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New Tech Promises Cheap Gene Sequencing In Minutes
Zothecula writes "Sequencing an entire genome is currently a highly complex, time-consuming process – the DNA must be broken down into segments and replicated, utilizing chemicals that destroy the original sample. Scientists from Imperial College London, however, have just announced the development of a prototype device that could lead to technology capable of sequencing a human genome within minutes, at a cost of just a few dollars. By contrast, when sequencing of the genome of Dr. James Watson (co-discoverer of the structure of DNA) was completed in 2007, it had taken two years and cost US$1 million."
can it sequence as fast as slashdotters can claim first post?
Now if we get it down to a second we can use it to control turnstyles...
Let's hope we heed the warnings of sci-fi.
If they can build those in bulk, the CSI episodes are becoming much more realistic
I can't get too enthused about a prototype of something that might one day lead to another prototype, "up to ten years away".
But the article in the sidebar titled "Breakthrough raises possibility of genetic children for same-sex couples" is at least amusingly illustrated with a picture of Bert and Ernie.
"Warning?"
That's an instructional video!
My first Journal Entry ever, in 8 years! http://slashdot.org/journal/365947/aphelion-scifi-fantasy-horror-poetry-webzine
have just announced the development of a prototype device that could lead to technology capable of
The prototype could lead to technology, which could lead to discoveries that could lead to clues that could lead to a one-armed man who could lead to some funding...
What problem were we trying solve again?
I hate over-hyped article titles and summaries.
Why are you letting these clowns ruin our country?
I hate scientific journalism. "New tech promises cheap gene sequencing in minutes" is complete bullshit. When I read interesting news on scientific research, I try to track down the actual research to compare. Usually what's in the media is something like "SCIENTISTS ONE YEAR AWAY FROM CURING CANCER!!!" and the research reads "Behavior of protein XYZ under high pH"
For those of us here that actually care about this kind of stuff, here is the real information: http://pubs.acs.org/doi/full/10.1021/nl103873a
It drives me nuts when the popular media article doesn't include a citation back to the original research. Here's a link to the article on the Nano Letters website: http://pubs.acs.org/doi/full/10.1021/nl103873a
At the heart of the Imperial College device is a silicon chip, with a 50-nanometer nanopore bored through it. DNA strands are propelled at high speed through this hole, and get their coding sequence read by a “tunneling electrode junction” as they come out the other side. This junction consists of a 2-nanometer gap between two platinum wires, with an electrical current passing between them, across the gap. The current interacts with the unique electrical signal given off by each of the DNA strand’s base codes, and the resulting data is then processed by a computer to determine the complete genome sequence. The chips are reportedly quite durable, standing up to repeated uses and washings with no loss in performance.
Doesn't sound too outrageous. I suppose this is one advantage of only two base pairs.
they are not gay! otherwise Bert would have been in the tub with Ernie instead of the duck.
Dr. OneEye: "We have a match on the Genome of the DNA we found and its a HUMAN"
Detective BRassBalls: "How did you find it that fast?"
Dr. OneEye: "With this new Instant Genome from As Seen on TV". "We can solve cases in minutes instead of 40 minutes with commercials and it only cost 19.95 with S&H".
Detective BRassBalls: "You total NERD. Do you know what you have done?"
Dr. OneEye: "No What?"
---- Later ----
Detective BRassBalls: "Now we solve cases in 5 minutes with 55 minutes worth of commercials and make 1/10th the pay we once did"
Dr OneEye, just learning his pay cut, just stares into nothingness and you hear the Instant Genome whirring in the background....
I can program myself out of a Hello World Contest!!
as in, every time- no matter how bad the power situation ever is, especially when 'shutting down to be electronically insignificant to detection' artificial gravity is always a constant.
Millenium Falcon, Jetstar 1, enterprise, firelfy, pigs in space, hitchikers, galactica, dr. who, farscape, stargate atlantis & Universe, starship troopers, tripping the rift....
every day http://en.wikipedia.org/wiki/Special:Random
The first one was also done in 'minutes', 1,051,897 of them.
Ignoring any one specific advance in technology, the cost per base pair of sequencing DNA has dropping exponentially. The cost to sequence an entire human genome has gone from billions of dollars in 1990 to about $40,000 in 2010. By 2015, it will probably cross the $1000 barrier.
By 2020, it will likely be under $100 - at which point it might as well be a standard part of a person's medical file.
By 2030, it could under $1 - amateur biologists could start collecting genomes like poleroids while hiking.
By 2040, it could be a fraction of penny - cough on a sensor, get a readout of all the microbes in your lungs, what strain they are and, by looking at the specific mutations between generations and comparing to a database of everyone else's microbes, the likely person who infected you.
At that rate maybe I will be able to order my cat-girl sex-slave by 2016!
2 years @ $500,000 a year doesn't sound like a lot. In fact it sounds completely implausable for something as valuable as the results they produced. Maybe in the 50's or something.
I wonder how they came up with that figure? I imagine the lab + scientists alone cost that much to outfit and rent; not to mention lawyers and research assistants
I went to battle M.C. Escher, but drew a blank.
By contrast, when sequencing of the genome of Dr. James Watson (co-discoverer of the structure of DNA) was completed in 2007, it had taken two years and cost US$1 million.
Yeah, but nowadays it can be done in a few hours and costs under $10,000. May as well say that the Human Genome Project took 13 years and cost $3 billion - true, but not very relevant.
And we're well on-track for sub-$1,000 genomes in a year or two (without any new breakthrough technologies); which is basically "good enough" for research purposes. As Lincoln Stein pointed out in a recent paper, we're already almost at the point where it costs less to sequence a base pair than it does to store it for computational analysis.
sic transit gloria mundi
No more long lines at the gene sequencing place!
No more frantically pulling everything out of the glove compartment looking for $1 million in change.
- sigh, that's all I got
DNA Sequencer Vending machines in convenience stores ?
Son, let's go to buy some candy.....
The base pair sequence is nice, yet there is much more to gene expression than that. Two cloned cats can look and act remarkably differently. In embryology, it is known that the same gene can act differently depending on the timing and circumstances of that gene's activation. So bravo for cheap fast sequences, but we will need to know more about gene expression for genomics to bring big changes to medicine.
Obi-Wan: "I felt a great disturbance in the Force, as if millions of voices suddenly cried out in terror and were sudden
Last weeks issue of Nature mentions gene hackers who study newly posted human genomes for interesting DNA. We are somewhere in the "third decade" of sequenced human genomes- that is between 100 and 1000 fully sequenced genomes published so far. There are interesting things remaining to be discovered in this huge mass of data.
Here's a small detail that the article leaves for the last paragraph:
“The next step will be to differentiate between different DNA samples and, ultimately, between individual bases within the DNA strand,” said study co-author Dr. Tim Albrecht. “I think we know the way forward, but it is a challenging project and we have to make many more incremental steps before our vision can be realized.”
In other words, they can zip DNA through this device quickly and measure some signal as the DNA passes through, but no one knows yet whether it is possible to extract accurate sequence information from the signal they get. Similar implementations (that admittedly have a less sensitive way of getting a signal from the different DNA bases) have so far failed to see significant enough differences between the DNA bases to be useful for sequencing. It's not clear that this method will work as advertised
Nanopore sequencing has been around for at least a decade in the lab. They admit that their method of using tunnel junctions to detect the DNA cannot even distinguish between different base pairs.
For background, here's the basic idea of a classical nanopore sequencer:
1. Make a solution with ions in it with a very thin membrane separating two different compartments each containing an electrode. The membrane has a very tiny hole (nanopore)
2. Apply a voltage. This will either attract or repel the salt ions, thus you get a detectable current passing through the nanopore.
3. Put DNA in the solution. The hole is hopefully small enough that the DNA can only go through as if stranded like thread through a needle. As the different base pairs move through, they block up varying amounts of the hole, manifesting as small changes in resistance across the hole.
4. Profit
The only real limiter is how thin you can make the membrane. Recently, some researchers used graphene, which is thinner than your average base pair, and so you do not get a resistance that is the convolution of many base pairs blocking up the pore at any given time. For more, google "Dekker DNA translocation through graphene nanopores" to see that they can already detect single pairs - and do it thousands of times a second.
Pacific Biosciences is already on the market with single-molecule sequencing.
http://www.pacificbiosciences.com/
Keep your eye out for Ion Torrent's Personal Genome machine. Reviewed on the same site http://www.gizmag.com/ion-torrent-personal-genome-machine-launched/17330/
I think this is the right paper for those who want to check it out, if you have the super $$ sub to this journal
Letter
DNA Tunneling Detector Embedded in a Nanopore
Aleksandar P. Ivanov, Emanuele Instuli, Catriona M. McGilvery, Geoff Baldwin, David W. McComb, Tim Albrecht*, and Joshua B. Edel*
Department of Chemistry
Department of Materials
Division of Molecular Biosciences
Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
Nano Lett., Article ASAP
DOI: 10.1021/nl103873a
Publication Date (Web): December 6, 2010
Copyright © 2010 American Chemical Society
Membrane - very thin sheet or plate ..driven through a nanopore by an electric field. This results in a drop of the current across the pore.
From this, information on molecular properties such as length, composition can be extracted.
With DNA, it may be possilbe to get seq data Unfortunately, the state-of-the-art detection based on
ionic current blockade or fluorescence spectroscopy seems to lack the spatial and temporal resolution necessary to
obtain structural information at the single base level.
An alternative method based on tunneling perpendicular to the DNA backbone has been proposed to alleviate these limitations.
Due to its quantum mechanical origin, the tunneling current
decays rapidly with distance leading to enhanced spatial
resolution and better molecular specificity (ability to tell which base is moving thru the pore)
Pore - a small hole in the sheet
current - ions (atoms such as sodium or chloride) per second; in a salt solution, current is carried between the electrodes (usually Platinum wire, or graphite) thru the liquid by ions; these ions have a size of roughly 1 angstrom, so they are, compared to electrons, really big.
when we measure the current, we are simply measuring the number of ions/second going thru the pore; if the pore has ~ the size of a DNA moleucle, then it seems obvious tht when the DNA fills the pore; fewer ions can go thru, so the current will drop
As the authors state (editied)
In a typical nanopore experiment, biological molecules are
Wikileaks Task Force!?!?! (WTF!?!?!) I saw the 5th element on TV a few months ago (saw it in theatre years ago), and they sequence an entire person (a superbeing actually) in less than 3 minutes! Mind you, its perhaps a bit like the computer tech I see on NCIS where every NP-hard problem is resolved in less than 10 seconds, and you can super-zoom-in on the most crappiest video and make it look like ultra-high-definition! K3W3L! Where's my youtube super-ultra-high-definition booster program! Anyway, I saw them do it in less than 3 minutes, the whole body, from only 2 or 3 cells. I saw it in the movies, so it must be true! Now these folk claim to be able to just read the DNA in a few days? Pfffft. Thats not like the movie I saw! ..seriously (finally), this is amazing work! Kudos to the whole Imperial College team!
According to [1] the cost of sequencing Watson's genome in 2007 was $2 million, not $1 million! Costs of the "original" genome sequences are often misquoted as well as $3 billion when that was the cost of the entire HGP which included the yeast genomes, the mouse genome and the development of a lot of technology that enable the sequencing of larger genomes. For an estimate of the actual cost of sequencing the original genomes (circa 2001-2003) a better source of information is the total amount of capital Celera raised from the late 1990s through 2003. Alternatively one could go through the NIH NHCGR budgets for the late 90's thru 2003 and separate out the grants actually awarded to the primary genome sequencing centers related to human genome sequencing. I believe the "common" number quoted for the first human genome is around $1 billion (~30% of the cost of the entire HGP), but I suspect that Celera never raised that much money so the real 1st & 2nd genome costs were probably less.
But it is clear that in the last 7 years the cost of sequencing a genome has declined by more than 5 orders of magnitude and that another order of magnitude will bring personal genome sequencing into budget realm (~$500) of individuals living in developed countries. However the fly in the ointment here is that there is currently little capability and will be little capability for some time [2] for using this information in medical settings to improve health care or reduce sickness, disease and aging.
Most people think that just because one sees reports on CNN that one can diagnose predispositions for breast or colon cancer that we are on the verge of curing all diseases. Not! The only way we will solve the primary problem driving our health care costs (aging) is by recognizing that the genome architecture is fundamentally flawed and the only way to solve the problem is to design a new more robust and reliable genomes. This can be done now. It could probably even have been started a decade ago [3]. Sure it will not be simple -- but neither was learning how to build automobiles or airplanes or rockets. But it is time that people start about transcending the current human OS just as Chromium OS will likely trump Windows and Linux and they in turn trumped VMS, UNIX, MVS, etc.
1. http://www.technologyreview.com/biotech/18809/
2. Scientists have not even begun to think about the "systems biology of specific human genomes" (vs. the systems biology of the "generic" human genome) and except for exceptional cases where defective genes have been directly tied to diseases in OMIM the information required is lacking and will only slowly accumulate through long term correlation studies. The only "short-cut" is to do full scale molecular dynamics simulations of all of the atoms in single eukaryotic cells (and then tissues, organs and bodies) and our largest supercomputers are still many orders of magnitude away from having that capability.
3. There will be people who claim designing a cellular OS is impossible until we completely understand how it works. I would argue that writing a program that prints "Hello World" seems difficult to people who don't understand programming or computers but is pretty simple to people who have been taught basic computer skills without the requirement of having to know assembly language or do arithmetic in binary numbers. There is also the problem that in designing cellular operating systems one is playing "God" -- so you will not see politicians touching this "third rail". Thus the demand and support has to come from private individuals or foundations who recognize that this is simply the logical and "right" thing to do.
If you read TFA, it turns out what they have done so far is drill a tiny hole.
Everything else is still TBD. Things like:
(1) Figuring out how to get a thread of DNA to enter the hole.
(2) Figuring out how to push it through the hole.
(3) Figuring out how to read the bases, which are electrically equivalent and somewhat shielded by the phosphorous backbones..
(4) Figuring how to keep DNA and other crud from getting wedged in this nanometer-width hole.
Somehow I think they're doing this all backwards-- doing the trivial part first and announcing what at first glance appears to be total success.