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Faster DNA Testing

ScuttleMonkey posted more than 7 years ago | from the sorry-sir-i-need-to-stick-you-again dept.

Science 187

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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187 comments

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Your DNA (5, Funny)

Jozer99 (693146) | more than 7 years ago | (#14089270)

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

Re:Your DNA (1)

TubeSteak (669689) | more than 7 years ago | (#14089376)

Your DNA says you don't have a bomb, so go right ahead and board! Have a nice day!
You have no chance to survive make your time

acid trip (4, Funny)

digitaldc (879047) | more than 7 years ago | (#14089387)

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

Re:acid trip (1)

Peldor (639336) | more than 7 years ago | (#14089672)

Then I'm okay, all my DNA is made up of base pairs.

Re:Your DNA (1)

DaHat (247651) | more than 7 years ago | (#14089394)

Not to mention the idea that the powers that be already have all of our dna on file so they know who is good... as well as the dna of every suspected terrorist. At last... we may be safe!

Chifrudo (2, Funny)

praedictus (61731) | more than 7 years ago | (#14089689)

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!

In a word.... (2, Funny)

conteXXt (249905) | more than 7 years ago | (#14089286)

Probably.

Re:In a word.... (1)

dascandy (869781) | more than 7 years ago | (#14089303)

What are you going to swab off somebodies skin? Best take a swab of saliva...

Accuracy (2, Interesting)

kellar (932533) | more than 7 years ago | (#14089289)

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.)

Re:Accuracy (1)

Red Flayer (890720) | more than 7 years ago | (#14089321)

"(it also uses 'leverage' as a verb.)"

from Random House College Dictionary (closest one at hand):
lev-er-age ...v.t. 5. to provide (an investment or equity) with operating or financial leverage.

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.

Re:Accuracy (1)

thetejon (798945) | more than 7 years ago | (#14089571)

I don't have a dictionary handy, but I believe that most dictionaries didn't recognize leverage as a verb until pretty recently. Leverage as a verb is something made up by middle managers to sound smart that has been accepted by (some of) society, and is now maybe considered a real word.

I still think that using it as a verb implies that you are trying to sound smarter and/or more important than you are, but if dictionaries are starting to include it, I guess I'll have to get over it.

Re:Accuracy (1)

Red Flayer (890720) | more than 7 years ago | (#14089640)

Well, my dictionary was printed in 1975, so it depends on your definition of recent.

Sure, middle-managers use it as a buzzword -- but upper-level management, and financial analysts, etc, use it as a meaningful verb. Sometimes even middle-managers use it correctly. ;)

Another possibility is that the public (myself included) is paying more attention to financial matters, and so are becoming more exposed to financial terms.

Re:Accuracy (1)

Imsdal (930595) | more than 7 years ago | (#14089753)

I agree that it happens that "leverage" is used correctly, but in my experience it is much more often used instead of "use" in order to sound fancy (i.e. like a consultant), even by upper management. But maybe finacial analysts use it properly more often than not.

Googling for "we will leverage" yielded 0 correct uses of the ten presented to me on the first page. (Just googling for "leverage" will not yield results where it is used as a verb.)

Re:Accuracy (1)

Red Flayer (890720) | more than 7 years ago | (#14089929)

Well, to be fair, "we will leverage" is a loaded search term. You're looking almost exclusively for the type of press release, etc, in which it will be used incorrectly.

"To leverage" would be a better search, and there are a couple correct usages within the first 10 results there.

I do agree that it is used incorrectly, and without real purpose, far too much.

Re:Accuracy (0)

Anonymous Coward | more than 7 years ago | (#14089329)

(it also uses 'leverage' as a verb.)
It is a verb, dumb ass.

Re:Accuracy (1)

jimbolauski (882977) | more than 7 years ago | (#14089469)

What if my evil twin gets put on the no fly list, fortunatly they all ready track me with rfid in my fillings so i might be set free before the proctology exam.

Only 5 minutes?? (4, Insightful)

SegFaultCM (617569) | more than 7 years ago | (#14089291)

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?? (0)

Anonymous Coward | more than 7 years ago | (#14089305)

Yes, because they will only do one person at a time... Thinking are we?

Re:Only 5 minutes?? (2, Insightful)

Exocrist (770370) | more than 7 years ago | (#14089318)

I imagine that in a facility like an airport, with that many people, they'd have more than one line going. Something like an airport would probably have more than one machine.
However, that does raise an interesting point about the number of people who can be tested at once.

Re:Only 5 minutes?? (4, Funny)

Stevyn (691306) | more than 7 years ago | (#14089393)

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?? (4, Funny)

yerfatma (666741) | more than 7 years ago | (#14089446)

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

It takes 5 minutes? Must require two semen samples.

Punchline to old joke.. (1)

mykepredko (40154) | more than 7 years ago | (#14089888)

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

Re:Only 5 minutes?? (1)

DoctorFrog (556179) | more than 7 years ago | (#14089902)

s / quickly escorted off either by trained guards or another piece of machinery for re-classification / conveyed further along in extreme comfort, past murals depicting Mediterranean fishing scenes, toward the rotating knives. The last hundred feet are heavily soundproofed, The blood drains into these gutters, and the mangled flesh slurps into..."

"Excuse me."

"Yes?"

"Did you say knives?"

"Ah, rotating knives, yes."

"Are you proposing to simply slaughter the suspects? Without trial?"

"Yes, does that not fit in with your plans? You see, I mainly design slaughterhouses."

"Actually, that's perfect. Do you own an apron and trowel, by any chance?"

(With apologies to Monty Python [jumpstation.ca]

Re:Only 5 minutes?? (1)

91degrees (207121) | more than 7 years ago | (#14089410)

This isn't number of people on a flight. This is number of people at the airport! How many people go through every 5 minutes? This could easily be in the thousands.

But the question is whether the process can be pipelined. Is the sample just sitting there for 5 minutes? Can several samples be processed at the same time? I still think that doing anything like 100 people at a time would be impractical though.

Re:Only 5 minutes?? (4, Interesting)

TheRaven64 (641858) | more than 7 years ago | (#14089464)

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.

Re:Only 5 minutes?? (2, Informative)

AndersOSU (873247) | more than 7 years ago | (#14089793)

Ignoring the fact that this is all impossible becasue DNA analysis consists of more than PCR and that PCR is never going to take 5 minutes - its just the kinetics of the reaction.

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, because as we all know airports are the hallmarks of efficiency.

Re:Only 5 minutes?? (2, Insightful)

Killjoy_NL (719667) | more than 7 years ago | (#14089488)

You really think they would only process 1 person at a time?

Weird (0)

Anonymous Coward | more than 7 years ago | (#14089297)

Have we go somehing agains using he leer 't'?

The next stage of biometrics? (1)

Dekortage (697532) | more than 7 years ago | (#14089298)

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? (0)

Anonymous Coward | more than 7 years ago | (#14089348)

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

Re:The next stage of biometrics? (3, Informative)

n0dalus (807994) | more than 7 years ago | (#14089390)

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.

Re:The next stage of biometrics? (1)

Dekortage (697532) | more than 7 years ago | (#14089445)

So maybe this particular device wouldn't work with hair. If not hairs, it seems like we leave a trail of other useful matter that could be used. Would it work with spit on a toothbrush, snot on a tissue, a band-aid over my paper cut, lipstick on a drinking glass, discarded condoms...?

Re:The next stage of biometrics? (1)

sabernet (751826) | more than 7 years ago | (#14089968)

I don't think snot would work well as it's mostly the stuff collected from the air (lots of contamination) and mucus is mucus is mucus. I may be wrong though.

What impact on UK ID cards (3, Insightful)

Silver Sloth (770927) | more than 7 years ago | (#14089307)

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 (1)

backslashdot (95548) | more than 7 years ago | (#14089339)

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

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 (1)

Turn-X Alphonse (789240) | more than 7 years ago | (#14089400)

DNA can easily be planted. Lets make a random scenario.

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 on someone.

Hey, is that your soap on the floor? (-1, Offtopic)

Anonymous Coward | more than 7 years ago | (#14089455)

Are you posting from prison?

Re:What impact on UK ID cards (1)

badfish99 (826052) | more than 7 years ago | (#14089398)

So then I'll have to stop leaving saliva samples everywhere I commit a crime? Shit. And I'd only just got used to the idea of wearing gloves because of this new-fangled fingerprinting stuff.

Re:What impact on UK ID cards (1)

arivanov (12034) | more than 7 years ago | (#14089429)

A classic example here is the so called cut hair murder. It is IIRC a murder case from a few years ago where the suspect deliberately left hair near the victim's body. He made a few mistakes though:

1. It was hair which usually does not have enough material for a good test unless it has been pulled out with the roots.
2. He cut it and the fact that it was cut was quite obvious under microscope.

AFAIK the police is still chewing the case and is nowhere near identifying neither the suspect nor the person whose hair was cut.

As you see it has already happened and I bet it is happening right now. In the Great Brave New World.

Re:What impact on UK ID cards (1)

DarkTempes (822722) | more than 7 years ago | (#14089680)

I do believe one major reason DNA testing isn't used for lesser crimes is because of it's expense. At least here in the states. That said, this quicker method doesn't say anything about being a cheaper method, so I doubt this will make that much of an impact with use in lesser crimes.

popular application (4, Funny)

Douglas Simmons (628988) | more than 7 years ago | (#14089315)

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.

Re:popular application (0)

Anonymous Coward | more than 7 years ago | (#14089413)

but my homies done seen her 'round the block. Dig?


Honestly? I have no idea what it was you just said.... oh, and before you ask, I'm 23.

Re:popular application (1)

brufleth (534234) | more than 7 years ago | (#14089465)

Translation:
Implying she's been unfaithful. As in, hanging out with other guys "around the block." Seemed obvious to me.

Re:popular application (2, Interesting)

zerocool^ (112121) | more than 7 years ago | (#14089436)


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 (0)

EwokMolester (918844) | more than 7 years ago | (#14089444)

You have some serious issues man.

Re:popular application (1)

Scoth (879800) | more than 7 years ago | (#14089448)

I've lately started hearing radio ads for a company that says all they need is a swab from the kid's and a swab from the "alleged father's" mouth to do the test, which doesn't seem too terribly difficult. Having never needed a paternity test, I have no idea what they entail and whether this is something new or not. I suppose it's still a philisophically hostile action, though ;)

you can do this today, (0)

Anonymous Coward | more than 7 years ago | (#14089657)

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.

Time rent "Gattaca" again... (1)

PSaltyDS (467134) | more than 7 years ago | (#14089319)

Time rent Gattaca [imdb.com] again...for a creepy "1984-like" vision a world with perfect identity tracking.

Obviously not perfect... (1)

interactive_civilian (205158) | more than 7 years ago | (#14089364)

One of the main premises of GATTACA (IMHO) was that the system could be circumvented by the dedicated.

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.

Weird (-1, Offtopic)

Anonymous Coward | more than 7 years ago | (#14089887)

It's bizarrely unsettling how you managed to keep leaving prepositions out of your sentences.

What about the research benefits? (5, Insightful)

achesterase (918544) | more than 7 years ago | (#14089326)

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. (5, Informative)

LiquidCoooled (634315) | more than 7 years ago | (#14089330)

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 [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. (3, Informative)

Reblet (671563) | more than 7 years ago | (#14089372)

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. (1)

AndersOSU (873247) | more than 7 years ago | (#14089406)

Not only that but current thermal cyclers used for PCR are pretty darn quick at changing the temperature. Maybe they can make them smaller and cheaper, but it's not like they invented the peltier chip...

Re:Whoa giddy. (1)

pgolik (526039) | more than 7 years ago | (#14089700)

Moder capillary based PCRs can run the amplification procedure within 20-30 minutes. If they use a system similar to the one in real-time PCR devices and do melting curve analysis instead of electrophoresis they might get the whole procedure done within about 40 minutes. Actual temperature ramping time is an insignificant fraction there, most of the time is what is needed for the enzyme to complete the elongation step. Unless you make a faster polymerase you won't speed PCR up significantly. The article is not very specific, seems like the actual improvement may lie in the size and portability of their device, they don't say however, how many samples in paralell it can run and if any disposable reaction vessels are used (and if not, then how they deal with cross-contamination issues). I guess you could make a single-tube size PCR block of a similar size using current peltier technology.

Re:Whoa giddy. (1)

njyoder (164804) | more than 7 years ago | (#14089616)

So taking minutes instead of hours and not requiring millions of dollars to be spent on a lab is a minor upgrade? What?

Re:Whoa giddy. (1)

pgolik (526039) | more than 7 years ago | (#14089747)

Current machines on the market can do it in about 1 hour (depending on the size of the fragment you amplify), you can't make it much shorter by just speeding up the heating/cooling steps, you need time for the enzyme to do the work. And you can buy a basic thermocycler for a few thousand $, add a few hundred $ for the equipment to do post-PCR electrophoresis, and some $ for the reagents. Hardly "millions of dollars", there are high schools that can afford to do it in the classrooom. And I doubt the new thing will be significantly cheaper than the current crop of thermocyclers.

Re:Whoa giddy. (1)

njyoder (164804) | more than 7 years ago | (#14089818)

Yes, you can speed up the process. By doing it on a microscopic scale with microfluidics, you can shortcut the process. This research has been done by people a hell of a lot smarter than you, and I wouldn't doubt them just because your understanding of traditional technology doesn't let you think you can do it. read my comment here [slashdot.org] for information on the past research on this. And I'm not taking your estimates at face value, especially if they involve low-end, crappy equipment that wouldn't be used for any real analysis. Your "doubts" are founded on nothing other than ignorance, as I somehow doubt you have any background in MEMS or microfluidics technology whatsoever.

Swim time is over! (0, Offtopic)

cdtoad (14065) | more than 7 years ago | (#14089334)

You! Outta the gene pool!!!!

DNA testing on job applications (2, Interesting)

digitaldc (879047) | more than 7 years ago | (#14089343)

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.

Health Insurance (0)

Anonymous Coward | more than 7 years ago | (#14089546)

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.

Re:DNA testing on job applications (0, Troll)

mrogers (85392) | more than 7 years ago | (#14089807)

Don't worry, the machine will have bright, friendly-looking lights labelled "crazy", "dishonest", "gay" and "Arab".

you forgot French (0, Offtopic)

digitaldc (879047) | more than 7 years ago | (#14089831)

and Insurgent

Yes (0, Offtopic)

paranode (671698) | more than 7 years ago | (#14089949)

And that's when it's time to call Jude Law.

fuck and off (1)

Turn-X Alphonse (789240) | more than 7 years ago | (#14089354)

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".

Re:fuck and off (1)

interactive_civilian (205158) | more than 7 years ago | (#14089385)

so says Turn-X Alphonse:
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".
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 (3, Insightful)

Mononoke (88668) | more than 7 years ago | (#14089355)

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.

Re:Tattoo us already (0)

Anonymous Coward | more than 7 years ago | (#14089945)

I call dibs on 666. With red ink and some plutonium for that neat glowy effect.

be skeptical (2, Interesting)

Anonymous Coward | more than 7 years ago | (#14089361)

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.

This doesn't seem so great... (2, Informative)

sowalsky (142308) | more than 7 years ago | (#14089366)

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.

Re: faster thermocyclers (1)

gringer (252588) | more than 7 years ago | (#14089440)

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 [roche-appl...cience.com] 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.

Re:This doesn't seem so great... (1)

King Babar (19862) | more than 7 years ago | (#14089484)

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.

I agree that this is obviously hype. For starters, PCR is an important part of finger-printing, but it doesn't give you the sequence. It just amplifies the DNA; you might be able to go a different way for rapid (but not completely accurate) identification. For people who don't do much PCR or sequencing or the whole process, it goes like this:

  1. Get sample including DNA. (Can be really fast with a cheek swab.)
  2. Extract DNA from the sample. (Minutes to hours; from a fruit fly, I can do this in an hour.)
  3. Set up the PCR reaction. (Can be automated to be very fast.)
  4. Run PCR. With miniaturization and with some other tricks (see below) this can get quite fast.
  5. Interpret what you've got. If you're doing this via sequencing, add (currently) hours to the process right now. If you're doing this by examining VNTRs, you might be able to get away faster. (VNTR = variable number of tandem repeats; if you look at enough sites that have these, you can get close to a unique identification, and I'm supposing you could get the numbers in at least a loose fashion via real-time quantitative PCR and a final melt curve analysis. That's faster than sequencing by a lot, but not 3-5 minutes that people are suggesting.)

So it would be nice to miniaturize and (thus) build faster thermocyclers, but it alone would not be a panacea. So the last point about 30-30-30: if you've got good primers, ideal sequence, and a short product, you can cut those times down quite a bit in some situations. I've seen (nominal) extension times in RT-PCR as short as 8 seconds being used for ~100 bp sequences. But that's still not the whole cycle, and you still need to multiply by 30-35 for the number of cycles, and the target article is just a hype-y blurb.

Just what I always wanted (1)

gringer (252588) | more than 7 years ago | (#14089367)

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 [appliedbiosystems.com] on PCR and associated technologies.

Test everywhere? Forget it. (1)

Alwin Henseler (640539) | more than 7 years ago | (#14089368)

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?

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.

When will they realize (4, Insightful)

Elrac (314784) | more than 7 years ago | (#14089373)

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.

Re:When will they realize (1)

sita (71217) | more than 7 years ago | (#14089425)

Confirming identity does nothing toward confirming non-terrorism.

Blatantly not-true. Not fully efficient, yes. Has to be combined with other measures, yes. May be insufficient, yes. May not be worth the price, yes. Does nothing, no.

Re:When will they realize (2, Interesting)

MrMickS (568778) | more than 7 years ago | (#14089497)

Blatantly not-true. Not fully efficient, yes. Has to be combined with other measures, yes. May be insufficient, yes. May not be worth the price, yes. Does nothing, no

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 present everything with the "it will prevent terrorism" tagline. "No it won't" comes the view from the opposition. Someone else then says "well, that's not strictly true" and the authorities can sit back and watch it all unfold. If they are lucky they also get "its true that it won't do anything unless all of these other authoritarian measures are invoked as well". They can then respond by proposing to implement them all in the name of safety and can point out that they didn't think of it first. The fact that they had the measures ready to roll was pure coincidence, they were just being prepared and it shows that they were in touch with public feeling.

DNA testing, in itself, is no defence against terrorism which I believe was what the OP meant.

Forensic audit trail (0)

Anonymous Coward | more than 7 years ago | (#14089377)

Now that we are coming out forms of identification that offer better certainty let's start working on the accuracy. DNA evidence is suprisingly easy to contrive. There's no way to determine the sample wasn't originally collected at a different place and time than the orginal crime scene. You can be convicted solely on a DNA sample and the police have been known to fake evidence. That's a bad combination. Even if you don't believe you will ever become entrapped in such a matter, you don't want to risk doezens of convicted felons having their convictions overturned because a dectective involved in their cases got caught faking evidence. This happened in NY where a dectective got caught faking fingerprint evidence (harder than faking DNA evidence).

Go ahead. Watch CSI and see how causually they collect and handle evidence. Pretty scarey?

If you haven't seen it yet... (1)

El Camino SS (264212) | more than 7 years ago | (#14089379)


    I would highly suggest renting Gattaca.

   

integrity check at speed of light now available (-1, Troll)

Anonymous Coward | more than 7 years ago | (#14089380)

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Not all that special... (2, Interesting)

J.Y.Kelly (828209) | more than 7 years ago | (#14089383)

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.

Insurance? (2, Insightful)

Savage-Rabbit (308260) | more than 7 years ago | (#14089388)

"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.

Best Collection Method? (1)

dc_dog (767092) | more than 7 years ago | (#14089389)

I would be happy to leave my DNA sample in the hands of a stewardess!

Big step? Not so much (1)

dedioste (797427) | more than 7 years ago | (#14089395)

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.

They stole this idea from the movies! (1)

PatHMV (701344) | more than 7 years ago | (#14089411)

Gattaca [imdb.com]

fiction becomes fact (1)

mustafap (452510) | more than 7 years ago | (#14089419)


Looks like "Gattaca" becoming reality

Gary T. Marx (3, Insightful)

daigu (111684) | more than 7 years ago | (#14089430)

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.

As seen in... (1)

tmk (712144) | more than 7 years ago | (#14089459)

Who shot Mr Burns Part 2: http://en.wikipedia.org/wiki/Who_shot_Mr._Burns%3F [wikipedia.org]

"Whoa, hey there, DNA testing takes 6 to 8 weeks ....did I say weeks? 'Cause I meant seconds."

Rochester Shopping (1)

scottennis (225462) | more than 7 years ago | (#14089478)

They can do this in Rochester but they can't revitalize Midtown Plaza? Oh well, at least they have Radio Shack.

maury's show (1)

jzeejunk (878194) | more than 7 years ago | (#14089549)

now you won't have to wait for an hour to know who's the father ;)

in rochester? (0)

Anonymous Coward | more than 7 years ago | (#14089586)

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)

Awesome! (-1)

Anonymous Coward | more than 7 years ago | (#14089648)

I can't wait until they come out with DNA fortune tellers!

share DNA with Uma Thurman (1)

peter303 (12292) | more than 7 years ago | (#14089670)

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.)

microfluidics PCR research (1)

njyoder (164804) | more than 7 years ago | (#14089681)

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.

Here is the text from Microfluidics: Fluid physics at the nanoliter scale:
http://thebigone.stanford.edu/quake/publications/R evModPhysJul05.pdf [stanford.edu]

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.

Prison Egress (1)

WindBourne (631190) | more than 7 years ago | (#14089685)

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.

Great (0)

Anonymous Coward | more than 7 years ago | (#14089691)

Maybe they can use this to help the families in New Orleans, since 3 months later there are still over 300 bodies [chinapost.com.tw] still unidentified, and over 4,000 people still missing.

"You're doing a heckuva job, Brownie!"

Gotta Love It.... (2, Insightful)

hotarugari (525375) | more than 7 years ago | (#14089705)

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.

Speed vs. accuracy (1)

Billosaur (927319) | more than 7 years ago | (#14089771)

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 [wired.com] ? A government-run DNA database [schneier.com] ? 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 [wikipedia.org] ?). Speedy DNA processing isn't going to solve the fundamental security problem, which is how do we read your mind.

DNA's hash becomes your world-unique name (0)

Anonymous Coward | more than 7 years ago | (#14089787)

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.
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