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Faster DNA Testing
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?"
Your DNA says you don't have a bomb, so go right ahead and board! Have a nice day!
Probably.
The truth about Led Zep should never be told on
anyone got thoughts on likely accuracy? false negs/pos's? speed vs quality? TFA looks too much like an advert to give out this sort of information. (it also uses 'leverage' as a verb.)
k e l l a r
Only 5 minutes? No, check the math. Assume 100 people (though it could be FAR more). Each person needs 5 minutes, so you'd need to be there 500 minutes early (8 1/3 hours). I really doubt they'd have that many machines laying around, so multitasking the scans is an improbability.
-- SegFault
"One day, some time ago, something important happened."
Have we go somehing agains using he leer 't'?
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!)
$nice = $webHosting + $domainNames + $sslCerts
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
init 11 - for when you need that edge.
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.
Time rent Gattaca again...for a creepy "1984-like" vision a world with perfect identity tracking.
Any technology distinguishable from magic is insufficiently advanced. - Geek's corollary to Clarke's law
Of course, the OP did not mention the huge positive effects accelerated PCR will have on research (particularly in molecular biology and biochemistry). It's fine recognizing new technology's potential for misuse, but this article's summary is just plain FUD.
They have a tiny oven which can:
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:
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.
liqbase
How long do you think it will be before they start testing people's DNA as part of a job application?
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.
He who knows best knows how little he knows. - Thomas Jefferson
When the hell did we become a society where you need "evidence" incase I do something wrong? Isn't it about time we stopped going "well maybe you'll do something wrong.." and start going "well 99% of people don't do this bullshit, maybe it's best we don't piss them all off for that 1 in a billion chance".
I like muppets.
I don't know why they haven't just gone ahead and tattooed serial numbers on the inside of our forearms yet. There's not much difference in the final result.
NetInfo connection failed for server 127.0.0.1/local
Hey folks I work in this field. Be highly skeptical. Department of Homeland Security is throwing large sums of money around trying to find a biological warfare agent detector that an untrained person can use. Some interesting work has come out of the spending spree - it has also brought out an army of slick talkers with a half baked idea.
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.
"Empathise with stupidity, and you're halfway to thinking like an idiot." - Iain M. Banks
Many companies have produced faster thermocyclers. And indeed, the rate of heat cycling is a major factor in the time needed for a 30- or 35-cycle PCR. However, what this article omits are necessary wait periods to permit the annealing, elongation, and melting stages in typical PCR. Unless they have also re-engineered a DNA polymerase and can sufficiently prove that denaturation and annealing stages can be completed much faster, we're talking about maybe a 30 to 45 minute decrease in PCR. That's it. I've never seen anything less than 30-30-30 before, even in the smallest of genotyping markers.
The company plans to leverage its patented technology in accelerated thermal cycling through licensing and internally developing devices for clinical diagnostics, general biotechnology, bio-defense and other related industries.
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 on PCR and associated technologies.
Ask me about repetitive DNA
Yes, and photographing every woman that walks by up her skirt, only takes a second, and doesn't hurt a bit. So why not do that?
Just because it's easy to do something, is a silly reason to do it. And DNA testing is one area where it is good to be extra careful, since there's so much more than just identity or generic features that you can derive from DNA.
Fortunately government/law enforcement is held to higher standards, and needs to show a need before being allowed to do things. Or at least should, in civilized nations.Confirming identity does nothing toward confirming non-terrorism. The attackers of 9/11 were fully legal American residents, maybe even citizens, and even the most expensive and invasive of identity tests would not have disclosed their terrorist intent.
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.
When one person suffers from a delusion, it is called insanity. When many people suffer from a delusion it is called Rel
Go ahead. Watch CSI and see how causually they collect and handle evidence. Pretty scarey?
I would highly suggest renting Gattaca.
This doesn't seem like as much of a breakthrough as they're claiming. PCR is basically a system where you can amplify DNA by putting it through a series of heating / cooling cycles in the presence of a thermostable enzyme which does the actual amplification. Labs already use expensive peltier heaters/coolers to make this pretty efficient.
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 step isn't the ramping between temperatures but rather the length of time you have to leave to let the enzyme to let it copy the DNA (normally calculated around 30secs per 1000bases - though it's probaby faster than that).
The only big win for this would be if you're amplifying very small stretches of DNA (a few tens of bases) when the temperature ramping times could be significant. Even so it's still going to be far from instantaneous.
Sorry, but you are not allowed to bring acid of any kind on board, not even Deoxyribonucleic.
He who knows best knows how little he knows. - Thomas Jefferson
"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?"
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.
Only to idiots, are orders laws.
-- Henning von Tresckow
I would be happy to leave my DNA sample in the hands of a stewardess!
Faster PCR is to Dna Techniques what Overcloking is to hardware performance.
Sometimes it could be a solution, sometimes it's just a buzzword, sometimes it's the door to your nightmares.
In a lot of applications, PCR speed it's not the bottleneck.
Gattaca
Looks like "Gattaca" becoming reality
Open Source Drum Kit, LPLC deve board - mjhdesigns.com
I recently read (Fall 2005) an interesting article in Dissent 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 has some material available online like Technology and Social Control: The Search for the Illusive Silver Bullet.
If you know of other people addressing this issue that would be worth reading, please reply with a citation or link.
http://www.imdb.com/title/tt0119177/Gattaca
There's a DNA preparation stage as well, which also contributes to the total time involved in a single PCR reaction. If you're willing to work with slightly smaller volumes, then the LightCycler is something that I consider to be pretty fast already.
An entire 35-cycle run can be completed in as little as 30 minutes (with 20 microlitre capillaries) or 60 minutes (with 100 microlitre capillaries).
When you're getting down near that speed, DNA preparation time can take longer than the PCR process itself (especially when the preparation is done by real people). As a side note, a 30-45 minute decrease in PCR from that speed (for the 20 microlitre volume) is going into the negatives.
Ask me about repetitive DNA
Who shot Mr Burns Part 2: http://en.wikipedia.org/wiki/Who_shot_Mr._Burns%3F
....did I say weeks? 'Cause I meant seconds."
"Whoa, hey there, DNA testing takes 6 to 8 weeks
They can do this in Rochester but they can't revitalize Midtown Plaza? Oh well, at least they have Radio Shack.
Read any good sonnets lately?
The HMO's would love, and likely require it as soon as it's feasible. They'd only insure you against things they don't find, and will "encourage" (read: extort) your potential employer demand you submit to the test to qualify for benefits, with their fee structure. No sample, no sub-COBRA discount.
now you won't have to wait for an hour to know who's the father ;)
sarchasm
where in rochester? sweet that sounds like a good co-op opportunity if they're actually a company thats been established for a little while?
(RIT Bioinformatics student)
without the woman finding out.
you can buy an over the counter kit with two swabs, mail them off, and call in a few days (week) to find out if the two are related or not. it is specifically for parental concerns, without everyone needing to know
doesn't help if it's your brother as much I suppose.
The movie Gattaca speculated on a future with instant DNA analysis. The story was people could think of ways of getting around it.
(Uma was the romantic interest in the movie.)
I did a quick search and came across a paper summarizing past research. It seems that some methods 'cheat' to simulate PCR and other use methods which simply aren't possible to achive on a macroscopic scale. I don't understand why people are criticizing what would essentially be a super cheap (by comparison to the expensive traditional lab equipament) chip which can do this in minutes. Keep in mind,microfluidics is helping revolutionize lots of areas of biology. It's already being used to create microchips that can detect individual genes in a blood sample given to it.
R evModPhysJul05.pdf
Here is the text from Microfluidics: Fluid physics at the nanoliter scale:
http://thebigone.stanford.edu/quake/publications/
Polymerse chain reaction PCR is a process used to
exponentially replicate double-stranded DNA, allowing
even a very small amount of DNA to be amplified into a
sufficient amount for sophisticated analysis. PCR involves
a three-step thermal cycle in the presence of a
reagent soup: i heating the solution to melt the DNA
by separating each ds-DNA into two single strands; ii
cooling so that DNA primers and DNA polymerase enzymes
bind each strand annealing; and iii warming
slightly to promote the base-by-base DNA replication
by the polymerase extension. Ideally, each PCR cycle
doubles the number of double-stranded DNA molecules.
Integrating PCR into microfluidic devices has been
achieved by many groups, typically by cycling the temperature
of a microfluidic sample to replicate the standard
macroscopic PCR Wilding et al., 1994; Burns et al.,
1996; Cheng et al., 1996; Woolley et al., 1996; Schmalzing
et al., 1997; Belgrader et al., 1999; Khandurina et al.,
2000; Chiou et al., 2001; Hong et al., 2001; Lagally, Emrich,
and Mathies, 2001; Lagally, Medintz, and Mathies,
2001; Auroux et al., 2004. An alternate strategy involves
pumping solution through various temperature zones to
mimic PCR Fig. 35a Kopp et al., 1998; Liu, Enzelberger,
and Quake, 2002, whose benefit is that cycle
time no longer depends on the time required to heat or
cool the solution and its surroundings. Another approach
exploits high-Ra buoyant flows to perform PCR
in a steady temperature profile without an external
pump Krishnan et al., 2002; Braun et al., 2003. The
basic idea involves establishing a large convective flow
whose roll fills the experimental cell. This flow advects
FIG. 35. Color in online edition Polymerase chain reaction
PCR in a steady temperature field. a Solution is driven
along a channel that winds through temperature regions i,
ii, and iii designed to cause DNA melting, extension, and
annealing. Thus the temperature profile seen by the solution
matches a standard PCR cycle. Reprinted with permission
from Kopp et al., 1998. ©1998 AAAS. b A PCR reactor in
which temperature gradients drive a convective fluid flow that
takes suspended DNA molecules through a temperature profile
designed to resemble that of PCR. Reprinted with permission
from Braun et al., 2003
DNA molecules Pe1 through the variable temperature
profile in the fluid. By properly designing the experiment,
the temperature profile experienced by DNA
can be made to resemble that of conventional PCR, thus
allowing the chain reaction to proceed. The underlying
convective flows have been established in two ways: i
uniformly heating the bottom plate and cooling the top
plate enough to drive Rayleigh-Benard convection at
Ra106 Krishnan et al., 2002, or ii heating the fluid
inhomogeneously Fig. 35b at Ra104 to establish
laminar convective flow Braun et al., 2003. Finally,
DNA molecules advect with the flow along the bottom
of the cell towards the center of the roll, but also move
outwards via thermophoresis itself poorly understood,
leading to trapping in a ring so long as Pe1 Braun and
Libchaber, 2002.
This could be useful for all these prison breaks in texas and other states.
Of course, I suspect that they are not even using something as easy as fingerprints.
I prefer the "u" in honour as it seems to be missing these days.
Jones family to service desk please! Congratulations Mr. Jones, the oldest child is yours, the other two have different fathers, but we managed to locate one, he's coincidentally on the same flight as yours. Flight 3485 now boarding, have an nice flight!
Watashi wa chikyubutsurigakusha desu.
Maybe they can use this to help the families in New Orleans, since 3 months later there are still over 300 bodies still unidentified, and over 4,000 people still missing.
"You're doing a heckuva job, Brownie!"
You gotta love all these new technology companies that claim to have something so innovative that they have to slashdot it. And then when it's all said in done, it reads more like a headline story from the Enquirer or something. The product is supposed to clone people, remove unwanted hair, reverse the aging process, and create gateways into an alternate dimension. In the end however, and after really reading the press release, you're lucky if their so called discovery is capable of making Julianne fries.
Until I saw a series of controlled laboratory tests and their results, I'll remain a bit skeptical. DNA isn't your garden-variety chemical and processing it is so tedious precisely because of that fact. Speed in testing DNA may be desireable (look at the trouble they have to go through identifying Katrina or 9/11 victims), but accuracy is more important. It has to be consistant to be regarded seriously as a security device.
What's more, so they have my DNA and know who I am. How? That data will have to be stored somewhere. An RFID chip in my passport? A government-run DNA database? Better yet, so what? Assuming I haven't faked the RFID chip or hacked the DNA DB, who's to say I'm not a terrorist? Maybe I don't have a criminal record and maybe I'm not Muslim (remember such golden oldies as the Bader-Meinhof?). Speedy DNA processing isn't going to solve the fundamental security problem, which is how do we read your mind.
GetOuttaMySpace - The Anti-Social Network
I hope eventually it can be used to fully sequence human DNA in 10 seconds or so. This would allow creeating a desktop or handheld device into which you spit and after a brief pause it will display the unique hash checksum of your unique DNA. This hash if displayed as a sequence of four letter pseudowords, could be used as the person's name. No longer would there be 25 million John Smiths and 250 million Xin Li Huas, every person in the world would have a unique name. No person could lie about his/her identity or use a pseudoname any more, since your DNA is you and your DNA hash is your name. Everybody could have his/her own pocket DNA sequencer, so you could positively validate the identity of the person you are facing. So perfect world, total transparency. Lie would disappear from mankind. Great happiness with security for all.
and Insurgent
He who knows best knows how little he knows. - Thomas Jefferson
Stevyn wrote: they move along, you take a blood, hair, or semen sample.
If I'm in a hurry, can I just leave my underwear?
myke
Mimetics Inc. Twitter
And that's when it's time to call Jude Law.
or maybe you don't, but the OP doesn't work for the TSA. His ramblings are inconsequential.
That the standard response around here when the subject of DNA is mentioned is
1) paranoia so extreme that it borders or mental illness
2) bring up Gattaca
And more importantly, why do these post routinely get modded insightful, when they NEVER say anything that some other paranoid Karma whore hasn't already said?
The world isn't looking to track your every fucking move, nor use your DNA to somehow subjugate you. Get over yourselves.
How pathetic are you that you follow me from topic to topic and waste all your mod points at once modding me down?
OK...
all your base-pairs are belong to us?
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 has been given a undeservedly bum rap by the Culture of Death.
I'm confused .. it was i who posted that physorg.com article yesterday , while logged on with my /. userid and password ..
who is 'scuttlemonkey' , anyway???
tkjtkj
tkjtkj@gmail.com
"There are 11 kinds of people: those who know binary, those who don't, and those who could not care less!"
I think you can see where I am going with this. The day they start something like this is the last day I fly, because IANAT (I Am Not a Terrorist) and deserve the anonymity I enjoy as a protection from government intrusion.
...Open Source isn't the only answer -- but it's almost always a better value than the alternatives...
it's a significant step towards the Brave New World
Ooooh, when do I get my Soma?
My Journal
It's just a device that does PCR faster than regular thermal cyclers. The DNA has to be "melted" (strands uncoiled and separated) for the heat-resistant DNA polymerase enzyme to be able to replicate the strands. This is just a tiny instrument with a lower heat capacity and microfluidics capabilities, so they can go from hot to cold and back in less time. Oh, and it seems they're using semiconductor tech to fabricate the suckers.
But it's by no means revolutionary like PCR itself.
Si la vida me da palo, yo la voy a soportar Si la vida me da palo, yo la voy a espabilar
"DNA just allows confirmation of identity" IF done right AND properly watched by well-paid guards. One can easily fool, GATTACA-style, automagic DNA recognition.
It's better to be the foot on the boot than the face on the pavement. ~~ tkx Kadin2048
Is that five minutes earlier then my flight or 5 minutes earlier then the two hours I usually get their early?
Speaking is NOT communication
1) Melt your DNA strands apart (95/96C for 30-45 sec)
2) Anneal your primers (~45C for another 45 sec)
3) Elongation of primers performed by DNA polymerase. General rule of thumb is 1 min for every 1000 base pairs. The speed of this reaction is limited by the inherent speed of the enzyme.
Repeat steps 1-3 for 20-30 cycles. Usually 30 unless you are concerned about fidelity of replication.
Who uses mineral overlay anymore? It's all hot top now. (mineral overlay is to prevent your sample from uselessly evapourating and condensing on the cool PCR tube cap and not being exposed to the correct temperatures, you can avoid this problem by heating the tops of the tubes and preventing condensation.)
Even with a very fast temperature ramp this still takes a while. I can't see where in the article they get their 5 minutes from, especially since they still claim 30 cycles.
The CSI's have had that for about 5 years in Las Vegas, and also Miami. and for a couple years in NY.
discussion here.
Human being (n.): A genetically human, genetically distinct, functioning organism.
You omitted the last two steps:
7. government employees sell info to malicious info-users/spammers/telemarketers
8. Profit!
"The difference between theory and practice is often much greater in practice than in theory."
You know, we talk about nuclear proliferation, but that's nothing compared to biotech proliferation. I think that should be on top of Bush's agenda. Once you can 'write' biological viruses that attack people based on their genetic heritage, that's gonna really suck. How long til another holier than thou Hitler shows up, and decides to purify the world? You don't possess the "officially approved" genetics, so down with you. With all the computer viruses that get written targeting a specific vulnerability, you have a solution, you can switch OS's and play the security by obscurity thing, or even stay with mainstream and play the patched-it-now-you're-it cat-and-mouse game. Worst thing that happens is all the computers going down and you get really pissed, but that's about it, so what. But you can't do that to your own software, to your own DNA, can't patch it on the fly, at least not yet, and the Almighty save your souls from a world where you can. And if your own DNA 'crashes' there is no reboot, unless you believe in reincarnation. There are always two sides to everything: a good side and a bad side, a dark side and a light side. Every power has benefits and dangers. Nuclear stuff at least can provide/get converted to heating, air conditioning, food, car fuel, what not, and even if something goes wrong - even after hiroshima and nagasaki - the rest of the world goes on, people live, the eskimos, the amish, the bushmans, and the jungle people live, whales, elephants, jaguars live on, even if the modern world 'crashes'. Nuclear stuff is not contagious. But there is nothing scarier that I can think of than biotechnology, what hell can get loose once we attain sufficient knowledge to tinker with the software with too much ease. Have you seen them cows with huge titties that they can barely drag around? Yes, biotechnology at your service, providing you lots of milk. But you will always have some idiots or pranksters who think it's kewl to make a fly or a grasshopper the size of an elephant, or a super-virus that attacks anything, just like you have it with all these creative computer virus writers. Just think of the sick doctors who kill their own patients. With sufficiently developed biotech viruses filled with intent, that freely jump from bacteria to plants to animals to humans, if one gets loose to proliferate, good luck to us all. Or even if it's not as destructive, just selective enough, just think of a special SARS or bird flu that specifically targets people with slanted eyes, but won't touch anyone else. Yeah, biotech has the potential to cure illnesses, I know. But still, please meditate over that other side too, once in a while.
This technology doesn't sequence your entire genome, so that shady corporations can make ill-founded predictions of a nervous breakdown when you reach 52 and not hire you on that basis.
It's just looking at specific markers, probably in a manner similar to current forensic tests. If you include enough markers in the test, each person will have his own unique 'fingerprint', enough to verify that person is really who he claims to be. Of course, they need a prior, verified sample to compare it to. More reliable than carrying documents which can be forged, but not so much different from fingerprinting or retinal scans.
The markers used aren't even coding DNA (genes).
a great excuse for a huge DNA database.