disease? (-1, Troll)

Anonymous Coward | more than 6 years ago | (#22150404)

scientifically maybe, but anyway it's going to be interesting to look for a genetic cause.

Did the late Heath Ledger have a buttfucking gene? (-1, Troll)

Anonymous Coward | more than 6 years ago | (#22150418)

Just curious. If not, he was certainly a talented actor.

HEATH LEDGER RIP (-1, Troll)

Anonymous Coward | more than 6 years ago | (#22150422)

Rest In Peace, Heath.
You could buttfuck with the best of them.

Ralph Macchio

Re:HEATH LEDGER RIP (0)

Anonymous Coward | more than 6 years ago | (#22150462)

I like this method of trolling. keep it up, good sir!

1000 Gnomes Project? (4, Funny)

Aereus (1042228) | more than 6 years ago | (#22150426)

I have no idea what they plan to do with 1000 gnomes, but I can only guess that whatever it is will end in a giant explosion.

Re:1000 Gnomes Project? (1)

Smordnys s'regrepsA (1160895) | more than 6 years ago | (#22150510)

...and Profit!

Re:1000 Gnomes Project? (3, Funny)

Hognoxious (631665) | more than 6 years ago | (#22150644)

I have no idea what they plan to do with 1000 gnomes
Replace them with KDE?

Re:1000 Gnomes Project? (1)

ecavalli (1216014) | more than 6 years ago | (#22150646)

Maybe they'll finally retake Gnomeregan.

Re:1000 Gnomes Project? (2, Funny)

PietjeJantje (917584) | more than 6 years ago | (#22150834)

Found them [wikimedia.org] . Commenting on this article may be closed now.

Re:1000 Gnomes Project? (1)

RuBLed (995686) | more than 6 years ago | (#22150836)

I have no idea what they plan to do with 1000 gnomes...

Hmmm... They could use the 1000 gnomes as a baseline data to determine:

- how many gnomes are needed to be joined end - to - end to encircle the earth
      - at the equator
      - at the horse latitudes
- how many are needed to drill from the america and out to china
- the number of gnomes needed to reach the moon and back
- the volume of gnomes needed to fill a library of congress
- the difference between a metric gnome and those other gnome measurements...
- find out what's the difference between a gnome and inome
- could gnomes vanish?
- what's the speed of an unladen gnome?
- are gnomes witches?
- is there a tall gnome and a short gnome?
- if a gnome farts what would it sound? if 1000 gnomes far...

anyway.. the things to do are endless..

Re:1000 Gnomes Project? (1)

xarak (458209) | more than 6 years ago | (#22151070)

An African or European gnome?

Re:1000 Gnomes Project? (0)

Anonymous Coward | more than 6 years ago | (#22157544)

Uh, I don't know!

Re:1000 Gnomes Project? (1)

tg2k (895772) | more than 6 years ago | (#22153150)

Maybe even an explosion of underpants [wikipedia.org] !

This is made of win (1)

Amorymeltzer (1213818) | more than 6 years ago | (#22150432)

This is really awesome. For too long, the "human genome" has been what we know of a few guys who ran the HGP. Since then, many more have been sequenced but not systematically, and not for the sole purpose of cataloging the countless variations present. This sort of database is the first giant leap towards effectively creating a solid understanding of human variation, allowing us to perfect everything from medical treatment to diet supplements (the GATTACA option in the poll is so relevant). Really, this is just setting the stage, paving the way for when we get to the Genomics X-Prize [xprize.org] and beyond. It's about time there was another push of serious capital in this arena.

Re:This is made of win (1)

graft (556969) | more than 6 years ago | (#22150992)

This is wrong. Craig Venter had his own genome sequenced, but the HGP used random, anonymous samples.

The 1000 Niggers Project (-1, Troll)

Anonymous Coward | more than 6 years ago | (#22150448)

We aim to find 1,000 niggers in the projects.

Wish us luck.

-The 1000 Niggers Project
RIP HEATH

See also Personal Genome Project (0)

Anonymous Coward | more than 6 years ago | (#22150540)

The Personal Genome Project [personalgenomes.org] is a similar effort except the volunteers get access to their genomes. There are a few levels of sharing for who gets your personal and genetic information. At the default it is just a supposedly select group of Personal Genome approved researchers. The next level up includes a larger set of the research community via some other authorization mechanism. And finally there is full open, all information totally available for all to see. I know, "what could possibly go wrong?"

Anyway, it's kind of cool to donate to science. And it might be nice to get a free sequencing if you think that kind of knowledge may help extend and enhance your life.

NB: This is a Harvard University sponsored research project.

Good News... (1)

Badgam (1219056) | more than 6 years ago | (#22150552)

Personally, I'm very excited by this because it will not only provide even more insights in to the human genome, but will also provide a way for researchers to lower the cost and resource intensity of genomic sequencing. This will accelerate falling costs for this sequencing and make it increasingly available as a medical technique. Overall, I think this study will be part of the tipping point for the era of genomics; once this has been performed, the doors will be open for huge advances at all levels across the board. It's especially remarkable considering we went from sequencing 1 genome in 2003 to sequencing over one thousand in a little more than four years.

It's hard to believe people actually opposed the Human Genome Project...if we had listened to them, I can only imagine how much progress in this essential field would have been disrupted.

This is fantastic news (4, Insightful)

Biotech9 (704202) | more than 6 years ago | (#22150600)

Anyone reading up on the progress in genomics over the last decade has seen the huge leaps in speed and accuracy and the insane cuts in cost to work with nucleic acids.

From a lab level where what used to be a weeks work with lots of chemicals and processing is now usually a 20 minute protocol with a kit from Quagen. what used to be massive amounts of work with hundreds of gels and digestions and labeling steps to analyse nucleic acid sequences is now a few days with an affymetrix kit, giving far more accurate and useable results. Across every step this progress has been rapid.

And in the future, near-term like within a decade, all these methods will become outdated and replaced with near-realtime analysis and diagnosis. The best point in all of this is that no matter how advanced medical tech has become, the limiting factor has been that it's necessary to actually BRING your disease ridden body to the hospital or doctor. The rise of companies like www.decodeme.com [decodeme.com] is what i expect DNA assesment to be like in the future. You send off some samples you scrape off your cheek yourself, and within a few days you get a full diagnosis on any known predisposition to disease or genetic problems.

Which is why a lot more attention should be put into the debate on morality and genetic profiling. It's going to be here before you can blink, it might be nice to know what you think about using embryo selection to wipe out CF before it becomes a possibility.

Re:This is fantastic news (0)

Anonymous Coward | more than 6 years ago | (#22155862)

From the linked sites: deCODEme and similar outfits process single nucleotide polymorphisms (SNPs), while the 1000 genomes project delivers genomes. Big difference. SNPs can of course be indicative of disease states, but they lack a lot of useful information.

That said, I don't see why genomic information has to be any different than bank account information. Anybody can deposit their goods, and depending on how you value your goods, you pay for the level of privacy/protection/convenience needed. Want to tell your mom you make $320k/year? Your business. Want to tell your landlord you're on welfare? Fine. Want to tell your healthcare provider you're predisposed for Alzheimers? Your call. Don't want to know at all? Cool, live off the grid, put your cash under the mattress, and don't gripe when you're giving a drug that treats a condition you don't have.

Parent post is confusing some (significant) details, but we agree in principle. Genomic data WILL be available sooner than one might think. By 2009, the national genome sequencing centers (listed in the 1000 genomes article) will be able to process most of a human genome in 1-2 weeks. And that ignores the cool new sequencing technologies.

Where do I sign up? (2, Interesting)

AndGodSed (968378) | more than 6 years ago | (#22150614)

I've got marfan syndrome. I am really eager to have my genome sampled so that this condition is better understood.

www.marfan.org

You don't match what they want right now: (0)

Anonymous Coward | more than 6 years ago | (#22152868)

Accoding to the article, these are the groups of people they want to start with:

Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Gujarati Indians in Houston; Chinese in metropolitan Denver; people of Mexican ancestry in Los Angeles; and people of African ancestry in the southwestern United States.

Question (1)

KidShaft (879082) | more than 6 years ago | (#22150658)

Does an individuals DNA structure change at all through out ones life time?

Re:Question (1)

nguy (1207026) | more than 6 years ago | (#22150718)

Does an individuals DNA structure change at all through out ones life time?

Not in the sense you probably mean: your DNA does not adapt or "change" during your lifetime. Some cells have some changes to their DNA, either by accident or on purpose, but that generally amounts to inactivating or removing genetic material that a specialized cell won't be needing anymore before its death.

Re:Question (1)

RML (135014) | more than 6 years ago | (#22150736)

Some individual cells' DNA may change (usually for the worse - that's how you get cancer), but those mutations are probably much less common than the errors generated by the DNA sequencing machines. Both sorts of errors are filtered out because each piece of the genome is sequenced several times for each individual, and a computer combines the results.

Re:Question (2, Informative)

David Munch (939296) | more than 6 years ago | (#22151092)

Does an individuals DNA structure change at all through out ones life time?

I believe you are talking about the DNA sequence, and not the structure of DNA itself? The DNA sequence is relatively unchanged throughout your life. The only things that changes it, are spontaneous mutations and pathogen-induced mutations (Bacteria, but especially viruses). Most of the time, cells with lethal malfunctions in their DNA undergo self-killing, known as apoptosis. Others that behave unnormally, either due to infection, infection-induced DNA mutations or due to spontaneous DNA mutations, are usually killed of by specifik immune defence killer-cells, that can recognize cells that are different from the others. But in the end, some persist and becomes uncontrollable, like cancer-cells that divide extremly fast. Many mutations are silent though, meaning that even though the end product, the proteins, are different from 'normal', they can act as if nothing had happened.

Re:Question (0)

Anonymous Coward | more than 6 years ago | (#22162614)

NO, but how your genome is used based on environmental factors that allow or suppress genetic expression changes based on your environment. This is called 'epigenetic' effects. This is how one identical twin can get cancer and another doesn't. Knowing one's genome is just one part of a greater picture, although it's a great place to start or, at the very least, the easiest place to start. :)

Not 1 in 2000 (3, Informative)

RML (135014) | more than 6 years ago | (#22150678)

The scientific goals of the 1000 Genomes Project are to produce a catalog of variants that are present at 1 percent or greater frequency in the human population across most of the genome, and down to 0.5 percent or lower within genes.
A frequency of 0.5% is 1 in 200, not 1 in 2000. That's much easier to find with a thousand genomes, especially since they're not trying to figure out what the variations do, just that they exist.

Human Genome project? It's about time... (2, Funny)

d4nowar (941785) | more than 6 years ago | (#22150696)

We've been needing the +1 talent in every base for awhile now, what with all of the drone riots these days.

Re:Human Genome project? It's about time... (1)

Badgam (1219056) | more than 6 years ago | (#22150810)

I'm waiting for the Network Backbone and Virtual World myself; that way, I can pretty much beeline to Ascent to Transcendence without the penalties of a Cybernetic civilization and get the increased happiness bonus for my cities.

The last thing I need is to see the University exterminated just because we got impatient and nerve stapled our drones instead of mitigating their anger with technology.

Astonishing (2, Insightful)

Anonymous Coward | more than 6 years ago | (#22150846)

What do we propose to do once we have genetic maps anyway? Scientists (especially within the drug industry) have no clue what they're doing - all we do is "best guess" diagnoses, and then pump people full of drugs that may or may not help, and that induce more serious side effects than they're supposed to be "helping".

This whole idea of "early detection" pisses me off; it just reminds me of the drug industry. It really does come down to the almighty human thinking they know what they're doing. Hopefully we find a genetic marker for depression... that way we can take 95% of people taking anti-depressants off their drugs for not actually having depression.

Every single other mammal on the planet survives without this bullshit; why can't we? Oh that's right, there's money to be made.

Re:Astonishing (1)

Martin Soto (21440) | more than 6 years ago | (#22152032)

Every single other mammal on the planet survives without this bullshit; why can't we? Oh that's right, there's money to be made.

Probably the difference is that we want to survive as individuals, not just as a species.

Re:Astonishing (1)

ErikZ (55491) | more than 6 years ago | (#22152126)

I know people who those "New Drugs" have worked wonders on.

And as we know more, genetic therapy will become more effective. But feel free to go to live in a tribe somewhere if you hate progress that much.

Re:Astonishing (1)

jd (1658) | more than 6 years ago | (#22164160)

There is some degree of truth to that. For example, the exact effects of a new drug aren't always clear until there have been several years of study - even after approval. It would not be particularly hard to use tracer isotopes in early pre-approval testing, and then use well-established imaging techniques to determine exactly what component of a drug affected what and how. I would not be at all surprised if this was already being done in some cases. You'd then obviously also need to use the same imaging techniques on the patient to determine what underlying mechanisms were responsible for the symptoms being observed.

A set of symptoms may have many, many causes (which is why there are many, many medications for "bipolar disorder") and ultimately it is meaningless to treat a symptom. A visible symptom is measurable, yes, but it has no independent existence, and not all symptoms are going to be outwardly visible. If you treat what is outwardly seen, then there may be all kinds of damage being done that won't be visible until much later. If you treat the problem at a much lower level, you also treat what you can't see.

In principle, genetic studies could reduce the problems and costs involved in imaging. If you know a specific gene impacts specific things, then corruption on that gene will impact (at least) that same set of things. It must. The impact could be broader, but it can't be narrower. With time and knowledge, it should be possible to link some specific types of damage to specific impacts to the components within the body. Since sequencing specific segments of DNA should be cheaper and quicker than using the very high-resolution imaging systems, it aught to be possible to get as good results (at best) more reliably and for more people.

In the case of, say, "bipolar", this is extremely important. Different treatments for bipolar will work with specific individuals but not for others. At present, doctors just try the different treatments more-or-less at random until something works or your brain explodes. (Ok, not literally, although I did lose colour vision for a while with one treatment, and another caused my blood pressure to sky-rocket temporarily.) I simply do not - and will not - believe that this is a viable approach to medicine in the long-term. If there is a way of using genetics to severely limit the options and have a good idea of what is most likely to work, then it should be pursued. To me, diagnosis of the symptoms is immaterial, it is diagnosis of the cause that allows one to speak meaningfully of a "cure", and perhaps of much more exact cures that don't try to solve over-broad ranges of problems that might look the same on the surface but be entirely unrelated mechanistically.

It also opens up the possibility of understanding why early attempts at gene therapy were only partially successful (and partially disastrous), maybe find ways of tailoring such cures to minimize risks, maybe find ways of quantifying what those risks are for different individuals. Let's face it, using a retrovirus to embed a full replacement gene or chromosome into DNA is going to be a bit of a sledgehammer method in some cases. If you can identify what those cases are and what alternatives would be subtler and safer, that would obviously be helpful.

Now, the parent post mentioned the animal kingdom. This would be the same animal kingdom that includes the Tasmanian Devil, which is at grave danger from going extinct due to a cancer-like growth that seems to be water-borne. The growth doesn't seem to affect any other organism. There is (currently) no known treatment. Once infected, death is pretty much guaranteed to follow soon after. Better biotech capability would lead to a better understanding of the agent, which the survivors could be protected against and maybe treated for. Better understanding of genetics could lead to understanding what made the Tasmanian Devil (and nothing else) susceptible, which could lead to a way to immunize all future populations by tweaking the genes. At present, if nothing is done, Taz will go completely extinct within a decade, possibly just a few years. And it will have been entirely preventable.

If Tasmanian Devils could speak, do you think they'd be saying they didn't need drugs and genetic cures? Hell, no. They'd be wanting to know why nobody was bothering to apply those skills to save them.

Do drug companies profiteer off the ill? Sure. They worked hard to suppress the discovery of heliobacteria's role in peptic ulcers and certain forms of stomach cancer associated with peptic ulcers. You are very unlikely to see Manuka Honey being used to treat MRSA, although it appears to be a vastly superior remedy to any drugs currently in use for it. More than a few medications have been pulled due to harmful side-effects that had been known about from clinical trials but omitted in reports. Medical journals are wary of publishing negative reports. Doctors are sometimes encouraged via sponsorship deals and sweeteners to push specific treatments as the first option to be tried.

Let's be fair, though. Regulations and scrutiny are lax, so it's more a matter of what is sanctioned than anything. Nobody wants to be uncompetitive, so everybody gravitates towards what is permissible. Don't blame the companies for not wanting to go broke. The practices are also common in many industries. Why do you think they had more electric cars in 1905 than they do today? Why do you think the legal battle between the ESA and California over pollution laws is filled with secrecy and dirty money? Why do you think SCO tried to pull its stunt in the computing industry? Or how Microsoft has gained a monopoly on so many sectors of it? The problems are far from unique to medical technology.

Do I like the status quo? No. The only status quo I like is the rock group of that name. For that matter, as nothing is ever perfect, I will never like the status quo. I will always believe that it is possible to improve on the current system, although this does not mean it is always possible to know how one should improve it. Better, cleaner, more rigorous and more enforceable regulations should be drawn up for all industries, and should be policed a whole lot better, with much less tolerance of corruption, neglect and abuse within the enforcing agencies. Doesn't mean I could tell you what those regulations should be, or how you'd watch the watchmen. I doubt any outsider could tell you that, either, which means you'd need people to want a level playing field before you'll get one, and that in turn won't happen until high-tech skills are so utterly common that it is totally uneconomic to not be on a level playing field.

I have wiped entire civilizations off of my chest (-1, Offtopic)

Anonymous Coward | more than 6 years ago | (#22151028)

"I have wiped entire civilizations off of my chest with a grey gym sock. THAT is special" - Bill Hicks

hmm (1)

noobstate (1224768) | more than 6 years ago | (#22151746)

"find conditions that might only appear once in every 2,000 people"

call me paranoid but i would much rather not take the chances of my genome being documented into the hands of others only to find such a rare illness

u never know what they will use it later down the line

these scientists and all . .. *caught government access or sneeze mutant hamster me sneeze*

At a glance... (1)

ikarys (865465) | more than 6 years ago | (#22151770)

At first glance I thought this was a story about 1000 Gnomes!

I was hoping to find out what that ????? step was before profit.. but alas, its just boring DNA crap.

I know this is off-topic, but.... (1)

maxhavelaar (1225386) | more than 6 years ago | (#22151780)

you might want to read on, anyway. Last week, I realised that Second Life's economy [valleywag.com] isn't the only economy that's a pyramid scheme benefitting above all the Guys at the top of the pyramid. I combined that with John Perkins [democracynow.org] story about how the super rich manage to rape the poorest people on the world, so I got a little worried, and decided to follow the money. Then, in a hunch, I decided to follow Hitler's money [guardian.co.uk] and also discovered a clear and credible link between the Nazi's and Al-Qaida [john-loftus.com] . A few more steps and reality [indymedia.nl] makes your worst nightmares look like a walk in the park. -- Multatuli --

Someone didn't... (1)

Deliveranc3 (629997) | more than 6 years ago | (#22151812)

finish grade 11-12 science did they...
(though how they intend to do that with half that number is unclear)
Here's how... [wikipedia.org] Alleles.

Re:Someone didn't... (0)

Anonymous Coward | more than 6 years ago | (#22151884)

Grade 11-12 science? Didn't we abolish the education system as a sacrifice to fund the War on XYZ?

Re:Someone didn't... (0)

Anonymous Coward | more than 6 years ago | (#22157300)

No, XYZ are our allies. They have always been our allies. We've always been at war with ABC.

misleading science (2, Informative)

cinnamon colbert (732724) | more than 6 years ago | (#22151826)

When scientists use the word "complete" they are being misleading. There are very large, difficult to sequence regions (, heterochromatin,, eg centromeres) that have not been sequenced, ever, and that are biologically important (centromeres are required in every cell division, to ensure that each cell has the proper set of chromosomes.)
Even within the "normal", euchromomatic, sequencable DNA, there are gaps that have not been sequenced.
Beyond this, you need to know haplotypes - that is, for most of your DNA there are two copies (except the x and y sex chromosomes) one from dad and one from mom
Since these two copies are different, it matters, a lot, what differences are where.

Funding through auction? (1)

zav42 (584609) | more than 6 years ago | (#22151924)

If companies like https://www.23andme.com/ [23andme.com] can get 1000$ for a very rough analysis of a persons genome, I wonder how much people would be willing to bid for the 1000 places in this program.

Obviously the 1000 candidates can not be choosen based on their bid alone, but a little online auction with candidates having to fill in a form on their health could probably help raise a significant part of the money needed for the project.

-Bernd

Invaluable to a cure for auto-immune diseases. (1)

jackpot777 (1159971) | more than 6 years ago | (#22152682)

I recently took part in a small genetic survey for the auto-immune disease Ankylosing Spondylitis [wikipedia.org] (AS), a disease my wife has had for nearly a decade. It doesn't have the publicity of Lupus, but there are far more people suffering from it.

Before the survey, only one genetic marker was known for the disease: HLA-B27, uncovered over three decades ago. If you have that genetic marker, you're almost certain to get AS ...but only 40% of AS sufferers actually test positive for HLA-B27. One survey later, we now know that testing positive for ARTS1 or IL23R counts too (70% of AS sufferers have one or more of the three).

The Wiki page does need correcting... it says "Over 95% of people with AS are HLA-B27 positive" where it should say "Over 95% of people that are HLA-B27 positive develop AS". Big difference. All whales are mammals, not all mammals are whales. I'll change that now.

1000 Gnomes... (0)

Anonymous Coward | more than 6 years ago | (#22152888)

Sheesh, welcome to Ironforge.

Oh, GEnomes. And Sourceforge.

OK, got it.

The 1000 Gnomes Project (1)

Anne_Nonymous (313852) | more than 6 years ago | (#22153304)

> The 1000 Gnomes Project

They probably stole them from gardens all over town and then set them up in various suggestive poses on the town hall lawn.

Chromosomes are diploid! (2, Informative)

bcwright (871193) | more than 6 years ago | (#22155064)

Remember that human chromosomes are diploid - we have two copies of (most) genes. (A few of the genes on the male Y chromosome have no analogue on the X chromosome, but that's a very small percentage of the human genome). So in total they will have roughly 2000 samples for each gene - 2 for every individual.

Of course, that doesn't provide a correlation with specific genetic diseases - but here classical genetics techniques allow you to get an insight on how some of those diseases might be related to specific genes. The easiest to understand are those genetic diseases that are dominant - that is, you need only one copy of the gene in order to have the disease. On average, a dominant genetic disease which has a frequency in the population of 1 in 1000 would have about a 50% probability of being represented in the sample.

The situation is more complex for genetic diseases caused by recessive genes - which form the majority of genetic diseases. People carrying only one copy of the disease will be asymptomatic but a 'carrier' of the disease so that their children would have some chance of getting the disease if their other parent was also a carrier of the disease. However even there, you often have a good idea who might be a carrier for the disease based on family history: how many others in that person's family are affected. If any of those individuals are the person's children, you know that that person is a carrier for the disease; if one of them is a (full) sibling, then there's (at least) a 50% chance that the individual is a carrier, etc.

These sorts of familial relationships are the bread-and-butter of traditional investigations into genetic diseases, and this promises the ability to multiply their effectiveness. In effect you are getting a window into the genomes of many more individuals than merely those whose genomes were sequenced.

Already happened (1)

philspear (1142299) | more than 6 years ago | (#22155584)

I was watching "Heroes" and they were able to identify individuals with super powers based on their participation in the human genome project. It helps that they identified the "codon" that was responsible for the super powers. I wonder which three nucleotides give you super powers... But I digress, everyone who has ever signed anything with the words "human genome progect" already has had their genome sequenced.

Hey! (0)

Anonymous Coward | more than 6 years ago | (#22160682)

What about the 1000 KeDEs project.

This makes me wonder (1)

CopaceticOpus (965603) | more than 6 years ago | (#22161688)

What would we get if we calculated out the averages for every sequence, created an artifical DNA strand with that sequence, and grew it using cloning technology? Some kind of perfect man, or a genetic freak?

I think I'd make a good mad scientist...
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