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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."
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.
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.
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.
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.
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!
Read the friendly Haplotype Map, that is:
http://www.hapmap.org/.
You can even browse the project data: Gbrowse
First of all, most SNPs are free information. dbSNP contains ~5 million validated SNPs and ~27 million reported SNPs in humans. Celera owns a lot of SNP finds, but most are junk (sequencing errors) and they will be giving them to the free databases soon.
However, the importance of this article has nothing to do with the number of SNPs available or the fact that the SNPs are common (because of the low sample size). The whole point is to have SNPs that exist in ~50% of the population so that the haplotype can be determined. The Haplotype shows which segments of the genome tend to be inherited together. This can be traced back for multiple generations of inheritance - essentially there are ancient haplotypes and more modern haplotypes. The importance of looking at haplotypes is that it allows researchers to see which region an important mutation relating to a disease may occur in. Note that just by knowing which haplotype the disease causing mutation occurs in does not let us know which SNP or insertion/deletion event causes the disease.
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.
Nature doesn't have goals to be tricked out of. Nature doesn't have beliefs to be fooled out of believing.
Coordinators
Abh
I saw this cartoon the other day. It is a classified ad on God's computer, with Him pushing the submit button.
The text reads:
Designer Wanted
Full-time position (6 days/week; 24 hours/day). Must be intelligent. Must be able to conceive and manufacture organisms and genetically modify 5000 species a minute. Fabricate evidence of evolutionary adaptation and carelessly cast said product about while transforming living organisms in an increasingly complex and generally miraculous manner. Must be detail oriented and create non-redundant internal networks of varying complexity in species with intriguingly systematic (but actually random) appearance. Proficiency in message encryption highly desirable. Salary to be determined according to evangelistic vigor of followers. Benefits include Medical, Dental, Immortality, Omnipotence, Dissolution of Science as a discipline, Disease, Pestilence, Famine, Destruction of the Earth.
I think someone at my work made it and posted it up (I work at a research facility), but it is hilarious.
First you animate. Then you SUSPEND!!!
I'd perhaps pay more attention to your concerns if you appeared to know more about the subject. An antibiotic is a drug that kills or slows the growth of bacteria. It has no effect on viral agents.
As such, a virus doesn't "learn" to get around them.
And THAT being the case, your comments strike me as little more than the semi-modern version of that hoary cry, "There are things man was never meant to know."
Any sect, cult, or religion will legislate its creed into law if it acquires the political power to do so.
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:
--JohnQuite 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?
Let me give you a couple of examples of what it is already doing. I have a dear friend with an inoperable brain tumor. It turns out this particular form of tumor has genetic markers that are strongly correlated with its response to chemotherapy. After a biopsy of the tumor they can run genetic tests and give you a much clearer picture of whether chemotherapy is likely to be effective or not. As you doubtless know, chemotherapy is no picnic, so it is a hard, hard decision figuring out whether you should undertake a treatment that may extend your life 5 years, or simply screw up the the last three months you have. Tools like this genetic analysis help a bit.
On the absolute cutting edge of genetic therapy, doctors in France treated several children who had no immune system (bubble boy disease in popular parlance) due to a genetic defect. They were able use viruses to transfer a correctly functioning copy of the broken gene into the children's bone marrow. All of the children developed fully functioning immune systems. Unfortunately three of the children developed leukemia and one died. Certainly here is an example of the unforeseen consequences you are worried about, but what do you do in the face of a lethal disease like this?
Do these sound like cosmetic surgery?
How is this different from any form of medical care now in existence? Across the world, even in countries with socialized medicine, the wealthy can get better health care then the poor. If you are going to wait to develop medical treatments until this inequity can be solved, you are going to wait a very long time.
But again I ask, what is your moral standing to make this criticism? How much of your time and treasure have you given? You could cancel your cell phone this very week, send the money to Doctor's Without Borders, and they might save several lives with the supplies that it buys. Are you going to do it? I don't mean to pick specifically on you here. I have a cell phone, and unfortunately I am not going to cancel it and give the proceeds to a worthy cause. I'm just trying to make the point the people are sometimes too quick to demand charity and sacrifice in others while not offering it themselves.