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?"

Comments

Your DNA

[Jozer99]

Your DNA says you don't have a bomb, so go right ahead and board! Have a nice day!

Only 5 minutes??

[SegFaultCM]

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.

Re:Only 5 minutes??

[Stevyn]

Jeez, have you no imagination?

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.

Re:Only 5 minutes??

[yerfatma]

As they move along, you take a blood, hair, or semen sample.

It takes 5 minutes? Must require two semen samples.

Re:Only 5 minutes??

[TheRaven64]

Since this is Slashdot, I'll give a computer-related analogy. Once upon a time, there were silicon chips which could do calculations. They did them one at a time, waiting for one to be completed before starting the next one. Then someone came up with the idea of pipelining. You would start fetching one instruction while the previous one was being decoded, and start decoding it while the previous one was executing. Next, someone came up with the idea of a superscalar design - you could have two or more of these pipelines, and as long as a pair of instructions didn't depend on each other, you could execute them at once.

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.

What impact on UK ID cards

[Silver Sloth]

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

popular application

[Douglas Simmons]

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. Dig?

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.

What about the research benefits?

[achesterase]

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.

Whoa giddy.

[LiquidCoooled]

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.

Re:Whoa giddy.

[Reblet]

minor upgrade, no digg.

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 can perform DNA-analysis in mere minutes anytime soon. Reblet

Re:Whoa giddy.

[rhombic]

The subject matter isn't confusing to me, at least. What we have here, folks, is a failure to communicate.

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 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.

Re:Whoa giddy.

[Noehre]

The problem is that this press release is incredibly short on details. They appear to be making the claim that they have a product that will replace conventional PCR equipment when, in fact, this is not the case.

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.

Tattoo us already

[Mononoke]

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.

When will they realize

[Elrac]

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.

acid trip

[digitaldc]

Sorry, but you are not allowed to bring acid of any kind on board, not even Deoxyribonucleic.

Re:The next stage of biometrics?

[n0dalus]

Normal hairs you shed off don't contain a usable DNA tag; contrary to what most believe.
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.

Gary T. Marx

[daigu]

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.