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Scientists Complete Map of Human Genetic Variation
UltimaGuy writes "A major scientific step in the field of genetics is set to speed up the search for the causes of common illnesses ranging from heart disease and cancer to Alzheimer's and asthma. Scientists have mapped patterns of tiny DNA differences that distinguish one person from another, a step that will speed up the search for genes that promote common illnesses such as heart disease and diabetes."
"... a step that will speed up the search for genes that promote common illnesses such as heart disease and diabetes."
That's all well and good, but can they cure my ugly face?!
No sig for now.
If there ever was a case for computational biology, this is it. :-)
I am defenseless. Use your button. Mod me down with all of your hatred.
First Post! Yeaaaa!!!
Here is a link to the mp3 of the Nature podcast on this.
I always think it is ridiculous how these genomic announcements happen. They choose to announce that they have ONE MILLION SNPs with big press release, but this data is available online as soon as its sequenced.
First you animate. Then you SUSPEND!!!
I'm not sure how they define "complete", but I bet in 30 years or so, after major discoveries have been made based off this, and all the patents have expired, and I'm dying of old age, this could really lead to some good treatments for a number of rare genetic illnesses, except for those so rare as to make developing a treatment unprofitable.
We're playing a dangerous game, where people can control what their baby's gender will be - now we get to play with their genes too? Ever hear of Natural Selection?
Hey, who knows, maybe companies will start buying gene sequences. Sure, you can make your kid immune to heart disease... for a price. Want them to have blond hair and blue eyes? We can do that, just fork over that cash.
This sentence is false.
This is precisely the process the bioweapons arms merchants needed to perfect in order to make their "ethnic bomb" work in my book Slatewiper.
Maybe the have a high degree of certainty .. but how do they a few people have got unique rare SNP mutations?
This brings us closer to confronting the issue of genetic discrimination on a large scale. IBM made a nice announcementhttp://www.out-law.com/page-6217> that they will avoid this, but there's not much legal protection from genetic profiling in the laws of most countries. Fortunately for those of us not currently in America, health care access in most developed countries won't be affected by this. Unfortunately, for those of us who intend to live in America at some point in the future, health insurance could certainly be affected by this. For example, it's well known that Amish, Ashkenazi Jews, and other groups suffer from certain genetic maladies far above the average. This kind of research will make it possible to pinpoint other groups with risks not yet known, and raise their health insurance costs, avoid hiring them (a la Wal-Mart's recent memo regarding hiring healthy people to cut down on benefits costs), etc. While I don't want to spread too much paranoia on the issue, I think it's very important that we make sure to protect people from genetic discrimination before it becomes widespread and harder to stop.
Although the moon is smaller than the earth, it is farther away.
All those tiny little variations they've mapped are either owned, or going to be owned by a company. This is good news, because curing almost any disease will be as simple as opening your checkbook. If you can write a digit followed by 6 zeroes in that checkbook, you're A-OK!
Fascism trolls keeping me up every night. When I starts a preachin', he HITS ME WITH HIS REICH!
Hurry up!
As a survivor of stage I kidney cancer, stage III colon cancer, arthritis, and diabetes I am a little anxious for progress in this field.
(Enter: the usual suspects.)
(From a speaker)
AAAAGGUATCUCGCUAGCUAUTCGGGCA...GTAC, please step forward!
(Suspects look around in confusion.)
(The third suspect tenatively steps forward.)
(From a speaker)
I said AAAAGGUATCUCGCUAGCUAUTCGGGCA...GTAC, AAAAGGUATCUCGCUAGCUAUTCGGGCA...GTAT! Get back in the line-up.
(AAAAGGUATCUCGCUAGCUAUTCGGGCA...GTAT shuffles back into the line-up.)
(The suspects look around in apprehensively and glance furtively at each other.)
Welcome to the future, invalid.
so if there are SNP mutations that only have a 1 in 270 or lesser chance of being present ..it's not going to be in their Map. You could be walking around with an SNP they missed cause the mutation happened recently (unique to you or maybe your grandparents etc) or is rare or whatever.
99.9% of your genes are belong to everyone!
my apologies for the ugly link. I should "Use the Preview Button! Check those URLs!" Feel free to learn from my mistakes.
Although the moon is smaller than the earth, it is farther away.
Read the friendly Haplotype Map, that is:
http://www.hapmap.org/.
You can even browse the project data: Gbrowse
"The achievement probably won't result in new disease treatments for five or 10 years or more, he said." - From TFA
Ah medicine, how impervious to progress you are.
Yippee!!!!!
The potential misuses of this are obvious, immediate and must be legislated against now:
That's a short list and others can think of more, I'm sure.
The first two are obviously evil, but the third is perhaps the most terrifying. It would be very tempting to have a magic wand to change your child's DNA in such a way that they would not have high blood pressure. But what else would that do? Scientist are just beginning to understand how RNA and proteins magnify DNA differences and no one understands the relationship to thought patterns or behavior. Informed consent, under such circumstances, is impossible and experiments are not ethical.
Formulating laws to deal with problems without halting reasonable research is difficult but must be persued.
Friends don't help friends install M$ junk.
Knowing the sequence of your genes will help you avoid or delay disease and make cures easier. The benefits may outweight the costs.
And what about people with good genes, should they subsidize the people with bad genes?
The University of Queensland's physics blog, Illuminating Science has a summary with some interesting thoughts about the implications of this project.
So, did they find the bit where God signed his name and copyrighted it?
(c) God, 5800BC
The author asserts His moral rights over this work.
Resemblence to all persons in history is expressly intentional.
For Ethel.
"Corporations complete patent applications for human genetic variations".
Yes, people with good genes should "subsidize" the people with bad genes. Everyone has their own ideas of a just society, but it seems pretty brutal to make everyone suffer for their genetic problems more than they inherently do. I know I certainly wouldn't want to live in a society where we just left the mentally handicapped to die on their own, instead of taking care of them, for instance. Some people disagree, but I think it's important that the genetically blessed help those not blessed. From each according to his ability, to each according to his needs. Or something like that, in an ideal world.
Although the moon is smaller than the earth, it is farther away.
The good news: drug companies might be able to resurrect some failed medications if they can determine which genetic variants are helped by the drug versus being harmed by the drug. Some promising but previously unapproved medications will make it on to the market.
The bad news: Current drug development focuses on blockbusters. Finding something that millions of people will need to take. This pushes development to help the greatest number of people. If the treatment works for most people (based on genetic screening), there's little reason to develop a cure for genetic minority populations. Genetic orphan populations will be marginalized.
Two wrongs don't make a right, but three lefts do.
except it will be patented and kept quiet for 5 to 7 yrs only for NEOSCO to sue all living persons for patent violations demanding $699 per set of cromozones.
aww the constitution
I have also: totaled three cars in crashes, been hit by a car while riding a bicycle, cracked my sternum in a freak lawn mowing accident, and overdosed on aspirin when I was 4. I cracked both shoulder blades by falling out of a tree when I was 6, got attacked by monkeys (twice), and I've been hit by lightning.
I'm 38, and I haven't died yet. I'm pretty sure I'm immortal.
There are so many things incorrectly implied about this finding that it's almost hard to begin:
1) The headline and idea: "New DNA Map Will Help Find Bad Genes". There are no bad genes. Evolution didn't just come around and place some miscreant gene in your body just to give you a hard time after living off a diet of pizza and Mt. Dew for ten years. Every gene has its own function. Genetic research is based more upon finding which variation of a gene is more beneficial to an individual and how to change/block the non-beneficial variations. Genes are either more or less successful, but definitely (minus the case or rare genetic diseases) not evil or bad.
2) "The project analyzed DNA samples from 269 people from Nigeria, Beijing, Tokyo and Utah." Well, this would be fine if everyone was of a direct Nigeria, Beijing, Tokyo or Utah decent similar to the test subjects. As for real world population, they probably contain mutations not near those found in any of these people. A native american, a man from agentina, and a guy from India I guarantee you would have completely different results. And that's assuming pure-bread people. Where would someone like Tiger Woods fit in? As an interesting side note, why do you think they picked Utah? Could it be that one of the principal investigators of the study is Mormon and thought it might be nice to bring government funds to his own people? I think that most of us can agree that politics and science rarely mix to give good results...
3) 269 People? You're telling me that out of 3 billion DNA basepairs, we can find all the parts that have changed over the last few hundred thousand (and more) years in only 269 people?
4) "This clustering greatly simplifies the task of analyzing what variations a person carries, because not all of them have to be identified." and "A person with one particular version of a SNP is highly likely to carry particular versions of other SNPs as well." When you begin to think about the error rates contained in "highly likely" and then start to cluster those rates togeter, your model falls apart.
Basically, from my own experience of working with data of thousands of whites, blacks, both male and female, the rates at which certain areas of DNA are linked vary directly upon the strata one looks at and the number of individuals in that strata. This project is a neat theorhetical idea, but until we can sequence the entire genomes of thousands of people overnight for a small fee, there is not enough realy data to really do anything with.
i keep reading the title as "Genetic Vacation".
it sounds like a nice break away from stresses of being made up of genetic material... this could catch on!
serenity now!
Nature doesn't have goals to be tricked out of. Nature doesn't have beliefs to be fooled out of believing.
Coordinators
Abh
Maybe now we'll find out why niggers run so fast.
Reuters will report that monkeys have have long had the ability to type Shakespeare but have never felt it to be a worthwhile endeavor...we are all actually such borderline genomic constructs that we shouldn't really exist...and that we are only using 10 percent of our genomic potential.
Is there some kind of overarching cause of all your health problems? I mean, arthritis and colon cancer at 38? What are the frickin' odds?
Laws do not persuade just because they threaten. --Seneca
A summary plus a discussion of some thoughts on the ethical issues involved in both intellectual property and discrimination are on the University of Queensland's physics blog.
Physicist, consultant, science communicator
You had me at "freak lawn mowing accident."
Paul Grosfield - the quicker picker upper.
I'm a little uninformed in this area of science. What exactly does this discovery mean? Does it mean that they now know exactly where the strain of DNA is that makes me white, or have dark hair, or have a weakness toward a certain type of cancer?
How is this going to help? Are they going to be able to reach inside me and change my DNA to fix my problems (gene therapy, this is called? Clueless there too i guess)?
Are we going to start engineering perfect babies, ala Gattaca? (http://www.imdb.com/title/tt0119177/)
...assuming I ever MAKE any kids, will they be able to figure out why I was born with 12 toes & zap that, so it doesn't get passed on?
Schatten Teufel
There is nothing "Common" about Sense
I'm headed home so I'm not going to RTFA but as someone working for a company that sells tools for identifying genetic sequences in solution, I can tell you that every time a "gene map" or such has been claimed it's been completely overblown. There are vast regions in the clusters that have iffy data or the clusters are in many pieces and no one knows how they fit together. It'll be a long while before 1 person's DNA has been fully sequenced, much less a comprehensive list of variations among all peoples.
r u going to tell me that a mutation that results in a stop codon, resulting in a painful death 5 years post birth, is not a "bad" gene ?
.....
/.geek and a human geneticist r at a party, and they c a super hot babe across the room. the geek says, lets go over and chat her up, the HG says its not worth it, because after we go half way, half remains, and so forth, and we will never get to the babe. /.geek say, yeah but we could get close enough to do...
u can quibble about semantics here, but sounds pretty bad to me
the rest of your arguments are more or less true but irrelevant, Yeah, they only did 239 people, yeah 1 million snps is not all of them,
the question is, are they close enough to do some practical damage ?
(old joke: a
and the
Many are owned by individual graduate students (and full PhDs) who "wasted" their weekends, social and family lives while certain people (not you...) were at parties, playing video games, or surfing the internet.
No, as long as you can't afford it, someone who works more than you do will pay for it through Medicaid (taxes) and higher premiums for health insurance.
I suggest you read Slashdot
...but you've got bad breath, too. :-(
--
Don't like it? Respond with words, not karma.
As of 2001 the location of the genes that causes Red/Green color blindness had not been located. We know that at least one of them is located on the X chromosome, but no idea where. In 1997 the gene that causes Achromatopsia, the complete inability to distinguish color, was located on chromosome 2 but this is the rarest form of color blindness. But say I had Achromatopsia, or that we located the gene for Red/Green color blindness, is there any hope of a cure? If you were to extract some of my stem cells, do some gene therapy on them, inject them into my eye and then flash my retina with a bright light would it grow back with a greater capability to distinguish color?
I know it's more sexy to cure debilitating genetic diseases but there's a lot more people out there with color blindness than there are people with hemophilia. Surely economies of scale dictate that we should get the first shot at a cure.
How we know is more important than what we know.
They can require selective breeding to eliminate bad genes, or offer gene therapy. Don't need to do any commie crap.
Actually, the HapMap is basically useless for "rare" genetic variants, because it intentionally is screening for common ones. Hence, it may actually be useful for common susceptibility alleles for heart disease or stroke but it isn't going to find the rare variants that affect only a few people.
From my weblog:
--Johnto evade tigers and law enforcement.
There are plenty of excellent scientific justifications for the HapMap project and if you're as unaware of them as it sounds, then I wonder what sort of human genetics you actually do. The HapMap is already transforming the way human genetics is being done and if you're unaware of its importance then you must be living under a rock. At the American Society of Human Genetics meeting where this was announced, there are literally hundreds of presentations that touch on the HapMap project in one way or another.
There are excellent reasons for focusing on common genetic variation as the HapMap project has done. One is pragmatic; there are billions of rare variants, but to catalog their relationships would take stupendous effort and would be nearly useless from a practical standpoint. Between any two individuals, nearly all of the genetic differences are common ones in the population. There is a ton of well established statistics that shows that most of the common variation can be captured using a limited number (250K, 500K, etc) of markers, and that these variants generally cross conventional "racial" boundaries because they predate the radiation of humans out of Africa.
One of the PIs is Mormon because there is an extremely well characterized collection of Utah Morman DNA samples (the CEPH pedigrees), that have been used for decades, that were chosen for the "European descent" portion of the HapMap. That guy has been working with those families since they were first recruited to participate in genetic studies. The amount of money that went to Utah had to be trivial because none of the laboratory work was done there.
Oxen's comment is the first time I've ever made this request, but to any mods who read it, please mod it up! It's brilliant.
It's worth at least a +6 (Miraculous)
I have to say though that the HapMap project is only a transient step to where this is all going. The NIH, NSF, and DOE are throwing significant amounts ofmoney incubating technologies to get us to the infamous '1000 dollar genome'. That's where things become really interesting.
The problem with HapMap, and frankly, the whole human genome project is that it's done on average people from diverse populations. Adults from diverse populations. Living Adults. What we all really want to know is what causes disease, and sequencing healthy people isn't going to completely get us there. There is a theory that common diseases are caused by large numbers of common varients or SNPs working in concert. In that respect, you can learn agood amount about things shuch as heart disease, certain psychiatric disorders, and cancers, but again, the SNPs most likely to be uncovered are those which have no deleterious effect.
Additionally, research using SNPs to find regions of interest on chromosomes (association or LD studies) require hundreds of thousands of data points in tens of thousands of people with disease and carefully paired controls. While the technology is there to do such projects now, it certainly isn't cheap. At some point, when technology allows, it will be way easier to just sequence the whole thing and look at the truely causitive SNPs and not the nearby SNPs with no biological relevance (which is what generally happens in association or LD studies- thus the name association, since they're associated, but not neccessarily the cause).
I certainly don't want to diminish the importance of the HapMap, as it is something that we could only dream of 10 years ago, and it will have a massive effect on medicine over the next 10 years, but the future is going to be absolutely incredible. At some point people will have themselves sequenced and have a comprehensive understanding of their suceptibilities for less than the cost of the prenatal screenings currently done on most newborns in the western world currently.
By that time, your doctor will be able to synthesize anything he needs on the fly, right there in the office.
Technoli
One way of looking at this study is the ramifications.
.01% of human DNA plays a huge role in difference between individual humans. The other factors being environmental and randomness.
.01% of human DNA plays a huge role in defects (ie sickness, bad growth,...) in any individual.
-
- Less than
Kind of blows your mind.
Anyway, face it Buddy, after 7800 years it's all public domain.
Quite a few roads to hell have been paved by eugenicists, so it shouldn't be surprising that many people now hesitate walking on paths that intersect them, knowing full well that there will always be people willing to turn at that intersection and follow in those footsteps, perhaps without even noticing.
The "real question[s]" you point to look more like pamphlet questions to me--the easy, obvious questions that guide the reader to predetermined conclusions. Then the segue into "the magic topic of race". A couple of statements of "fact" to get the nod of agreement, and then,
"How will people react to the mounds of evidence that will continue to build that the races are not indeed equal as they would want to believe?"
Hello! How easy is that jump from issues of medicine to issues of sociopolitical philosophy?
Bioinformatics.
And with it, all hell has been unleashed?
For example, it's well known that Amish, Ashkenazi Jews, and other groups suffer from certain genetic maladies far above the average.
h tm
Yes, but it's important to note that they don't suffer from more genetic difficulties than other populations. You won't cut your health care costs by excluding the Mennonite bretheren (i.e. Amish.)These populations are homogenous, not defective. Since intensive study always turns up particular defects, there has been some concern about the political consequences of studying a particular population.
Jewish individuals are in a unique position to assist scientists in the understanding of genetic disorders. Due to a long history of marriage within the faith, which extends back thousands of years, the Jewish community has emerged from a limited number of ancestors and has a similar genetic makeup. This allows researchers to more easily perform genetic studies and locate disease-causing genes.
http://www.hopkinsmedicine.org/epigen/ashkenazim.
___
It's the end of my comment as I know it and I feel fine.
Here's another study regarding mapping genes. There's a lot of research being done and it is being more and more interdisciplinary, which is a good thing if you want a big picture to find clues and solutions.
GeoPlace reports a story on project METAFUNCTIONS from Informationsdienst Wissenschaft about mapping environmental clues to decipher the function of genes. "Another innovative aspect of this project [METAFUNCTIONS] is the use of geographic information systems (GIS). GIS tools provide for the simulation and analysis of events from a geographical or spatial perspective. Novel patterns - for example, the physical clustering of genes within a genome - will be correlated to the contextual habitat data."
Animoog.org
This map can also show the human family tree, which originates from 1000-odd individuals around 200,000 years ago. It can also explain if we have Neanderthal genes, and if there were other ancestors of ours we dont know about.
"Give orange me give eat orange me eat orange give me eat orange give me you." -Nim Chimpsky
This is great. This means in 10 years we'll be able to do soemthing like this:
/dev/bioformer0
diff me.dna wife.dna | sed -e 's/sex=female//' -e 's/skin_burns_easily=y/skin_burns_easily=n' -e 's/good_at_soccer=n/good_at_soccer=y' > child.dna
cat child.dna >
who needs sex?
It's just a matter of mixing the right reptile genes with some Leonardo di Caprio DNA into your dailly dose of caffeine.
Then we just need to chop off your head and a new (less ugly) one will grow.
I've actually got most of a short story written around a similar concept, but in my case (and I think in the real world too) such a thing would never work.
The reason being is that the concept of "ethnicity" is more tribial/social/religious than it is genetic.
I'm willing to bet that there is no set of genes that uniquely identifies a given ethnicity *right now*, and that as time goes forward, the probability of discovering a set of genes that identifies "most" of the population of a given ethnicity is steadily dropping, due to population intermingling and interbreeding.
DG
Want to learn about race cars? Read my Book
made my day, "special attack"! "User ID in heaven"! HA!
"patterns of tiny DNA"
Is there any other kind?
An even more interesting set of data is the data from Iceland, where the entire population's genealogy is known and recorded and the country has a nationwide health care system. This has allowed extensive studies using the current population's data along with their history (privacy concerns heavily addressed, really!).
Roseanne: I fully support this. Who doesn't take pleasure in a well maintained lawn? Fresh green grass, a pleasure to the eyes, nose and toes. Some even take pleasure in hearing the distant sound of the mower across the street on a summer afternoon...
Chase: That's LAWS.
Roseanne: Well then, that's different...Nevermind.
There is no right to feel safe thru security vaudeville at the expense of everyone's freedom, privacy and tax money.
Five years after Craig Ventor's DNA was decoded, they still dont have a precise number of human genes. Thats partly because the the first draft was very rough, being gradually completed by per-chromosome working groups. The other is because there still some ambiguity in how DNA maps into proteins. Mammal DNA with all its introns and exons can have multiple, ambiguous mappings. Some simpler, sub-mammal organisms its easier to do this.
A mouse DNA decoding project has been more precise. They specific match the gene and its resulting protein(s). Then they reverse manaufacture cDNA from the protein and archive these. I recall they are around 30K genes and 60K proteins. Human genes are being analysed in this fashion too, but not as complete yet.
Don't you mean 2 people 4000 years ago?