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Biotech Medicine Science

1000 Genomes Project Releases Pilot Genome Data 55

Posted by Soulskill from the see-what-they're-made-of dept.
eldavojohn writes "Three pilot projects have been completed for the 1000 Genomes Project and as a result, the pilot data has been released. This makes the data of nearly 700 people available for analysis via FTP (Americas mirror, European mirror). Dr. Eric D. Green of the National Human Genome Research Institute said, 'The 1000 Genomes project has a simple goal: peer more deeply into the genetic variations of the human genome to understand the genetic contribution to common human diseases. I am excited about the progress being made on this resource for use by scientists around the world and look forward to seeing what we learn from the next stage of the project.' There's not a whole lot of information on their site about this data, but the repositories have many readme files explaining the data layout."
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1000 Genomes Project Releases Pilot Genome Data More

1000 Genomes Project Releases Pilot Genome Data

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  • Why pilots? (Score:2, Funny)

    by Anonymous Coward

    Do we really suspect there are genes for flying planes and bedding down stewardesses?

  • Stupid question (Score:3, Interesting)

    by Locke2005 ( 849178 ) on Monday June 21, 2010 @02:43PM (#32645062)
    Does the database also include MD5 checksums for each of the genomes, to make sure they don't get corrupted?

    • Re: (Score:3, Funny)

      by fatnickc ( 1259582 )
      No, but it probably gives clues about which people are more susceptible to hash, if that'll help you.
    • This is nice and all but I'm gonna wait until I can just Google 'ACTG' and get all this in a neat little package ;-)

    • Re: (Score:3, Informative)

      by jcmurray ( 975686 )
      Although they offer FTP access to the genomic data--including population, alignment and sequences (traces, calls, etc.)--the NCBI has hosted the files with a README [nih.gov] and guide [nih.gov] (aspera_transfer_guide.pdf) about Aspera's "fasp technology" [asperasoft.com] that the NCBI claims to incorporate automated checksum verification for both casual downloaders, via a browser plugin, and bulk downloaders, via a cross-platform command-line application. Aspera is new to me; they claim to have some throughput (bandwidth) advantages as well.

      • Aspera actually works quite well for transferring large data-sets such as these, it can fully saturate a 100Mb internet connection without a problem, it is only limited by connectivity and disk speed, and not troubled by things such as latency as opposed to TCP based transfer tools.

    • YES, apparently if you read the sequence.index file, you know, this one: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/sequence.index [nih.gov] The second tab is an MD5 check-sum, so don't go about freaking out =)

  • Would you guys stop messing with the godamn code (Score:1, Funny)

    by Anonymous Coward

    Why can't Slashdot, which is supposed to be run by nerds, test their code modification on test servers?

    Every other week, there's either HTML, CSS or Javascript errors.

    This time, they broke the mod system. I select "funny" and it does nothing. How the hell can you break something as basic as "onchange"?

  • Double edged sword (Score:3, Insightful)

    by Wowsers ( 1151731 ) on Monday June 21, 2010 @02:50PM (#32645136) Journal

    The genome project has the potential to help people with their illnesses, especially with tailored treatment instead of the generic drugs that work on some people, but not on others and might cause toxicity with certain combinations of drugs which you won't know until you are subjected to that combination.

    On the flip side, this could be a governments wonder weapon. Target a specific trait in the DNA, ie. people with black hair, or men, etc. etc. and kill them off, or make them weaker... all sorts of nasty things.

    • Just about everything in life is a double edged sword.

    • I'm not sure if you could really DO that though, I mean in some cases you might be able to (like say men vs women) - but I don't think you could have something target specifically people with black hair. I don't think working with genetics is like working with program code - you can't simply do an if statement to test for a condition and then execute if true. I was under the impression you could simply target the genes you'd want to change.

      But then again, I didn't even take Bio in high school, so I have no

    • It's something that's been thrown around a lot but I have to wonder if targeting those kinds of traits with a disease is really possible. The easiest way to target a cell is to target the binding receptors on the outside of that cell, unless the genes that code for the trait you want to eliminate are also expressed in the binding receptors I think that creating such a disease is way beyond our current technology.

      But maybe I'm wrong, any experts out there want to weigh in?

      • OF course it's not possible, at least not yet. There isn't really any drug that has been developed starting with a genome sequence as in "oh, so that's the gene. Now I know how to cure x". There seem to be a few drugs like anti-depressant that have been found to work better in people with a certain version of a gene, but these effects were only found after many trials, and the mechanism is not always known.

      • Re: (Score:3, Informative)

        by Turbio ( 1814644 )
        Most genes are used to produce proteins. Samples of all the proteins present inside a living human cell are exposed on the cell's membrane, as part of the immune system machinery. (See Mayor Histocompatibility Complex http://en.wikipedia.org/wiki/Major_histocompatibility_complex [wikipedia.org]) Those proteins can be targeted using homing peptides (think of it as a specific antibody) on a liposome (http://en.wikipedia.org/wiki/Liposome [wikipedia.org]). That liposome can contain anything from drugs to viral RNA. Right now, you can make

      • Re: (Score:2)

        by glwtta ( 532858 )
        But maybe I'm wrong, any experts out there want to weigh in?

        No, no, that's exactly how it works. Let's not forget that as long as you use the word "genetics", science is whatever you want it to be. If you say that sequencing a couple of human genomes allows you to instantly create weapons that will simply wipe out vaguely defined groups of people, who's to say you are wrong?

        It's not like anyone can actually understand biology. Why that would be preposterous - clearly anyone claiming to have any kind

    • Re: (Score:3, Insightful)

      by Anonymous Coward

      On the flip side, this could be a governments wonder weapon. Target a specific trait in the DNA, ie. people with black hair, or men, etc. etc. and kill them off, or make them weaker... all sorts of nasty things.

      Stop it with the ill-informed conspiracy mongering. There are downsides to human sequencing, but not for the reasons you've described. A lack of DNA sequencing has never stopped people from killing individuals with the traits you enumerated. So what are the problems?

      • Genetic testing without genetic counseling: What does a 1.2 increased risk of Alzheimer's mean?
      • Genetic discrimination: Sorry, you have a 1.1 OR risk allele for multiple sclerosis. We can't insure you.
      • Racism: Ah, your blood isn't pure enough, you
    • Your doctor could also target a particular trait and try to kill those people off who have said trait. (S)he also wouldn't need a database of any kind. Just FCFS.

    • Id be very wary about having my Genomes mapped. The likelihood of having some pharmaceutical corporation owning the patent on your own genetic makeup is a little too creepy. I wonder how long it is before this kind of stuff joins a growing database where insurance companies can pay subscription for access fee's.

      My tinfoil hat is not coming off to play today.

      • One of the major advantages of projects like this, funded by NCBI and EBI and other government agencies, is that the data will be a lot harder for anyone to put under IP restrictions than it would be if it came out of private labs.

    • On the flip side, this could be a governments wonder weapon. Target a specific trait in the DNA, ie. people with black hair, or men, etc. etc. and kill them off, or make them weaker... all sorts of nasty things.

      If we had the technology to do that, which we do not.

      If someone has black hair, their physiologies are very similar to anyone else, receptors are likely to be identical. Blondes would likely be susceptible to the exact same things. We don't have the capability to target specific genes in cells within a patient to, say fight cancerous cells.

      An ability to deploy something into the environment that would specifically target black hair genes yet can't be used to target cancer cells? I don't believe it.

      Before

  • Am I the only one who read that as "1000 Gnomes Project to Release Pilot Gnome"?

  • I'm gonna make a were-pig! Delicious aggressive angry bacon.

    • Re: (Score:2)

      by Kozz ( 7764 )

      Beware the boar taint [wikipedia.org]. Listen to segment 1 [wpr.org] for a fantastic related story (not for the faint of heart).

      I'm sorry this stuff is very much all OT, but it's a fascinating story and I had to share it. You mentioned pig, so here we are.

  • 4% genes of 2% total DNA of 700 people (Score:3, Insightful)

    by peter303 ( 12292 ) on Monday June 21, 2010 @04:24PM (#32646246)
    Tis probably more comprehensive than marker studies, but not really whole genomes. Who knows how important the so-called junk regions will be eventually?

    • Re: (Score:2, Informative)

      by Turbio ( 1814644 )
      Hey, I work with junk regions! (satellite DNA) And I completely agree with you. But I see that centering on the variability of those few regions rather than sequencing a second complete genome will probably be better for health-care research. The project's title is completely misleading. That's for sure.

      • Remember, this is a pilot project. The ultimate plan is, indeed, to get deep sequencing on 1000 people. Personally I suspect (and hope!) that by the time the project is finished, the "thousand-dollar genome" will be a reality and it will be possible to do, e.g., clinical trials which include deep sequencing of the genomes of arbitrary sets of several hundred or several thousand people. If that happens, we'll probably have 1000G to thank for a lot of it, just as we have the HGP to thank for a lot of the s

  • The most important question I have when i hear about datasets is:

    How much data are we talking about here, 1tb? 5tb? 50 megs?

  • 1000 gnomes project - ooh i'd like a gnome of my own!

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