1000 Genomes Project Releases Pilot Genome Data

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."

Comments

Why pilots?

[Anonymous Coward]

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

Stupid question

[Locke2005]

Does the database also include MD5 checksums for each of the genomes, to make sure they don't get corrupted?

Re:Stupid question

[fatnickc]

No, but it probably gives clues about which people are more susceptible to hash, if that'll help you.

Re:Stupid question

[WrongSizeGlass]

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:Stupid question

[jcmurray]

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 and guide (aspera_transfer_guide.pdf) about Aspera's "fasp technology" 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.

Nevertheless, the sequence data files embed MD5 checksums directly, per NCBI documentation, which I would expect bulk downloaders to take advantage of independent of any third-party "technology."

Re:Stupid question

[jamesdood]

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.

Re:Stupid question

[Locke2005]

I tried googling GATTACA, but I couldn't find any genomes in the results...

Re:Stupid question

[ZirconCode]

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

Would you guys stop messing with the godamn code

[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

[Wowsers]

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.

Re:Double edged sword

[Favonius Cornelius]

Just about everything in life is a double edged sword.

Re:Double edged sword

[Monkeedude1212]

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 idea.

Re:Double edged sword

[MozeeToby]

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?

Re:Double edged sword

[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, your children can't attend our schools.
• Inconsistent genealogy: You can figure this one out.

None of these rely on bizarre science fiction weapons to cause harm. Please don't spread FUD.

Re:Double edged sword

[shriphani]

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.

Re:Double edged sword

[gandhi_2]

Except single-edge swords.

Re:Double edged sword

[matt4077]

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:Double edged sword

[zill]

Let's not be too hard on the guy. He can't help it.

The FUD spreading is caused by a dominant allele in his jeans after all.

Re:Double edged sword

[gilleain]

Except single-edge swords.

Or "knives" as most people call them.

Oh, no, wait. Katanas.

Re:Double edged sword

[rainmouse]

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.

Re:Double edged sword

[city]

You gotta watch out though, those things can be kind of a double-edged sword.

Re:Double edged sword

[mattack2]

It's in his genes.

Re:Double edged sword

[Anonymous Coward]

Most of the technological and Scientific advancements have been created by Jewish Scientists. From Physics and Mathematics, to Biology and Chemistry. Jews compose the highest percentage of Nobel prize winners, Field medal winners, best writers, and chess masters on the planet. What have you, or your pathetic race ever accomplished?

Re:Double edged sword

[Turbio]

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) Those proteins can be targeted using homing peptides (think of it as a specific antibody) on a liposome (http://en.wikipedia.org/wiki/Liposome). That liposome can contain anything from drugs to viral RNA. Right now, you can make a solution with liposomes (or polymersomes), that when injected only kills the person if he/she has a certain trait. But I gess that is not a weapon of mass destruction... Anyway, making it a disease is another story. It could involve modifying the HIV virus, which already has a lipid bilayer just like a liposome. And then you have the problem of keeping that disease specific to the target population. And viral genomes tend to mutate at a very fast rate.

Re:Double edged sword

[glwtta]

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 of scientific expertise is a hubristic zealot, so blinded by the allure of infinite profit that they will wreak unspeakable misery on the human race; for, after all, they are meddling in God's Domain.

That, or they could use this data to possibly find genetic markers for a few diseases... It's one or the other, really.

Re:Double edged sword

[Anonymous Coward]

Yup, basically the SF written on this subject tends to have the virus maker as one of the first victims. The virus mutates until it targets him, and by the time he realises it has spread into the wider population. If the author doesn't know their stuff they usually have everyone die (in reality humans vary a lot, the virus probably doesn't work on a small minority of people for one crazy reason or another).

Re:Double edged sword

[interkin3tic]

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 anyone suggests to me that the government or pharmaceutical industries have such a cure for cancer but are keeping it a secret... there's really not much point in us talking if either you're that paranoid or I'm this naive. Except to say that if they were that smart, they wouldn't be announcing this.

Anyway, why would the government want to kill off people with black hair or men in a given population specifically? A simple bomb that doesn't discriminate is cheaper, easier, and more effective.

Re:Double edged sword

[ZirconCode]

I have a Moebious Sword you insensitive clod!

Re:Double edged sword

[DMUTPeregrine]

Or sabers, falchions, hangers, or pallasch among others...

Re:Double edged sword

[Daniel Dvorkin]

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.

Re:Would you guys stop messing with the godamn cod

[gandhi_2]

Protip: Don't use IE.

Re:Would you guys stop messing with the godamn cod

[Monkeedude1212]

I select "funny" and it does nothing.

That's not an error, Slashdot just doesn't agree with you.

Re:Would you guys stop messing with the godamn cod

[Anonymous Coward]

Hint: I'm not using IE.

Re:Would you guys stop messing with the godamn cod

[Yvan256]

I tried to mod you "funny", but the moderation system is indeed non-working. Also, after hitting "reply" I was sent to a new page with a messed-up "Reply to this" button, instead of simply having a comment textarea below your post on the same page.

Someone's messing around with the live website.

Re:Would you guys stop messing with the godamn cod

[Anonymous Coward]

Yeah, thanks, I'm using Seamonkey and I can't even show all comments anymore. Slashcode has been fucked up (bloated, slow, etc.) ever since the "ajaxification", but now it's fucked up and broken. Fucking amateurs.

Re:Would you guys stop messing with the godamn cod

[Yvan256]

It seems to be broken for everyone with mod points: there's already 15+ comments and nothing has been modded yet.

Re:Would you guys stop messing with the godamn cod

[Anonymous Coward]

Yep, they are messing with live code again and some AJAX stuff is broke at the moment. Slashdot needs a beta interface AND a place to moan about bugs so it doesn't (rightfully, at the moment) have to be discussed off-topic in other stories.

    No Karma Bonus - is that new?

I currently see

    No Karma Bonus and Post Anonymously as options. Also, caving in to the forum growth around /. and allowing BB code would be neat.

Re:Would you guys stop messing with the godamn cod

[Monkeedude1212]

Did you try clearing your AOL cache?

Re:Would you guys stop messing with the godamn cod

[WrongSizeGlass]

AC complaining != /.ers caring. I'm just sayin'

Gnomes

[Kell Bengal]

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

Re:Gnomes

[Anonymous Coward]

Am I the only one who read that as "Am I the only one who read that as "1000 Genomes Project to Release Pilot Genome"?"

Re:Gnomes

[ascari]

I'll be damned, Dan Quayle! We haven't heard from you in a while!

I'm gonna..

[e2d2]

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

Re:I'm gonna..

[Kozz]

Beware the boar taint. Listen to segment 1 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.

Especially

[Anonymous Coward]

Especially these:
http://wasteawarebusiness.files.wordpress.com/2010/01/double-edged-sword.jpg

4% genes of 2% total DNA of 700 people

[peter303]

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:4% genes of 2% total DNA of 700 people

[Turbio]

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.

Re:4% genes of 2% total DNA of 700 people

[Daniel Dvorkin]

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 sequencing technology we have today.

How much data is this?

[Mage Powers]

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

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

Re:How much data is this?

[Anonymous Coward]

You could download it and find out, but that would be like 3 minutes of work to do an ls in the directory on the FTP site and add some numbers.

Re:How much data is this?

[karlnyberg]

Approximately 3.5TB. That's the math.

Re:How much data is this?

[Anonymous Coward]

I stopped scanning at 9TB - I really would like to know how big the dataset is. As much as I like this data, though, I can't afford to dedicate that much hard drive space to it.

Re:Would you guys stop messing with the godamn cod

[interkin3tic]

Or Opera, because that ain't working either.

Misreading mornings

[tommten]

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