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Faster DNA Testing
Posted by
ScuttleMonkey
on Tue Nov 22, 2005 07:29 AM
from the sorry-sir-i-need-to-stick-you-again dept.
from the sorry-sir-i-need-to-stick-you-again dept.
tkjtkj writes "Physorg.com is reporting that a Rochester,NY, company, 'Thermal Gradients, Inc' has produced a new method of DNA analysis that can reduce the required time from hours to minutes that the usual 'Polymerase Chain Reacion' (PCR) takes to produce the large quantity of sample DNA needed to identify the donor. This could,conceivably, make "Instant DNA Identification" a reality! Will air travel now require one to arrive at the airport 5 minutes earlier than usual, to provide a skin-swab sample before boarding the plane?"
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Your DNA (Score:5, Funny)
Re:Your DNA (Score:2)
acid trip (Score:5, Funny)
Parent
AYB-PABTU (Score:3, Funny)
all your base-pairs are belong to us?
Re:Your DNA (Score:2)
Re:Your DNA (Score:3, Funny)
"Been there, done that." -- Santa Claus
In a word.... (Score:3, Funny)
Accuracy (Score:2, Interesting)
Re:Accuracy (Score:2)
from Random House College Dictionary (closest one at hand):
lev-er-age
And of course it's an advert, it's based on a press release. You can be pretty sure they're looking for capital to bring this to market.
Only 5 minutes?? (Score:4, Insightful)
Re:Only 5 minutes?? (Score:2, Insightful)
However, that does raise an interesting point about the number of people who can be tested at once.
Re:Only 5 minutes?? (Score:5, Funny)
Here's how a system could work. You load people one by one on a conveyor belt. As they move along, you take a blood, hair, or semen sample. Then a machine quickly and painlessly prints a temporary barcode on their forehead. Then they continue to move along the conveyor belt.
In about 5 minutes, the DNA is determined and compared against a database of known Un-Americans. At this time, a laser barcode reader down the line scans each head and if an enemy of the state is found, they are quickly escorted off either by trained guards or another piece of machinery for re-classification.
So what's the problem? Barcodes and conveyor belts have been around for years.
Parent
Re:Only 5 minutes?? (Score:4, Funny)
It takes 5 minutes? Must require two semen samples.
Parent
Re:Only 5 minutes?? (Score:3, Funny)
That's terribly inefficient, since you already have a laser trained on their head. If the person is known to be Un-American, just up the power. Seeing the head of one terrorist instantly vaporized will
Re:Only 5 minutes?? (Score:5, Interesting)
You see how this fits? You take the DNA sample, let people proceed to the next phase (e.g. baggage checking). Then, you scan their passports five or more minutes later and stop them if their DNA doesn't match.
Parent
Re:Only 5 minutes?? (Score:3, Informative)
The only real way to get rapid DNA testing is a test that forgoes the amplification step and can identify single strands of DNA. Of course you then have the what if they get someone elses DNA because I just kissed my mom^H^H^H girlfriend goodby.
If all of those were accomplished I see no problem implementing such a solution, becaus
Re:Only 5 minutes?? (Score:3, Insightful)
The next stage of biometrics? (Score:2)
Forget fingerprints and retina scans -- how long before my computer will require my personal DNA authorization to log in? (Actually that wouldn't work. Someone could just steal a few hairs off my pillow and log into my computer!)
Re:The next stage of biometrics? (Score:4, Informative)
Not always (unless a root is intact), but Mitochondrial DNA can still usually be found. mDNA, while more expensive to test and not as conclusive, is still useful and I think it's been used in some high profile murder cases.
Parent
What impact on UK ID cards (Score:4, Insightful)
If, and it's a big if, this is not vapourware and near instant (a few minutes in TFA) DNA testing is near it's going to add a certain spin to the UK ID card debate. The current use of DNA testing only for major crimes could be extended to practically any crime. And if your DNA profile is on your ID card then placing people at crime scenes will become a doddle.
Ok, so only those who have something to hide have somethng to fear - yeah right - but it's a significant step towards the Brave New World
Re:What impact on UK ID cards (Score:2)
DNA testing assumes people don't frame others for crimes. So maybe we'll catch criminals, but don't expect it to reduce the amount of innocent people convicted of crime due to overzealous prosecutors and a public that screams for revenge.
Psychos and boring people are the only ones who don't want privacy.
Re:What impact on UK ID cards (Score:2)
You goto a club, fuck some girl (who's high/drunk/out of it but still wants it and makes all the moves), she then waddles home and ends up being raped. Your DNA (and possiblely sperm) is on/in her, so is some other guys. If she doesn't remember you (or others) then you're now up for gang rape charges.
DNA is seen as some miracle cure, but it's so easy to get a hair, or a bit of spin or whatever. Planting DNA is insanely easy, more so then pinning a crime
Re:What impact on UK ID cards (Score:2)
popular application (Score:4, Funny)
Picture your own scenario. A paternity test is probably the most hostile confrontational gesture one could make toward a woman with whom one's engaged in a relationship; but sometimes, let's face it, it has to be done. What would make this less confrontational would be if DNA testing was quick and easy, not a whole to-do schlep. Just like signing a pre-nup in a world where lawyers weren't needed for that.
So if paternity testing could be relegated to a "By the way, would you mind" kind of matter, the greater piece of mind could-be dads would have jumping into a shotgun wedding. In short, the quicker we can tweak up the ol' Polymerase Chain Reacion, the more red state skanks we can get with safely.
Re:popular application (Score:3, Interesting)
Not to mention the possibility that CSI will now become something of a reality: Now, they submit those DNA samples to the lab, and get results back in a matter of minutes, when we all know that in reality, forensic investigative DNA testing takes a week or two minimum.
And good lord, my brain doesn't function at this time of morning - my fingers just wrote "DNS" when I asked them to write "DNA".
~W
Re:popular application (Score:3, Funny)
They'll get the results before they put the DNA sample in the machine!
In defence of pro-life red state skanks... (Score:3, Funny)
Sometimes I envision doomsday scenarios, like getting a call from a pro-life booty-call saying she's having my baby, but my homies done seen her 'round the block... In short, the quicker we can tweak up the ol' Polymerase Chain Reacion, the more red state skanks we can get with safely.
Alternatively, after she gives birth to that child of yours, you just might discover that that whole Miracle of Life thang [loudeye.com] has been given a undeservedly bum rap by the Culture of Death.
Time rent "Gattaca" again... (Score:2)
Obviously not perfect... (Score:2)
Granted, the main character was found out, but that lead to the (again IMHO) main premise of the movie: Genetic testing does not necessarily define one's abilities. Granted, this particular statement is off-topic, but the idea that it can be circumvented is not.
What about the research benefits? (Score:5, Insightful)
Re:What about the research benefits? (Score:3, Interesting)
Re:What about the research benefits? (Score:3, Insightful)
Whoa giddy. (Score:5, Informative)
While other miniature PCR devices exist, they are limited in the rate at which they can change temperature, Grover said. "Our first prototype has demonstrated that we can expose the sample to the required temperatures at unprecedented rates," he said.
Now, lets look at just whats needed to do the PCR reaction (just one of the variations taken from here [nih.gov]:
If you are using DNA Thermal Cycler (TCI, the DNA Thermal Cycler Model 4800 or any thermal cycler requiring light mineral oil overlay.
* Place the tubes in the thermal cycler and begin thermal cycling as follows:
* For the first cylce only, ramp to 96 C for 1-5 minutes to completely denature DNA template then proceed with sequencing PCR steps.
* Rapid thermal ramp to 96C
* 96C for 30 seconds
* Rapid thermal ramp to 50C
* 50C for 15 seconds
* Rapid thermal ramp to 60C
* 60C for 4 minutes
* Repeat Step 2 for 25 cycles
* Rapid thermal ramp to 4C and hold. Samples can be started in the evening and purified the next day if necessary
* Proceed with Purifying Extension Products.
They might be able to change temperature quicker, but they haven't invented a new way to perform the reaction.
minor upgrade, no digg.
Re:Whoa giddy. (Score:3, Informative)
Exactly. Having actually performed DNA analysis in the lab, I can tell you that while very rapid temperature changes are benificial, you still need to take some time to let the new DNA strands form. In addition, there's more steps involved in actual DNA analysis (isolating the DNA, running it through a poly-acrylamide gel to get the familiar stipe patterns, etc), some of which can take far longer than the actual replication of the DNA itself. I doubt we'll be seeing machines that
Re:Whoa giddy. (Score:2)
Re:Whoa giddy. (Score:4, Insightful)
The heating/cooling process is not the rate limiting step in this reaction. Read that last part again if you don't get it. Taq, Pfu, all the other polymerases that are used for PCR are processive. The fastest possible way to duplicate a strand of DNA is to have a single copy of the polymerase run down that strand, making the copy strand as it goes along. There is only one priming site, so a given template can only be used to make one copy per cycle. And for all of the enzymes I'm familiar with, and I'm pretty familiar with this area, the rate is in the ballpark of 1min/ 1000 bp. The fastest system I'm familiar with, Stratagene's FullVelocity QPCR, takes about 1 hour to run a 40 cycle reaction. Regardless of what other posters may be saying in the thread, their product literature [stratagene.com] agrees with this number, so I'd suggest asking some of the other posters for documentation of their much faster qpcr numbers. There are ways you can speed it up by giving up some accuracy and sensitivity, but five minutes? Not unless you can warp time or suddenly make a thermostable enzyme do its thing 20-30x faster. In which case TFA wouldn't be talking about heating & cooling rates, but would be addressing their hugely better enzyme.
Parent
Re:Whoa giddy. (Score:4, Informative)
Microfluidic heating methods only significantly increase PCR rates in cases in which the amplicon length is less than 1,000bp. In fact, the average amplicon length in a recent review of microfluidic PCR devices (Analytical Chemistry, 77(12):3887-93) is only 330bp. Dependending on what polymerase is used, a 330bp piece of DNA can be replicated in 10-20 seconds. This, obviously, is a completely different situation from one in which a researcher is amplifying a 7kb vector in which elongation is the rate-limiting step. I'm sure that microfluidic devices could be adapted to work with amplicon lengths >1kb, but at that point the reaction rate improvements become negligible. Microfluidic PCR lends itself primarily to SNP genotyping, not general research.
Furthermore, the difficulty inherent in working with nanoliter volumes of reagents makes these microfluidic PCR devices somewhat less useful for general lab use. Naturally, they mesh well when coupled with lab-on-chip applications, but again that is currently a niche use.
Traditional thermocyclers aren't going anywhere any time soon. They're cheap, they're functional, and they're flexible.
Parent
DNA testing on job applications (Score:3, Interesting)
I can see it now....Trevor wasn't hired because his DNA showed a tendency of autosomal recessive gene disorders and another defect affecting his mitochondrial enzymes.
fuck and off (Score:2)
Re:fuck and off (Score:2)
Or 1 in a hundred chance, based on your own percentage. ;p
But, no, seriously, I do agree with Turn-X Alphonse. The paranoia in current society is ridiculous. It would be nice to see the majority of society no longer considered to be potential criminals just for existing.
Tattoo us already (Score:3, Insightful)
be skeptical (Score:2, Interesting)
This doesn't seem so great... (Score:3, Informative)
Just what I always wanted (Score:2)
Yay for another patent on PCR technology, only a few months after the original PCR patent has expired. But of course they're only going with the trend -- there's other patents [appliedbiosystems.com] on PCR and associated technologies.
When will they realize (Score:5, Insightful)
Reasons why this would be considered for TSA purposes: (1) It will make some ignorant people feel more secure; (2) It will facilitate all kinds of other investigations, mostly related to the War On Drugs; (3) it will provide another opportunity for pork projects and kickbacks for government officials.
Re:When will they realize (Score:3, Interesting)
DNA just allows confirmation of identity. If the people committing the terrorist acts are not under suspicion then it does nothing. It is just a matter of context.
Your comments demonstrate why its so difficult to argue against the reduction in liberty and privacy that the authorities are attempting to implement in the western world. They pr
If you haven't seen it yet... (Score:2)
I would highly suggest renting Gattaca.
Not all that special... (Score:2, Interesting)
All this company have done is make a machine which heats up and cools down faster. The basic biochemistry is still the same. For most PCR reactions the rate limiting
Insurance? (Score:3, Insightful)
I'd worry about other consequences of this technology. For example will it enable Insurance companies to more effectively bill you for every genetic disorder that you are N% more likely to get than the next guy? Yes it probably will, as soon as they refine it into a low cost, high volume, technology to test for various disease causing genes. Insurance companies are aching to use such cost effective genetic diagnostic technology to stick consumers in higher risk groups (which translates in being able to bill them more money) based on their likelyhood to get some genetically caused disease later on in life. There are already many people that are unensurable as a result of having some chronic disease and this technology will swell their numbers. People show no outward signs of a genetic predisposition to get some disease and seem perfectly healty today might become ill or even uninsurable in the future thanks to this technology.
Gary T. Marx (Score:3, Insightful)
I recently read (Fall 2005) an interesting article in Dissent [dissentmagazine.org] magazine from Gary T. Marx on this issue called: "Soft Surveillance Mandatory Voluntarism and the Collection of Personal Data."
He makes a number of interesting observations on how DNA as a soft means for the collection of personal data - for example, where police go in and ask everyone in a community for a mouth swab "in order to solve a crime" or in airports as the poster suggests. Marx argues for a system based on clearly defined rules based on meaningful consent. These rules could center around questions like: Would the information collector be comfortable being the subject, rather than the agent, of surveillance if the situation were reversed?
Imagine for a moment a community database of DNA information and the potential for abuse. For example, a criminal might collect hair from a hair brush and plant it at the scene of a crime. Perhaps a swab might be a precondition for health insurance? Etc.
There are many potential problems with the widespread availability of DNA technology. It is also an issue many of us have not given a great deal of thought. Gary Marx [mit.edu] has some material available online like Technology and Social Control: The Search for the Illusive Silver Bullet [mit.edu].
If you know of other people addressing this issue that would be worth reading, please reply with a citation or link.