Briefcase Sized DNA Analysis System

An anonymous reader writes "Japan's NEC Corporation along with Aida Engineering have developed a briefcase-sized DNA analysis system that enables the police to perform comprehensive DNA testing at crime scenes in as little as 25 minutes. The same test would take at least a day to a week (if re-testing or conformation is required) in the lab. The system is compact enough to be carried to crime scenes or other locations where quick DNA analysis is required, making it the world's first portable DNA analysis system."

Comments

Oh, yippee!!

[$RANDOMLUSER]

Can't wait to see the minimum-wage TSA employees using this.
Coming soon! To an airport near you!!

Re:Oh, yippee!!

[Anonymous Coward]

Can't wait to see the minimum-wage TSA employees using this.
Coming soon! To an airport near you!!

The parent might have said something to fire up the crowd, but in all honesty, don't be suprised if it appears at passport office as a part of getting your passport, then becomes a part of your driver's license acquisition, then lands in every police car and station and finally at the checkout counter as part of using your credit card or purchasing certain items. The real flamebait is going to be when a true patriot spits in the eye of the first bureaucratic employee to tell him they have to have a DNA sample from him. Ptui, there is your sample.

Even the article states this can be used by law enforcement, so don't be suprised when DHS decrees that the parent is correct. Hope the samples aren't taken via blood as enough errors have proven fatal in the past in that regard and by professionals, much less low wage bullies at the airport. I hope this doesn't happen and perhaps the parent should have waited to say anything till it did, but I fear he is most prophetic in this regard. His prophecy may fire up the crowd, but we honestly should fear such abuse of our rights by the government and it is absurd that we put up with what they are already doing.

Everyone here knows of certain Ben Franklin quotes, but here is something he probably would agree on, a little manipulation of some of his old quotes: A liberty saved is a liberty earned. Take care of minor liberties and the major liberies will take care of themselves.

The gadget is cool and all ...

[ScrewMaster]

and I wouldn't mind sharing my DNA with the girl in the photo.

Re:The gadget is cool and all ...

[mooingyak]

You tricksy fiend! You made me RTFA!

Great

[Anonymous Coward]

So now the police can tamper with the evidence at the scene, rather than having the lab do it.

but officer are you allowed to do that

[Anonymous Coward]

I cannot imagine my rights being violated by some brash badge or overzealous detective. Never. I imagine all of the data collected will be kept private and secure. I cannot imagine my dna ever falling into the wrong hands. I cannot fathom an hmo denying to insure me due to my genes. No another tool which has added another layer of security and safety to the average true blooded american citizen. And for those nasty criminals (ahem *citizens*) we can use those new fangled pain guns to get them to give samples so we arrest them for all the horrible things they (ahem ahem *may* (g0d I have a sore throat today)) have done.
I love to see the principles of the constitution being upheld(ahem ahem ahem *read as trampling* (must be pneumonia(bad genes I guess))).

f

Re:but officer are you allowed to do that

[Anonymous Coward]

If the only reason you're not getting your rights violated is because they don't have the technology, technology isn't the problem, your government is.

Gattaca

[Nick Driver]

I guess it won't be long now until we see a sampler/scanner that fits into a turnstile.

Confirmation

[cataclyst]

From the blurb:

The same test would take at least a day to a week (if re-testing or conformation is required) in the lab.

Um, correct me if I'm wrong here, but the 1-7 days is still gonna be the case if/when you're verifying your results. This is just a "quick and dirty" test that will gain more acceptance and weight that it will deserve (::cough::POLYGRAPH::cough::). My guess is that it will just be a tool that Homeland Security/Your Average Cop will use to hold you until other tests *conclusively* provide a definite presence/absence answer (like PCR done by an ISO certified lab, HPLC done by an ISO certified lab, GCMS done by.. well you get the point.)

Just my $0.02 here.

Methodology

[cephalien]

I wonder how this works; obviously, 25 minutes isn't enough time to perform any PCR (even something like hot start PCR), so does it rely on having sufficient amounts of DNA available to perform whatever test they're using? Sometimes that can be a not-inconsiderable amount.

I didn't read the article, but eh. Just wondering.

processing time claim is very optimistic.

[mauthbaux]

From TFA:

The compact unit can be used to:
(1) take cell samples,
(2) extract the DNA,
(3) perform polymerase chain reaction (PCR) amplification to generate copies of the DNA,
(4) perform electrophoresis to measure the spacing between DNA bands (to create the genetic fingerprint), and
(5) perform short tandem repeat (STR) analysis to create a unique genetic profile for the individual,"

As I'm currently a grad student in biotechnology (and am performing similar processes in the lab), I feel compelled to respond to their claims on processing time. Taken step by step;
1: simple enough, although some cells are more suitable to DNA work than others.
2: the main obstacles in extracting DNA are proteins and prokaryotic contamination in the sample. DNA is almost always complexed with proteins like polymerases and histones. These proteins effectively prevent the DNA from migrating through agarose or acrylamide; the resulting electrophoresis bands would be almost meaningless. Prokaryotes are pretty much ubiquitous. The problem is that they carry their own DNA which can confuse results, and they carry endonucleases which chop apart most any DNA they come in contact with; destroying the reliability of the gel electrophoresis. Endonuclease digestion of DNA is standard fare for genetics, and I'm assuming that it's performed here, but the contamination of unknown endonucleases from uncharacterized bacteria causes problems regardless. Time required to separate the DNA from the proteins: 1 hour at best.
3: PCR incubation time depends on the length of the DNA chains being amplified, and the initial size of your sample. 10 minutes would be a best case scenario, and that's with ideally sized DNA fragments (whole-genome DNA is far too large), and a large initial sample (not likely).
4: As mentioned previously, protein contamination can make the electrophoresis results almost unreadable. Furthermore, moving that much DNA through a gel in such a short time requires very high voltages. The banding which results from high voltages is generally very blurred, making the 'fingerprint" unreadable. Moreover, whole-genome DNA doesn't really separate into bands; it makes big long smears, so standard staining practice is useless for diagnostics. The last gel I ran with genomic DNA (corn in this case) required about 45 minutes, and that was a small gel using high voltage.
5: STR analysis is touchy. Basically, you use a radioactive or chemoluminescent probe on both the genomic DNA, and a DNA with known STR lengths and compare how bright the sample is compared to the standard. An accurate reading requires a fairly precise estimate of the amount of DNA in your sample; a measure that usually requires a well-calibrated photospectrometer that also needs time to warm up and be calibrated. To further complicate matters, your DNA is in a gel. Getting the tagged probe into the gel (or getting the sample DNA back out of the gel) so that annealing can occur takes time. A southern blot (process involving the removal of DNA from a gel) is usually allowed to run overnight. After annealing takes place, the extra probe molecules are washed away. If excess stray probe is allowed to sit around, or if the annealing isn't complete in the first place, the measurement becomes unreliable. The minimum time I would think feasible for this step would be an hour. In a lab, the labeling alone is normally a 3 hour process. Accuracy would suffer tremendously as time decreases.

So yeah, in conclusion, their time frame for getting results is obscenely short. Severly truncated time frames produce equally severe errors. I don't personally know any scientist who would vouch for the validity of these results.

Re:processing time claim is very optimistic.

[jhfry]

I don't suppose you considered the possibility that this device was engineered and built by PHD's who have worked in the field longer than you knew it existed, and quite possibly are doing things you didn't even know were possible because they are the result of private, unpublished, research.

I am not saying that your wrong, only that your making an assumption that is, quite possibly, false. I'd imagine that they would not announce that something like this is available if it more or less completely failed to yield usable results.

I also suspect that it's not really designed for an untrained or inexperienced user... I'd imagine it's more useful for quick, on site, elimination of suspects performed by a field technician specially trained in DNA sample collection and analysis. Very useful if your one of the potential suspects who says... "I didn't do it, test me and send me home!".

Finally, I suspect that it's absolutely worthless in obtaining high 'resolution', and highly reliable results... however I would imagine it's great for determining if a suspect matches the sample found at a crimescene with a fair margin of error. Or, for example, to determine if the sample found is even human. I can see a lot of uses for a device that gives "close enough" results, as long as any positive results are verified through more precise methods.

Re:processing time claim is very optimistic.

[flushingmemos]

I imagine they can do it in the time they say. I also imagine the results are very simple, like looking at one STR sequence and counting how many lengths of it are in the person's genome in a process similar to qPCR, less RFLP/southern, as parent seems to think. Despite what TFA might imply, I don't think there's endonuclease digestion involved. I may be wrong, and they could have a really, really fast breifcase thermocycler making this work. Maybe, doubt it.

I'm not any kind of STR expert, but from cribbing Wikipedia http://en.wikipedia.org/wiki/Short_tandem_repeat, here's my impression of what's going on with this kit:

1. get cells = blood and semen. yum. In fact, I'd infer this kit is probably a "semen-only" deal in practice, which makes isolating the DNA that much easier, since semen is largely DNA.
2. isolate DNA. Do it yourself, kids! (http://learn.genetics.utah.edu/units/activities/extraction/) 2-5 minutes with a kit.
3. PCR. Here's where things get interesting. What are their primers? I think they're using 5-10 nucleotide STR sequences that are already conjugated to a fluorescent dye. Since STRs for human identification use are just, according to wikipedia, 4-5 STRs (10-50 nucleotides) long, each cycle can probably be as short as 30 seconds. With ramping the temperatures we can call that 1 minute per cycle. How many cycles do we need? 10 cycles gives us 2^10 copies of the original STR, that's (biologist math)1000 copies(/biologist math). Add 2 minutes for our hot-start polymerase, and that's 12 minutes for PCR. Whoo! It well may be less, i.e. shorter elongation, fewer cycles. This is where they're claiming to save time, so who knows.
4. electrophoresis. Undoubtedly capillary, you can see it in the photo (at least I can), and since we're looking at stuff that's only 75 nucleotides max, can be done very quickly. I don't really know capillary gel electrophoresis, but it apparently kicks the shit out of slab gel electrophoresis: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=330505. We'll call that 10 minutes, lol. Could be a bit more? Balances with the PCR.
5. Of course, we added a 10-100 nucleotide standard conjugated to a different fluorescent species from the primers (i.e. the primers glow green and the standard glows red), so we can use our shitty little built-in 2-wavelength spectrophotometer to see where our unknown sample's bands are.

And now we have our data! And that only took... 25 minutes! Of course, this isn't a full-blown RFLP, like parent seems to assume. But just for doing a quick-and-dirty count of STRs, this could work. That's how I'd do it. Maybe I just invented a competing type of kit, lol. In any event, looking at the picture, I get the feeling their pipettes are crap.

Note this doesn't show how many repeats of a given legth the accused has, so the asshole could have 3 5-repeat ones and 2 4-repeat, and the machine would show that as being the same as a person with 1 of each. Also, they may use more fluorescent dyes to look at more STR sequences without too much difficulty. But in general, the samples will be unclean at best, total crap more often than they'll like to admit, and, in the end, only good as a blood-type-and-then-some test. How juries will react to this, I don't know.

To get even farther from parent, the real threat to your privacy is coming from gene chips, the next generation of sequencing technology. This kit is comparatively rudamentary, and obviously expensive. Yet more overhyped crap, whee!

Re:processing time claim is very optimistic.

[Biotech9]

Rubbish, you obviously haven't worked in a nice lab. You think they are using full sized SDS gels for this? Agilent systems have capillary gel chips that run samples far more accurately and in a fraction of the time of SDS-Page.

And you think they're using a SPEC to check nucleic acid levels? Christ! just because you're using equipment form the 90s doesn't mean everyone else is!

A southern blot (process involving the removal of DNA from a gel) is usually allowed to run overnight.

!!!!

OK, i give up, you've been locked in a room since the 1960's right?

Re:processing time claim is very optimistic.

[reverseengineer]

I was in complete agreement with the parent on the subject of the processing time- I figured 25 minutes could only possibly be the figure if PCR were unnecessary, as I considered 25 minutes to be quite impressive for just running the gel and the STR analysis. Then I looked at the Pink Tentacle post that the "article" blog post cites (the original NEC press release is in Japanese). According to Pink Tentacle's summary, PCR is part of the process, and from start to finish is under 25 minutes.

Now, I've been away from molecular bio for a few years, so I was curious to know if this sort of speed was even remotely possible. I mean, I remember this whole process requiring a pretty solid afternoon's worth of work at minimum- and depending on the circumstances, often involved setting stuff up to run overnight. Having Googled "fastest PCR" and having found this paper, I have to admit NEC might not be full of crap about this.

Basically, they find workarounds for all the time-intensive steps in the analysis. DNA extraction? They add proteinase K and guanidine to whole blood, then put it through a solid-phase extraction that they say takes only 6 minutes.

For PCR, there's really only so far you can go to speed things up due to limits imposed by reaction kinetics, but the tiny sample size allows them to run through each temperature station in a couple seconds (it should be noted that the fragments they're replicating are only about 200 base pairs).

The separation by electrophoresis is where the magic really happens. See, the parent and I were thinking about how this is usually done, by moving a band of DNA across a slab of polyacrylamide or agarose gel. The setup is labor-intensive, and as the parent notes, it does take awhile for the gel to run to completion They instead do high voltage capillary electrophoresis- and their capillaries are channels etched into a glass chip. Fluorescent intercalating dye was present in the sieving matrix, and detection was done with laser-induced fluorescence- no Southern blot. Everything runs on a single chip, and in 25 minutes goes from bodily fluids to genetic fingerprinting.

I know there's been a lot of hype about "lab-on-a-chip" systems and what the future holds. What's mentioned in this Dec. 2006 paper is of course a research proof-of-concept system- if you look at their PCR setup, their "thermal control system" is a heat lamp and cooling fan controlled by a laptop. A year later, is NEC about to debut a 25 minute DNA lab-on-a-chip as a commercial product? I don't know, but I no longer think the idea is as crazy as it sounds.

Potential Uses outside of Law Enforcement

[teebob21]

I've already preordered mine.

I've been wanting to find out which one of my neighbors is leaving the uhhh...deposits on my sheets while I'm at work and the wife is home. Obtaining reference samples will be easy: both of them flick their cigarette butts in my yard. I'm certain this will be cheaper than hiring a divorce attorney. (The quote does not apply to me; those words were uttered by a co-worker with whom I shared this article.)

Of course, there are alternative input methods ...

[timothy]

which also fit into a briefcase.

(In the category "Things I want vs. things I need" ...)

timothy

Overconfidence.....

[IHC Navistar]

Criminal : "I didn't kill anybody!"
SGT. "So, you say you're not the killer eh? We'll see about that. We just got this new test that'll tell us if you murdered him or not."
Officer : "Aight Sarget. I got the kit. It says we need parental supervision before handling chemicals."
SGT. : "Set timer for five minutes."
Officer : "Check."
SGT. : "Fill Vial 'A' with 25ml saline solution."
Officer : "Check."
SGT. : "Warm to 85 degrees Fahrenheit. Then add suspect sample to Vial 'A'."
Officer : "Check. No wait....Ok. Check."
SGT. : "Activate timer. After 2.5 minutes, Add 2ml of liquid from evidence sample in Vial 'B'. Stir with enclosed plastic rod."
Officer : "Check."
--5 minutes later--
Officer : "Time!"
SGT. : "Using enclosed eydropper, place ONE (1) drop onto test strip in marked area. BLUE=MATCH, CLEAR=NO MATCH"
Officer : "What if it's pink?"
SGT. : "He's pregnant."

I would seriously question the accuracy of these tests, since there a many factors, both environmental and analytical that can affect the outcome of the test. Laboratory tests are meant to be conducted in a LABORATORY, not a Samsonite briefcase. Now, you will be giving every rookie officer who can hold a Q-Tip the same credibility as an educated, trained, and well-experienced forensic technician.

Laboratory setting are ideal for conducting tests and experiments: The are well-equipped, well-engineered, staffed by technicians with years of experience (discounting interns, of course), don't sacrifice accuracy for space, and allow a consistent, managed environment for evidence analysis, storage, and custody control. Treating DNA evidence as if it were a case of bad breath is just wrong. If I were a judge, I would seriously question the integrity of such tests and their results.

This is treating Forensic Science less like science and more like a "Conviction-In-A-Can".

Chimerism

[BuGless]

Given that DNA tests become more mainstream, it would be rather interesting to see how large a percentage of the population actually is a chimera. If it turns out to be "popular", DNA tests could lose a lot of their credibility (in which case DNA-tests-at-the-counter become a hazard instead of a benefit).

Re:Awesome!

[daniorerio]

Indeed, I had a lecture from the director of our national forensic institute (Dutch) once, explaining the whole procedure of obtaining DNA, what they actually analyze and how they verify the validity. There is a reason why these tests take up to 2 weeks to give a result: Once you as a scientist say "we have DNA evidence, we got him!" it pretty much seals the deal. So you got to be damn sure you are right: -what are the odds that an identical DNA pattern from someone else came there (no they don't sequence your DNA, so there's a small chance that another person with a similar pattern was on the crime scene, usually the chance is close to zero though) -how was the evidence collected, could it be contaminated etc. etc. -is there other evidence that contradicts the results And after that an analyzis has to been done estimating the chances that you are wrong in saying that the DNA is from the person you are accusing, and that he/she actually commited the crime. I wouldn't be very happy to let an untrained (in forensics) police officer do those things, because most of them hardly known what DNA is, and what exactly is analyzed. Another reason why you wouldn't wnat that: in the lab everythinh is done anonymous, the analyst just has sample numbers and suspect, X, Y, and Z. The police will know the name of the suspect and stop looking as soon as they think they can nail him, regardless of the presence of any other evidence contradicting this. PS. This forensics guy wasn't too happy with CSI, it creates really unrealistic expectations about what cases the police can actually solve (and the amount of time it takes them to do so).