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Scientists Complete Map of Human Genetic Variation 190

Posted by samzenpus from the one-of-these-things-is-not-like-the-other dept.
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."
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Scientists Complete Map of Human Genetic Variation More

Scientists Complete Map of Human Genetic Variation

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  • If there ever was... (Score:3, Insightful)

    by Seoulstriker ( 748895 ) on Wednesday October 26, 2005 @10:23PM (#13886260)
    If there ever was a case for computational biology, this is it. :-)

    • Re:If there ever was... (Score:4, Insightful)

      by CyricZ ( 887944 ) on Wednesday October 26, 2005 @10:29PM (#13886285)
      Indeed, these researchers are on the cutting edge of technology. They're pushing today's computing systems to the limit. It is research like this that will truly help drive forward computer hardware. Much like the Apollo project resulted in so much technological spin-off, we're bound to see the same happen with this sort of research, too.

      • I think this is were being stuck with the obtuse P4 is going to hurt us. We have special processors for Graphics, and now physics. will one day we have a chip designed to speed up the math needed for this.

        Is IBM's cell processors expandable to more than just vector co-processors? Say maybe a GPU, a PPU, and now BPU or two of each?
    • Yeah. My paper was just accepted to nature genetics, and uses the hapmap as one of the data sets. Interesting that they claim it's finished now, when I had the 5K data back in may...

      Ok, so this is to reflect the nature paper that is just comming out now, where a variation was looked for every 5,000 bases. The new map is 5x as dense (every 1k bases), and was released on the 10-24-05. The new map should provide a lot more resolution for interesting questions.

      Funny, David Altschuler is my former boss, and

  • Podcast from nature (Score:5, Informative)

    by Oxen ( 879661 ) on Wednesday October 26, 2005 @10:30PM (#13886289)
    Here is a link to the mp3 of the Nature podcast on this. [nature.com]

    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.
    • Parent makes an interesting point. Here is a link [cshl.org] a website where one can find additional information and even tab-delimited datafiles of SNPs variation and linkage.

      Here is an additional site [u-tokyo.ac.jp] with even more information and datasets available. I'm going to download these and see what I can find.

    • Re:Podcast from nature (Score:4, Insightful)

      by clarabellabo ( 874040 ) on Wednesday October 26, 2005 @10:41PM (#13886346)
      Maybe so but how many people are actually keeping track of this kind of research? I do to a certain extent because I have Usher Syndrome (a genetic condition) but I bet most people don't. I think it's great that they make announcements like this so the masses get to know about it. Maybe this kind of exposure will help more stem cell research to get done someday. If that happened then I might not have to face a future where I'm blind and deaf...and other people with genetic conditions may see cures in their lifetimes too :)
      • While I'm all for stem cell research, isn't gene therapy more suitable for curing defects in protein-producing genes? In Usher's case, the affected genes are already known (thanks to the mapping!) and the methods for either knocking off the defective gene or replacing them with a healthy one are probably already being devised or fine-tuned.

        Meanwhile, check out if carnosine might slow down the damage to your retinas. It is being used as eyedrops to alleviate the degeneration of proteins associated with aging

  • Great (Score:4, Insightful)

    by dtfinch ( 661405 ) * on Wednesday October 26, 2005 @10:33PM (#13886304) Journal
    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.
    • Long before then, it'll likely be used for stuff like this [guardian.co.uk]... or master race ala carte.

    • Re:Great (Score:2, Informative)

      by jrau ( 880696 )
      Biotech companies get special compensation by the U.S. government to develop treatments for so called "orphan" diseases. They get tax breaks and exclusive market rights if they develop drugs for these conditions, and as a result there are really quite a few advancements in the treatment of rare diseases when it normally wouldn't be monetarily feasible... but of course there are tons of different wierd conditions that people have. Here is a link for the FDA website discussing this: http://www.fda.gov/fdac/ [fda.gov]

    • No rare alleles in data (Score:4, Informative)

      by John Hawks ( 624818 ) on Thursday October 27, 2005 @12:23AM (#13886846)

      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 [johnhawks.net]:

      The HapMap is an incredible step forward in characterizing human genetic variation. It's a challenging dataset to work with, though. It's like an old map showing continent margins and little else -- we can see many of the common SNPs, but for most we have no idea which ones are functional or what they might do.
      --John
    • By that time, your doctor will be able to synthesize anything he needs on the fly, right there in the office.

  • Genetic Discrimination (Score:3, Interesting)

    by 246o1 ( 914193 ) on Wednesday October 26, 2005 @10:38PM (#13886330)
    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.
    • Yes if there was only some way that everyone could pay a fixed amount out of their income and have it fund healthcare for everyone. A "public" health system if you will. What an idea!! I've got to patent that asap.
    • Naw. We'll just use gene therapy to change the variations in any direction we want. Someday, those Penis Enlargement pills will actually work; unfortunately your spam filter will protect you from this amazing enhancement in medical science. :(
    • For example, it's well known that Amish, Ashkenazi Jews, and other groups suffer from certain genetic maladies far above the average.

      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

  • Patented (Score:2, Insightful)

    by Profane MuthaFucka ( 574406 ) *
    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!

    • Re:Patented (Score:4, Informative)

      by lockefire ( 691775 ) on Wednesday October 26, 2005 @10:57PM (#13886431)
      First of all, most SNPs are free information. dbSNP [nih.gov] 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 think the essential bonus of the haplotype is that you can infer data without directly measuring it. According to people at the Broad (where David Altschuler hangs a lot of the time), with the 5K map (1M snps), you can effectively measure 90% of the human variation that exists (about 10M snps).

        The haplotypes let you determine that if SNP 1 is an A, then SNP 2 is always a G, etc. Ok, for people who like things more technical, the R^2 values of a lot of the snps are high, so they can use these snps, or se
    • That is sad indeed, although I'm sure that many governments will violate the said patents, if the disease is important enough - like Brazil does wrt AIDS or Taiwan plans to with bird flu. Things like these affect people on too personal a level. But then, that's me being optimistic - hunger is personal too, and look at it go!
    • If you can write a digit followed by 6 zeroes in that checkbook, you're A-OK!

      Oh, I could write a check right now and if would cure my Type II diabetes I would. Of course, there's no chance that check would clear the bank, but so what? I'd already be cured!

  • Well all I can say is... (Score:5, Insightful)

    by Create an Account ( 841457 ) on Wednesday October 26, 2005 @10:39PM (#13886335)
    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.

  • They only analyzed DNA of 269 people (Score:3, Informative)

    by backslashdot ( 95548 ) on Wednesday October 26, 2005 @10:43PM (#13886361)
    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.

  • Obligatory... (Score:4, Funny)

    by RavenChild ( 854835 ) on Wednesday October 26, 2005 @10:45PM (#13886371)
    99.9% of your genes are belong to everyone!

  • RTFHM (Score:4, Informative)

    by Anonymous Coward on Wednesday October 26, 2005 @10:47PM (#13886383)
    Read the friendly Haplotype Map, that is:
    http://www.hapmap.org/ [hapmap.org].
    You can even browse the project data: Gbrowse [hapmap.org]

  • Design...? (Score:3, Funny)

    by GaryPatterson ( 852699 ) on Wednesday October 26, 2005 @11:05PM (#13886463)
    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.

    • Re:Design...? (Score:3, Funny)

      by Oxen ( 879661 )
      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 ori
      • 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)
    • The labels were removed when the design was commoditized by knock-offs which flooded the market.

      The original product is the Homan and the most popular knock-off is Human. You might have difficulty seeing the difference in the label but there is a huge price and quality difference.
    • Anyway, face it Buddy, after 7800 years it's all public domain.

  • "Corporations complete patent applications for human genetic variations".

  • Genetics & drugs: good news/bad news (Score:3, Informative)

    by G4from128k ( 686170 ) on Wednesday October 26, 2005 @11:09PM (#13886486)
    Genetic variations affect how people absorb drugs, metabolize drugs, are helped by drugs, or have dangerous reactions to drugs. People can vary more that 10000:1 in the rate of deactivating (or retaining) drugs and drug metabolites. This variation impacts clinic testing and drug approvals. The result is that some promising medications are knocked out by clinical testing when too few people are helped or too many people are hurt. Genetic testing would help determine which drugs work for which people. Already doctors use 3 different drugs for childhood leukemia as determined by a genetic test (the wrong drug can be lethal). Increasing use of genetic testing will have good and bad effects.

    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.

  • A Human Geneticist's Point Of View (Score:5, Informative)

    by kid_icarus75 ( 579846 ) on Wednesday October 26, 2005 @11:18PM (#13886521)
    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.
    • 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.

      While it may sound like falling into the pathetic fallacy to call a gene "bad," there are many traits which are almost certainly highly genetically dependent that most people would rather not have. Not just rare "genetic disorders," either. Is there really any function for myopia, for inst
      • Yup.

        Or fun ones like sickle cell anaemia which have a purpose, but a purpose which in the near(ish) future we won't need (hopefully -- and I mean malaria defense, for those not familiar).
      • I think you're missing the point. It's really a matter of symmantics, but genes are the strings of sequences which make a protein (there are other functions, but for the moment, we'll just stick with those). Genes coding for proteins (which is what most people consider the definition of genes, though there are a lot of small regulatory genes which are an entire PhD thesis in and of themselves) for the most part all serve an additive effect. There aren't a lot of genes I would rather not have (a lot are a
      • >Is there really any function for myopia, for instance? What about colorblindness?

        Semantics are interesting. The cause for those are mutations in some of the genes, but the genes themselves are not "bad". Each of the variations of a gene is called an "allele [google.com]", and different alleles of a gene can vary on how they perform and, thus, be considered to be "good" or "bad". Talking about good or bad genes is conceptually incorrect, and it doesn't help anyone when these terms muddy the waters for the already c

      • Given a choice, no one would want to be born knowing they'll need eye correction at some point in their life.

        Given that most 'nerds' need eye correction, while less intelligent people do not, I hypothesize that there is a relation between intelligence and needing eye correction. If this is the case, then I will choose wearing glasses all my life to being less intelligent. (but that is just me who can't see the floor without glasses)

        I of course am not sure how you would test this hypothesis, but that i

        • Im not so sure about that. I've been visiting the good old eye doctor since an early age because of lazy eye, and various corrections for that. I've been told more than once that overusing your near vision will make you near sighted (hence the need to take a few minutes off every couple hours). Surprise, I'm a nerd and i'm nearsighted.
    • 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 ?

      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 /.geek and a human geneticist r at a party, and they c a super hot babe across the room.
    • I suggest that you
      a) Read the paper.
      b) Read the followup papers that also discuss in more detail how to use this data to perform analysis.

      Q#2: If you're interested in how well this data transfers over to people from other populations, then read the "tag transfer" paper, which should be out in a month or so. Paul de Bakker will have a paper comming out that studies how to apply this data to other populations. The quick summary: you can use this data for other populations. By studying groups like Yoruba (a
  • A summary [illuminatingscience.org] plus a discussion of some thoughts on the ethical issues [illuminatingscience.org] involved in both intellectual property and discrimination are on the University of Queensland's physics blog [illuminatingscience.org].
  • ...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?

  • Can you cure my color blindness? (Score:3, Insightful)

    by QuantumG ( 50515 ) <qg@biodome.org> on Thursday October 27, 2005 @12:02AM (#13886733) Homepage Journal
    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 [nature.com] 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.
  • As someone working in the genomics and molecular biology field, I have to say that it's been an amazing ride over the past 6 or 7 years, since the human genome project really kicked in to full gear, the HapMap project took off, the National Cancer Institute's Cancer Genome Project, and comparative sequencing of countless genomes has and will be done.

    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 ofm

  • 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.

  • 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 ma

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