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IBM Researchers Working Toward Cheap, Fast DNA Reader
nk497 writes "IBM scientists are working on ambitious research where nano-sized holes will be drilled into computer chips and DNA passed through to create a 'genetic code reader.' A DNA molecule would be passed through a hole just three nanometers wide, while an electrical sensor 'reads' the DNA. The challenge of the silicon-based 'DNA Transistor' would be to slow and control the motion of the DNA through the hole so the reader could decode what is inside it. IBM claimed that if the project was successful it could make personalised genome analysis as cheap as $100 to $1,000, and compared it to the first-ever sequencing done for the Human Genome Project, which cost $3 billion."
All that remains now, I guess, is a device that can write arbitrary stands of DNA.
If God forks the Universe every time you roll a die, he'd better have a damned good memory.
Now, if we added the storage and compute power necessary to complete the picture, imagine the ability to store massive populations of DNA information and then apply BI-like analytics. Genetic research could be greatly accelerated. The implications and applications of this technology at first glance seem broad and promising.
will introduce myself as your newly appointed, genetically self-modified, cybernetic overlord once I get my hands (manipulators?) on one of these bad boys.
"Be prepared, son. That's my motto. Be prepared." --Joe Hallenbeck
If you can read DNA through a fabricated chip, possible next step is fabricating microcircuits from transistors scaffolded on DNA.
Yours In Belarus,
Kilgore Trout
Why is it that multibillion dollar companies are constantly researching exciting new tech that makes it more and more impossible for us to remain annonymous? Just once, I want to see IBM or somebody backing Tor or Freenet or something similar.
Please remember that IBM is, like most corporations, a for-profit entity. Which means that the vast majority of their research is going to be aimed at projects that will allow them to make a buck.
In short - Tor and Freenet don't spend gazillions of dollars on technologies, while governments do.
Don't tell me to get a life. I had one once. It sucked.
âoeUltimately it could improve the quality of medical care by identifying patients who will gain the greatest benefit from a particular medicine and those who are at most at risk of adverse reaction,â he added.
Insurance companies will use it to deny health insurance outright or label any diseases that this thing finds as "pre-existing conditions".
Travelers to the US will have to stick their fingers and give a DNA sample along with their finger prints and photo.
Government will use for the "war on [insert buzzword here]"
Genetic propensity for mental illness, well, we'll have to keep an eye on you! Especially, if there is some sort of genetic predisposition towards pedophilia - think of the children!
Have to take this DNA test as part of our drug screening. Predisposition towards alcoholism or any other disease or disorder that will send our health care costs through the roof? Well, you don't have the necessary "skills" for this job. Sorry, best of luck finding another job. (Yeah, good luck in proving that we violated the ADA or EEOC!)
nothing but good (TM) can come of this!
It's interesting. While editing this post, my cursor stays as a pointer on the right side of the entry field. To edit, I had to click to the left and then use the arrow keys to get to the right. Any spelling errors left are Slashdot's fault so flame them.
It's NOT me! It's the meds! I'm on 1000mg of Fukitol.
Say hello to DNA code readers.
"Please insert your DNA in the hole for authentication"
Well I would imagine that slowing and controlling the motion of the DNA wouldn't be all that difficult. DNA has a net negative charge due to the backbone. However, how the EM fields they'd use to manipulate it would interact with the circuitry of the reader I do not know. That might be the real challenge.
You look at this as a potential privacy invasion, which I supose that it is technically, although it is way overkill for mere identification purposes. I look at this and see the possibilities for huge medical breakthroughs. Having one human DNA sequenced is neat, but it isn't really enough to tell us much about what our DNA does. To really discover or rule out genetic causes of disease, we'll need tens of thousands of sequenced genomes that we can cross reference and compare; something that is within the realm of posibility if the cost can be pushed down to $1000 a sequencing.
Before we continue this conversation I'm going to need access to your source code to verify that you are not trying to corrupt me with your ideals. I promise that if I make any modifications I will distribute them with any clones that I produce of you.
Account -> Discussions -> Disable Sigs
High speed, computer-assisted, genetic analysis technology should go beautifully with IBM's existing expertise in Data-driven eugenics solutions...
Will this be able to identify viruses? Mass availability of this capability could help significantly if a significant pandemic actually hits.
The New York Times published an article in August about a technology that decoded a human genome for less than $50,000. The inventor speculates that the technology will be able to decode a genome for just $1,000 in 2-3 years.
That being said it will be amazing to see the IBM project succeed. Either way the cost of decoding a genome is dropping so quickly it puts Moore's Law to shame.
Perfect DNA = read DNA - unwanted DNA + wanted DNA
Soon everyone will have to jump through this thing and we'll all be the same.
The way this works is quite easy to understand, however the method used for the first few decades was rather different but no less ingenious. I remember they used enzymes to first replicate the DNA a few thousand or more times, then other enzymes to cut these in random places and then some other trick and then you can, after re-reading a certain spot 20-30 times, say whether an A, T, G or C was there. Right-ish?
Could someone provide a better description of this process?
GATTACA! GATTACA! GATTACA!
Kiss and tell!
If you think that fast and cheap DNA reading applies only (or even mostly) to monitoring of individuals, you do not have a real grasp of the scope and applicability of DNA sequencing.
There are enormous resources in scientific research that goes toward generating datasets. Sequencing of humans is a significant part of it, but most of that applies to medicinal uses, such as cancer genotyping (which uses sequencing to identify specifically the genotypic characteristics of a particular tumor colony so it can be treated much more effectively than just trying to guess by looking at it "from the outside"). Also, a huge new area in medicine is going to be "personalized" medicine. Medicine that's actually tailored to the specific genetic traits that YOU have, so that the chances of side-effects are reduced and effectiveness is increased.
Then there are the thousands of researchers that need to collect sequence datasets on organisms that have NOTHING to do with humans. A big chunk of this is plant genetics: crop stress tolerance (e.g. make wheat grow more reliably in colder or dryer climates, or resist disease better), natural product optimization (e.g. make canola plants produce 10% more of the kinds of oils you care about, and less of the crap you don't). Another big chunk of this research is basic science: figuring out the specific details of how evolution has progressed, or to identify the core biological processes that make organisms tick. That's core evolutionary biology and biomechanics research.
Then there's the people trying to do constructive genomics: actually build organisms that do specific things. Like modifying yeast to produce some complex bioproduct that requires a network of potentially hundreds of genes. Or creating organisms that filter waste from water. Or building algae variants that run on sunlight and produce oil.
All of these things could desperately use robust, cheap, accessible sequencing platforms. Genetic sequencing is not all about your privacy. It's a platform which has the scope to save scientists and researchers millions, and put that towards more research and better results than towards trying to scrape out a few bases from a tissue sample.
IBM is trying big time to get into the life sciences (that's wrong actually, they actually already HAVE products they market to the life sciences, like systems for large-scale data processing). It is worth billions to them, and they want to tap it.
-Laxitive
G A T T A C A
-S
At $100 for a reader, who is to say they cant screen job applicants to see if they will have future medical issues and deny them a job (and health insurance).
Who is to say medical insurance wouldnt require such a test, to flag any possible "pre-existing conditions"
Gattaca, here we come
It cost a lot more than that. I mean first we had to evolve from amoeba and create a civilization.
Once I was a four stone apology. Now I am two separate gorillas.
A reader for all sorts of diseases, especially communicable ones. It'd cut costs in countries with relatively modern health systems by wasting less of medical professionals' time, and since it'd likely be small (and hopefully very cheap) it'd help countries with very poor or non-existent health care systems. Would also be very helpful during/before epidemics break out. I know some of these exist for specific diseases, but we need ones that can test for thousands at once.
A reader specifically for STDs. Would revolutionize casual sex and libertine lifestyles. Meet, test, have sex without worry. Very liberating.
A nutrient reader. No more relying on labels for store-bought food. Would also allow you to test food from eating establishments that do not supply nutritional information. Stick your reader in your food, find out the exact calorie, fat, etc. content instantly. Would also help with obesity/portion control.
I know I'm feeding the troll, but, we have our priorities in order because this is more important than one horny old comedian. One person's actions/crimes are way less important than accurate, cheap DNA sequencing.
I completely agree that the technology can be used for awesome and amazing things. I just have a feeling that most of the things it's going to be used for are things that aren't going to benefit humanity in such lofty ways.
Support the EFF and Creative Commons. The war is coming, and they're supporting you...
It's about time someone did this. People have been talking about real nanotechnology for about two decades. Most of what's now called "nanotechnology" is surface chemistry of finely divided powders, or simple self-assembling structures like carbon nanotubes. Real nanotechnology, useful mechanisms made of deliberately placed individual atoms, hasn't been happening much. A DNA reader is one of the few applications where building a very small number of devices at the atomic scale is useful. You don't need self-replicating assemblers turning out vast numbers of nanomachines. Small numbers of devices can be created, slowly, with STM-type devices.
At least readers are safe. DNA writers are going to be an issue.
Wait. A modified "clone"? With--say--only 50% of my DNA included? Isn't that what they call a "normal child"!
So just what is it that you're volunteering for here, and are you sure it's legal in this state? Tell you what. Bend over, pick up that pencil I just dropped, and let me see if I might be willing to let you "access" my "source code". :)
You could argue that the entire purpose of mankind is to acquire, and then use to his benefit, information. This has been the ongoing work of mankind since the dawn of mankind. Our appetite for information is insatiable, as the ways to benefit from information seem endless.
Consequently, privacy is doomed.
A work that expires before its copyright never enters the public domain and thus enjoys eternal copyright protection.
Well, yes. But it does mean that we need to work out reliable, mathematically provable to be correct, robust, and so on and so forth, methods to give close control to you over data pertaining to you. Laws alone are not enough, technology alone is not enough, most of all we need to understand why it is important and how to go about it. We need to make sure everyone knows that, from average joe to managers to congress critters and worse. We have to make it a basic human right. And we do need to do this stat.
Why is it that multibillion dollar companies are constantly researching exciting new tech that makes it more and more impossible for us to remain annonymous?
Look at it this way, with so many more people's genomes sequenced, there will be that much more data to sort through to find yours. Security through obscurity!
Anyway, DNA is useful, they're developing it for other uses, it's not IBM's fault your ancestors foolishly chose to make everyone have unique DNA that can be used to identify you.
(Yes, this was a joke, but I prefer to believe dyingtolive was also joking.)
I completely agree that the technology can be used for awesome and amazing things. I just have a feeling that most of the things it's going to be used for are things that aren't going to benefit humanity in such lofty ways.
That second part is true of every single technology ever invented. The first sharpened stick man ever made may have been used to kill food, but the second one was probably used to kill another dude and steal his woman.
Tor isn't a holy technology that can only be used in good ways either. I'm guessing 5 seconds after it was finished, someone said something like "Think of the children! This will be used to transmit child porn." You probably scoff at that objection and, and rightfully so, but that's exactly our reaction to your objection to the DNA reader.
'If you think that fast and cheap DNA reading applies only (or even mostly) to monitoring of individuals, you do not have a real grasp of the scope and applicability of DNA sequencing.'
Indeed. For a great summary of what some of the people who really do grasp it think, check out the answers to Nature Genetics' question of the year in 2007 - 'What would you do if it became possible to sequence the equivalent of a full human genome for only $1,000?':
http://www.nature.com/ng/qoty/index.html
Right now, commercial genome sequencing is about $50,000 USD with the Solexa/Illumina system. Several teams are currently competing for a $10 million USD Genomics X-Prize, which will bring it down to the $10,000 USD level:
http://genomics.xprize.org/
You can't accuse them of being under-ambitious (e.g., from Reveo: "The ultimate mission of this proposed program is to commercialize an instrument in 5-10 years that will cost less than a $1000 and sequence the whole genome and simultaneously the epigenome (methylation code) nearly error free in a minute for pennies per genome.").
Am I the only one here thinking of the slight parallel with the coulter counter and the way it made such a huge difference to blood counts once a tech no longer had to sit behind a microscope staring at a haemocytometer? Only real diff is that one does whole cells and the other is planned to read sections of individual macromolecules. Only a matter of scale really. Definitely a "darn, why didnt anyone think of that before?" moment. Hope they make it work.
I had a
In their movie it looks like the DNA has to be single-stranded to be read by the chip. One of my friends has been working on a way of doing the reading with double stranded DNA, which is easier to work with:
http://pubs.acs.org/doi/abs/10.1021/nl9020232
IBM Researchers Working Toward Cheap, Fast DNA Reader
Cheap, Fast, Good. Pick any two.
For example, Pacific Biosciences:
http://www.nytimes.com/2008/02/09/business/09genome.html
``There, Pacific Biosciences has been developing a DNA sequencing machine that within a few years might be able to unravel an individual's entire genome in minutes, for less than $1,000."
And if they DID back Tor, would you trust it?
Agreed, I don't think a cheaper / more rapid DNA sequencer is really going to provide the health benefits that most seem to think it will. Much of ones genetic code is controlled by epigenetic markers such as methylation and acetylation of DNA and various transcription factor levels. These markers seem to be even more pertinent to whether or not we get a particular disease than our actual code sequence. So unless this sequencer can read methylation and actylation states, it won't provide more info than current genotyping microarrays that are already exist below the $1000 cost point. So in all actuality, an insurer wouldn't pay to get your "full genome"
The real world uses will likely be as you suggested, to sequence unknown and engineered genomes; Monsanto is no doubt rooting for IBM
There is a private company called Pacific Biosciences that is doing something very similar, single DNA molecule sequencing. They managed to get reads from a single DNA molecule, and this was sort of the hot topic at a few computational biolgoy conferences I went to last year. It's not clear who is going to win this race, but I think a lot of people think this is the future of DNA sequencing.
For most extant species on the planet, we don't even know how many chromosomes they have, let alone having sequenced them. This will speed things up enormously.
sub f{($f)=@_;print"$f(q{$f});";}f(q{sub f{($f)=@_;print"$f(q{$f});";}f});
It sounds like the major problem with this technology is controlling the rate of passage of a single DNA strand through the detection pore. Instead of trying to solve that "hard" problem, why not design the system so that you don't need such tight control over the speed of the DNA strand?
In the current system, if the strand moves to slowly between reads, a base will be scanned twice. If the strand moves too quickly, some bases may be skipped altogether. You could slow down the rate of strand passage relative to the scanning frequency, but then you couldn't differentiate between a sequence of 3 G's in a row or a single G getting scanned three times.
If you design your DNA reader with multiple reading points in series (i.e. read the strand simultaneously at multiple points along it's length), this problem would go away. Here's how it works:
1. You assume that the entire strand moves at the same rate (this rate can vary, but must be slow compared to the scan rate of the base readers).
2. If any of your serial DNA readers record a change in base, you interpret this to mean that the DNA molecule has moved down the pore by one base height. Any detectors that did not record a base change are likely reading their next base as well, but it just happens to be the same kind as the one they read just prior.
By allowing for multiple scans per base, you increase the likelihood of making a correct call. In fact, you may be able to distinguish a C from a methyl-C from a hydroxymethyl-C and get epigenetic information at the same time you get sequence information! By using multiple detectors in series, you are able to detect when the DNA strand has moved one base height and get another crack at making sure you read the right bases.
If anyone from IBM sees this and thinks it might work - drop me a note. I would be very interested in participating in the development/testing of this technology. - Cancer genetics researcher / clinician.