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Device Can Extract DNA With Full Genetic Data In Minutes
vinces99 writes "Imagine taking a swab of saliva from your mouth and, within minutes, having your DNA ready for genome sequencing. A new device from University of Washington engineers and a company called NanoFacture can extract human DNA from fluid samples in a simpler, more efficient and environmentally friendly way than conventional methods. It will give hospitals and labs a much easier way to separate DNA from human fluid samples, which will help with genome sequencing, disease diagnosis and forensic investigations."
GATTACA here we come!
Obama's legacy: (N)othing (S)ecure (A)nywhere and (T)error (S)imulation (A)dministration
...you gotta sequence a lot of DNA RIGHT NOW! In all seriousness though, this is pretty neat. Not every step in technology has to be earth shattering.
I can see this drastically reducing the cost of getting your DNA sequenced, and at the same time I can see police starting to take it anytime they would take fingerprints.
http://interserver.net/
... sequence the bacteria or virus DNA, not (usually) the human DNA.
One of the huge advantages of sequencing DNA from blood draws is that, assuming it was done properly, the collection was sterile and thus any DNA you find and subsequently amplify with PCR was human.
Of course, people tend not to like blood draws as much as cheek swabs.
The big question I have about this tech is: does it preferentially isolate human DNA? There are a LOT (capitals justified) of bacteria around, particularly near orifices but coating every non-sterilized surface. Without that, it's much less useful than it seems.
This would be the ultimate goal in Identity Verification... And then we find ourselves being cloned...
Awesome, soon we'll be able to have a paternity test included by default for every birth.
I'm just going to wait for cloning, to get a real live version of South Park.
You know what for.
I got a feeling that the implications that result from this will be worse than what that great movie, GATTACA, projected it might be. De-gene-rates, indeed. Although, to be honest, this has all be happening silently for a long time so...all women are experts in genetics. As I know, there is only one way to defend from all this.
More FUDDY FUDDY FUD for the stock pumping, what else is new? Instant DNA sequencing is like "quantum computing", which keeps getting "invented" over and over and over again. What a joke. Queue the scam defenders in 3...2...1.... (gotta keep up the hoax, or else they have to find REAL work!)
Some people are missing the point here, so for emphasis: this product only prepares DNA for sequencing, it doesn't do the sequencing itself. Half an hour of preparation is reduced to minutes, but the actual work still takes days.
This will be serious competition for these guys
Don't fight for your country, if your country does not fight for you.
You can also do it in minutes with common household items: http://learn.genetics.utah.edu/content/labs/extraction/howto/
Extraction's not the problem. Sequencing is not actually a problem, either (~$150k gets you an ION Torrent Proton that will come close to sequencing a person in a few hours). Data analysis is currently the hardest and costliest part of sequencing. Of course, that's getting better, too.
Don't get me wrong, incremental process improvements such as this are important, they're just not groundbreaking anymore.
-Chris
You get sequencing too...
http://www-03.ibm.com/ibm/history/ibm100/us/en/icons/dnatransistor/
W engineers designed microscopic probes that dip into a fluid sample – saliva, sputum or blood – and apply an electric field within the liquid. That draws particles to concentrate around the surface of the tiny probe. Larger particles hit the tip and swerve away, but DNA-sized molecules stick to the probe and are trapped on the surface.
I read through the entire article link, and didn't learn a whole lot about how it actually performs. The above paragraph was the only technical information included. From what I can see, neither really tests performance against really challenging samples with a lot of crud or difficult-to-extract material. We only have the PR blurb's claim that it's better than a typical Miniprep column.
Found a couple of papers that might be more relevant:
Size-Specific Concentration of DNA to a Nanostructured Tip Using Dielectrophoresis and Capillary Action (Has downloadable PDF)
Nanotips for single-step preparation of DNA for qPCR analysis (Paywall)
Ok, from the first paper, we find out what this is really for:
Extracellular DNA is of great interest in the fields of disease diagnostics and environmental molecular biology. Unlike the genomic DNA in normal cells, extracellular DNA is the free DNA released from dead cells. Thus, extracellular DNA circulating in body fluids can be used as an early indicator for various acute diseases such as cancer. For example, the concentration of extracellular DNA for a normal person is 30ng/mL, but the concentration is increased to 300 ng/mL for a cancer patient. When the issue comes to environmental monitoring, extracellular DNA dissolved in lakes and soil is an indicator for environmental quality because the dissolved DNA is generated from cell lysis and excretion. In spite of such a great potential, the study of extracellular DNA is limited by the standard sample preparation methods.
The conventional methods begin with filtering, centrifuging, and collecting DNA from a raw sample. In aggressive experimental protocols, genomic DNA from normal cells is released and mixed with extracellular DNA. In addition, a few hours is required for the sample preparation process, which can degrade and mutate extracellular DNA.6 As a result, the original information of extracellular DNA is partially or completely lost. Therefore, a rapid process that can concentrate extracellular DNA is very important for identifying pathogenic information. This paper presents a size-specific concentration mechanism directly extracting extracellular DNA from a sample mixture using a nanostructured tip. The concentration process is performed with two sequences: (1) an alternating current (AC) electric field is applied to attract DNA and other bioparticles in the vicinity of a nanotip; (2) only the DNA is size-selectively captured onto the nanotip by the combination of dielectrophoresis and capillary action. In the analytical section, the forces involved in the concentration are estimated to investigate the capturing process. An analytical model is presented for capillary induced size-selectivity that is described as the function of the ratio of a particle to a tip diameter.
Basically, this is a special purpose method for concentrating extra-cellular DNA while leaving whole cell material intact. It's not meant to compete against a Miniprep, but analyze a whole different type of sample material; you are trying to fish out what genetic material is already floating around outside of your cells. Really a niche kind of research thing, I don't know if this will make a whole lot of impact, either practically, academically, or economically.
If you could splice genes into people to "improve" them could you not do it, not even once? If you could find out what genetic defects, what dispositions to diseases, what aptitudes or weaknesses they had, could you say, nay, I don't need to know that, or would you need to know. What would you< do with that information once you had it.
Well, I see we're preparing ourselves for the PHAGE (http://en.memory-alpha.org/wiki/Phage)
Some people are missing the point here, so for emphasis: this product only prepares DNA for sequencing, it doesn't do the sequencing itself. Half an hour of preparation is reduced to minutes, but the actual work still takes days.
It used to take days, and still does if funding is short but an Illumina HiSeq 2500 can produce 150-180 Gbases in 40 hours in rapid run mode [1]. Most labs still run it in high output mode because of the reagent cost but the option is there. This means that if I was prepared to pay the extra and I sent a sample into "core sequencing" where I work, they could potentially return mapped DNA in a week. After that there's still some improvement tools we'd need to run to clean up artefacts, followed by calling and filtering variants, those bits can take weeks. Whilst it is true that the bottleneck is currently the physical sequencing process of things but pretty soon that is going to shift to the informatics.side.
[1] http://www.illumina.com/systems/hiseq_2500_1500/performance_specifications.ilmn
what is it about biotech that causes, even for slashdot, any lack of critical thinking
The use of electric field to purify DNA has a long history - i think the first commercial company that did bio sample to pure dna was McConnell research, who focus on plasmids
Even assuming this works, and (as nanogen found) the toxic chemicals produced at the electrodes don't damge the dna, everyone
*already knows*
that isolating hte DNA is the easy part - there is a long, complex process to get teh dna ready for sequencing, eg emulsion pcr in the ion torrent, or solid phase bridge amplification; this process often includes random shearing, size selection, adaptor ligation etc
I though it was already possible - dont u guys see CSI?
"Imagine..."
having no privacy.
and no health insurance.
the problem is how do you define "defect"??
I could see kids getting "edited" to correct things like excessive intelligence or self will (can't have a 95% person smarter than a 5% person or be able to get "uppity" )
Plus its been proven that if you select for %trait% and don't balance things out the person tends to be somewhat NUTS.
Any person using FTFY or editing my postings agrees to a US$50.00 charge
The main problem with your argument is - the only technology that can replicate itself these days is biotech. This and the incredibly low (and exponentially dropping) prices of this technology are the real reasons we must be far more cautious with biotechnology than other technologies. Sooner will a nutjob create a superbug in a garage lab than he would create skynet.
The created a new class of genetically gifted in society. This caused class tension with the ordinaries and defectives.
Unlike GATTACA, rapid testing would mean everyone is analyzed and databsed at birth or before. Then just rapid sub-testing of a few markers culd match the database instead full resequencing every identity check.
Expect serious pushback against home paternity tests from Women's groups, as it becomes evident that a large number of men are raising children that are not their own (biologically).
Everyone bashes conservatives on science ignorance or bias. As you pointed out the libertarian slashdoters have their version of junk science. Whenever I post a list of leftist junk science I get bashed too. All parties need to be more open minded and enlightened.
I see more and more of that. Right now fairly simple things are done. But with cheap sequencing and all the genetic unknowns out there I would not be surprised by some significant science fair discoveries.
full dna scanning and forced disclosure of your dna traits. The government and private corps can now scan you for undesirable traits
I give it 6 years. Then we will have a complete scanner. Another year or two after that and it will be included in the handheld-bio-metric-scanner-device-thingy.