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Fight Counterfeiting With Handheld DNA Sequencing

In previous articles (see Counterfeiting as an Art Form and Anti-Counterfeiting DNA Marking Gets a Boost), I wrote about DNA marking as an anti-counterfeiting measure. A few of the commenters suggested that the technology for sequencing authentication was too pricey to expect widespread deployments. My response was that costs will come down as a function of technology introductions that will put DNA sequencing equipment on the desktop at company receiving stations.

I mentioned that we might be looking out two to four years before this portable sequencer might become available. Also in the article, I wrote about a technology breakthrough that might make this a reality at $1,000. Well, I am delighted to say that there is a working handheld sequencer available using nanopore protein structures that can sequence up to 70,000 base pairs in a very short period of time.

Prior to this, turn-around sequencing times for even short sketches of DNA could take hours or days. To sequence just a few hundred base pairs, scientist had to mince up thousands of copies of the target DNA, sequence all the fragments, and use software to perform the reconstruction work by matching overlap within the fragments.

Lab in Your Hand

The MinION USB stick DNA sequencer costs under $1,000 and  sequences up to 150 million base pairs in its six-hour lifetime.

The MinION USB stick DNA sequencer costs under $1,000 and
sequences up to 150 million base pairs in its six-hour lifetime.

Time saver
The nanopore technology virtually eliminates the need for overlap analysis, and saves an incredible amount of time and effort in the sequencing process using very long strands of DNA. The human genome consists of about a billion base pairs so 70,000 seems like a small number in comparison. But DNA marking that only uses segments for DNA taggants may now become more economically viable as an anticounterfeiting methodology.

So, open your hand and consider the breadth of your palm. The unit called “MiniON,” pronounced “Min-ion” from Oxford Nanopore Technologies, fits nicely in your hand and includes a USB port that can plug into a laptop or a desktop PC. Here is how it works once you have swabbed the taggants and prepped the DNA:

  • Drop the DNA sample into the integrated port on the MinION. Within the device is a silicon chip with thin polymer membranes with tiny pores.
  • An enzyme carries or shuttles the DNA to the protein-based nanopore inserted through the polymer which is only a couple of nanometers in diameter. This is about 100,000 times thinner than a human hair. The enzyme unzips the base pairs and feeds one end into the nanopore. Imagine a railroad track that is divided such that only one rail goes through the tunnel at a time.
  • Electrodes put a small current through the nanopore and as each base type, A,T,C, and G are passing through the pore, the current is interrupted and sensed in such as manner as to be able to identify what base has caused the interruption. Each base has a characteristic response.

Software analysis
A software application in the laptop analyzes the electrical signal and records the different bases as they pass through the portal in the linear progression. The software then stitches together the sequence of bases of the entire strand.

Lastly, the DNA reading is enhanced through the additional capability of reading the complementary strand. During the unzip process, the strand is prepared with a “hairpin” connector that links the complementary strand that is subsequently pulled through the same pore for a “check” sequencing step. This is a kind of biological error detection much like a checksum on an EPROM program.

Blood DNA can also be sequenced in this application, so we are not too far from localized and mobilized DNA identification and authentication for security identification purposes. The nanopore technology could possibly open the door for low cost, DNA anti-counterfeiting measures. It seems like all of the technologies that are brought into being with human and business protections in mind, can also be subverted into loss of privacy concerns as information retrieval for various uses becomes more readily accessible.

I think this is a trade-off we may have to accept in order to ensure that we are not inadvertently endangering lives by using counterfeit electronics in mission critical and medical systems. We are in the business of industry and trade-offs.

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20 comments on “Fight Counterfeiting With Handheld DNA Sequencing

  1. Ariella
    April 5, 2013

    Wow, it's amazing that this is readily available now. DNA sequencing for data storage was estimated to only become financially feasible in about 10 years, as per Storing Digital Data in DNA. 

  2. t.alex
    April 6, 2013

    Wow, I think the idea of using DNA sequencing for authentication is so cool! Perhaps we need to achieve super fast sequencing with powerful computing by then.

  3. _hm
    April 6, 2013

    Very interesting but little difficult to understand it in detail. What are other apllications for this?

     

  4. dalexander
    April 6, 2013

    @hm … Google MinIon DNA and look at all the applications Pretty impressive technology for sure.

  5. SunitaT
    April 7, 2013

    @Douglas, thanks for the post. This is really good news, I am sure devices like “MinION” will definitely help us to reduce the counterfieting which is one of the biggest challenges that the electronic industry is facing today.

  6. SunitaT
    April 7, 2013

    Perhaps we need to achieve super fast sequencing with powerful computing by then.

    @t.alex, true. Currently i t's capable of sequencing 150 million base pairs in six hours, and uses the computer's own CPU to perform the analysis. I am sure this time can be brought down significantly as the transistor size shrink.

  7. SP
    April 8, 2013

    Wow that is just great. Using DNA sequencing to avoid counterfeit. While its definitely a full proof method and no doubt can avoid cunterfeit but can it be done in Asian counties too, because infrastructures is still a challenge. For sure it can be deployed in US, UK, many parts of Europe.

  8. prabhakar_deosthali
    April 10, 2013

    If the process can be implemented in US, UK then surely it can be implemented in Asia also.

    Though the underlying technology looks complex the process to implement the same looks pretty simple .

    I am slightly confused as to what process is applied at the source ( DNA stamping) and at the destination ( DNA verification)

  9. ddeisz
    April 10, 2013

    Applying DNA by the semiconductor companies directly to their products has not been accepted as reasonable cost or a reasonable anti-counterfeiting measure, regardless of this potential sequencing device. While in-field validation of who marked the part is important, this part of the anti-counterfeit flow ignores the handling chain before this validation occurred.

    Anyone can mark parts with DNA after they purchase them through fully Authorized channels, but that channel has already ensured no counterfeit. Marking of fully Authorized product is a waste of time and money unless your own supply chain can't keep track of where parts were purchased. In that case, perhaps this is the problem that should be solved first!

    Great – there is a DNA sequencer on the market. Ooops, nobody who manufactures semiconductors and not almost entirely funded by the US government (SRI) agrees to put it on their product for good and well-documented reasons.

    Dan Deisz

    Rochester Electronics

  10. dalexander
    April 10, 2013

    @ddeisz.. you sound almost angry. I can appreciate the technology without knowing a specific application. I think it is awesome that they can make a protein-structured nanopore than can be electrically charged and that an enzyme can unzip and subsequently escort the DNA through the pore one base at a time while detecting what base is passing through the pore. They can also identify individual molecules, nucleotides etc. All of this in a hand-held device. Wow! Considering the previous technology that took days to sequence just a hundred bases and this will do a single chain of 70,000 in minutes, I gotta say that I am amazed at the inginutiy and brains that went into this product. IF it is ever used in anti-counterfeiting is another issue entirely. Just the fact that such tech is available will help make criminal forensics much more affordable and maybew put away some of the real bad guys and let those who were false accused go home to their families. I am pumped about this breakthrough.

  11. ddeisz
    April 10, 2013

    Douglas,

    Not angry, just reacting to the title of the article with respect to semiconductors and counterfeit. If your article is just on the technology and nothing to do with semiconductor counterfeit, then I read into your title too much. The technology is cool and it is great advancement along the lines of what to do or could be done with DNA. This is awesome for criminal forensics as it relates to human DNA. Anything that can more simply remove extended lab work fraught with human error in handling is a good thing when it comes to processing human DNA samples for criminal investigations.

    Semiconductors…..not so much,

    Dan Deisz

    Rochester Electronics

  12. dalexander
    April 10, 2013

    @ddeisz…I strongly agree. In terms of authentication, there are many twists and turns yet to come, but this can be one of the foundation technologies that add the next, nearest twist.

  13. owen
    April 15, 2013

    Just when you think you've developed the best thing since sliced bread along comes another development. This was published yesterday, 4/14/13 by Japan Today… “DNA testing chip delivers results in one hour…,  TOKYO –  Panasonic, together with the Belgium-based research institution IMEC, has developed a DNA testing chip that automates all stages of obtaining genetic information, including pre-processing.”

    http://www.japantoday.com/category/technology/view/dna-testing-chip-delivers-results-in-one-hour-paves-way-for-personalized-drug-treatments

    With regard to Mr. Deisz's comments, given that Congess, in Sec 818 of the NDAA2012, specifically requires the DoD to develop means to ensure traceability of parts and that he has acknowledged the benefit of DNA for such purposes, it seems his hostility toward that solution is somewhat misplaced. Indeed, he has called for that solution to be addressed first!

  14. ddeisz
    April 15, 2013

    Owen,

    DNA marking of semiconductor products makes no sense how it has been mandated by DLA. The semiconductor supply chain for DLA has clearly articulated the reasons why and you can find this on the SIA web page. If you are a proponent for DNA marking of semiconductor products, you must not be an employee of a semiconductor company because they have all rejected it. DNA as a technology has some fantastic opportunities. DNA marking of semiconductor products by the original component manufacturers isn't going to happen. I have not heard of a single SIA member who cares if DLA wanted to mark parts with DNA THEMSELVES after procurement to solve their internal supply chain issues. Unfortunately, this proposal by the SIA was rejected by DLA.

    I mostly applaud the NDAA and Section 818 (aside from vague terms like “trusted” or “trustworthy” in the language). However, until legislation reflects exactly how the semiconductor supply chain can ensure fully authorized product, we have a disconnect. Those vague terms allow wiggle room to avoid fixing a purchasing priority to favor fully authorized FIRST before going independent.

    The number one issue causing counterfeit continues to be a procurement issue. Buying from fully Authorized first when available solves this. DLA has chosen another path and a much riskier path for procurement of 5962 product. All this, because they issued a mandate they can't seem to back away from. They would rather buy from brokers, refund brokers most of the DNA cost, and pay more per part, than buy fully authroized product with no DNA tagging and guaranteed no counterfeit. None of DLA's 5962 purchases in Q1 2013 have come with any OCM warranty. Zero. But the parts all had broker DNA marking on them.

    Douglas has pointed out how quickly human forensic DNA analysis has become more affordable and he is psyched about the technology advancement. I agree.That's what the article was originally about.

    Dan Deisz

    Rochester Electronics

  15. dalexander
    April 15, 2013

    @All, Authentication has been and always will be the key to widespread deployment. As long as the integrity of the authentication can be questioned, the marking worthiness is in question. What can be made, can be stolen. What can be stolen can be resold. If one of the sources for counterfeit is used parts being recycled back into the supply chain, then part of the authentication has to include a time/date stamp with RFID rules type management. Where the parts were in transit after leaving the OCM. Clearly, the authorized distributor channel with front and back end anti-counterfeit detection measures, is the first line of defense. But, if counterfeit parts can slip by these safeguards, then only DNA marking that is covertly marked and protected, will absolutely guarantee authenticity to the end user. So, I think that a combination of anti-counterfeiting technologies may be called for until statistically proven that DNA can stand on its own. That is a challenge that any DNA marking company should be willing to accept with open arms. Staging that challenge and gathering the statistical proof, is a necessary process that would be part of the market worthiness evaluation. I believe the DLA did that before issuing the current DNA marking mandate. I suggest we wait and see if the DLA publishes any data that a counterfeit part slipped by them because it seemed to have authorized DNA marking. That will be the final argument giving evidence to the fallibility of the DNA marking solution.

  16. ddeisz
    April 15, 2013

    Douglas,

    Counterfeits through fully Authorized supply don't happen. Every supposed documented case where this happened has turned into a red herring. Independents have tried to say this happens but specific cases have not come forward and held up when thoroughly investigated.

    Prior to the mandate, DLA did not do anything but try to crack the DNA code itself and see if an ink-based product could be marked in an ink-based flow. Unfortunately, the mandate came as a surprise to all of their tier 1 suppliers (Arrow, Avnet, Rochester, Landsdale) and did not involve any of their suppliers before the mandate. DLA does not buy from OCM's directly for a vast majority of their 5962 purchases.

    The truly tragic part of this story is that nobody will know until counterfeit product is well-within the chain at DLA. Their usage is so low that it may take years for this to happen. When it does happen, I really hope it's not in a bad way.

    Here is what we do know. DLA is mainly buying from 5 brokers for Q1 2013. One of those brokers just entered a GIDEP report where they passed on a part they didn't realize was counterfeit because they didn't have enough expertise in-house to catch the issue. They bought the part from another broker who bought the part from somewhere in China and they are surprised! What? The part wasn't to DLA, but it tells an interesting story about who is supplying to DLA today when DLA could be buying from fully Authorized sources.

    DLA didn't do their homework before the mandate.

    Dan Deisz

    Rochester Electronics

  17. dalexander
    April 15, 2013

    @ddeisz…Counterfeits through fully Authorized supply don't happen. That's a huge statement Dan. If that is the case, then we do not need any anti-counterfeiting tech at all if people only buy through ADs. I think the red herrings argument is convincing. Can you cite a couple of articles that uncovered the AD's innocence after being accused of passing along counterfeits. It seems you are well-connected to SIA and can resource some key rebuttals. Please forward the links. Thanks.

  18. ddeisz
    April 15, 2013

    Douglas,

    I would rather put it out there this way as a challenge. Let the IDEA members come forward with a documented case of where they think a fully Authorized supplier (for the product in question of course) has supplied counterfeit product. If they can produce a GIDEP report where this happened, I would be glad to investigate and report back. The same goes for you too. Bring a case where a fully Authorized source for a product has supplied a counterfeit of that product. There was one GIDEP report I know from several years ago which turned out to be a customer pushing the Authorized source to buy from the open market to fully source an order rather than have two seperate orders. Then the end customer wrote them up in a GIDEP report conveniently leaving out how the order went down to begin with. Let's see if this old favorite comes back. I would love to hear specific OCM and specific product instances rather than hearsay. 

    Authorized sources are found here:

    //www.authorizeddirectory.com

    Your statement about not needing anitcounterfeit is inaccurate only because the Fully Authorized channel cannot supply all products. There are products no longer available where even the Authorized channel has no ability to supply the product. That being said, once you are buying from this type of source, all kinds of other mechanisms should kick in. Of course, if all product was available through fully Authorized sources then no anticounterfeit would be needed.

    It should be as simple as:

    1. Buy Authorized First if available = no counterfeit

    2. When buying from Independents, do way more than just visual detection methods which should include full dynamic testing across temp/voltage ranges. Visual-only methods (including SAM) which avoid full dynamic testing are inadequate. I don't care what standard they are part of.

    Dan Deisz

    Rochester Electronics

  19. dalexander
    April 16, 2013

    Dan….I agree. Not all goods go through ADs. We will.need anti counterfeiting strategies to cover all the bases. I hope someone can take you up on that challenge. It would be good to have concrete proof once and for all.

  20. dalexander
    April 16, 2013

    @Dan….Did you see this? http://science.dodlive.mil/2013/04/10/sneaky-discovery-can-identify-counterfeits-track-materiel/?goback=%2Egde_157971_member_231182789. Nobody is sitting on their hands. That is for sure. I think this must use an optical method that detects distance like refractometers and colorizes the surface anomalies. They can do this in free 3D space where you can look down a hallway and know the distance from an object by its color. If you throw the object the entire distance, it changed colors in flight in real time. It seems like an optimum surveying tool…at the very least.

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