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The 1000 Genomes Project
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."
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.
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.
Libertarian Leaning Political Discussion Forum.
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...
i didn't think Republicans believed in genetics..
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.
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 and beyond. It's about time there was another push of serious capital in this arena.
I live in constant fear of the Coming of the Red Spiders.
I like this method of trolling. keep it up, good sir!
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
Just -1, Troll talking to another.
The Personal Genome Project 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.
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.
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 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.
I've got marfan syndrome. I am really eager to have my genome sampled so that this condition is better understood.
www.marfan.org
Seven Days with Ubuntu Unity
Does an individuals DNA structure change at all through out ones life time?
Human/Ranger/Zangband
We've been needing the +1 talent in every base for awhile now, what with all of the drone riots these days.
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.
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.
Human/Ranger/Zangband
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.
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.
Hell, most of them believe in eugenics!
yeah, but they can't actually pronounce it.
"find conditions that might only appear once in every 2,000 people"
.. *caught government access or sneeze mutant hamster me sneeze*
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 .
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.
you might want to read on, anyway. Last week, I realised that Second Life's economy 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 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 and also discovered a clear and credible link between the Nazi's and Al-Qaida. A few more steps and reality makes your worst nightmares look like a walk in the park. -- Multatuli --
You can fool some people all of the time and all people some of the time, but you can't fool all people all of the time.
finish grade 11-12 science did they...
(though how they intend to do that with half that number is unclear)
Here's how... Alleles.
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.
If companies like https://www.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
I recently took part in a small genetic survey for the auto-immune disease Ankylosing Spondylitis (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.
...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).
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
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.
Shiny. Let's be bad guys...
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.
Sheesh, welcome to Ironforge.
Oh, GEnomes. And Sourceforge.
OK, got it.
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.
> 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.
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.
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.
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.
What about the 1000 KeDEs project.
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...