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Breakthrough In Detecting DNA Mutations Could Help Treat Cancer, TB

Posted by samzenpus on from the narrowing-it-down dept.

vinces99 writes "Researchers have developed a new method that can look at a specific segment of DNA and pinpoint a single mutation, which could help diagnose and treat diseases such as cancer and tuberculosis. These small changes can be the root of a disease or the reason some infectious diseases resist certain antibiotics. The findings were published online July 28 in the journal Nature Chemistry. 'We've really improved on previous approaches because our solution doesn't require any complicated reactions or added enzymes, it just uses DNA,' said lead author Georg Seelig, a University of Washington assistant professor of electrical engineering and of computer science and engineering. 'This means that the method is robust to changes in temperature and other environmental variables, making it well-suited for diagnostic applications in low-resource settings.' The researchers designed probes that can pick out mutations in a single base pair in a target stretch of DNA. The probes allow researchers to look in much more detail for variations in long sequences up to 200 base pairs while current methods can detect mutations in stretches of up to only 20."

25 of 42 comments (clear)

  1. Detecting Mutation by i+kan+reed · · Score: 4, Funny

    When reached for comment, Magneto promised that this would spell inevitable war between mutants and humans.

    1. Re:Detecting Mutation by aled · · Score: 1

      People with no mutation to hide have nothing to fear. What could go wrong?

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  2. Patents? by delt0r · · Score: 3, Informative

    Is it patented? And as someone who is working in the field. Most diseases, even inherited ones, are not due to single mutations...

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    1. Re:Patents? by Beardo+the+Bearded · · Score: 1

      My takeaway from this means that they can isolate each of the responsible mutations. This is a tenfold increase in precision, is it not?

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    2. Re:Patents? by delt0r · · Score: 1

      In precision no. We can do that right now. But its not that cheap yet. Perhaps this is cheaper. However for most inherited disease there is no identifiable mutations. So this is still only a niche detection tool for typically quite rare diseases.

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  3. Great news... by Steve_Ussler · · Score: 1

    But I certainly need help for athletes foot.

    1. Re:Great news... by Anonymous Coward · · Score: 1

      I think I'll just keep my jock itch suffering to myself...

  4. Re:Patent by Antipater · · Score: 2, Informative

    Given that "...our solution doesn't require any complicated reactions or added enzymes, it just uses DNA," it should be unpatentable thanks to the recent Supreme Court decision.

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  5. It's a press release by Anonymous Coward · · Score: 2, Insightful

    The link points to a university press release, I would therefore not put too much on the claim. The text in the press release is so inflated with flowery prose the subject matter looses credibility. Since the original paper is behind a pay wall most of us will never know if it was a 'breakthrough' or not. Plus I see it will be patented but the research was paid for by public funds!

  6. Sounds like BRCA1 and BRCA2 case... by parkinglot777 · · Score: 1

    This may becomes BRCA1 & BRCA2 case in the future if they can "patent" these genes... I hope they fail miserably on getting a patent if what they called "technology" is actually "genes"! Below is from TFA...

    The researchers have filed a patent on the technology and are working with the UW Center for Commercialization. They hope to integrate it into a paper-based diagnostic test for diseases that could be used in parts of the world with few medical resources.

    1. Re:Sounds like BRCA1 and BRCA2 case... by Qzukk · · Score: 2

      Really, it comes down to what they do with the patent once they have it. They could charge a penny for it as a token licensing fee. Or they could demand 50% of all the revenue of anyone using it which would make sure it never sees use in the "parts of the world with few medical resources" (except for those nations that routinely ignore patents).

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    2. Re:Sounds like BRCA1 and BRCA2 case... by pepty · · Score: 4, Informative

      There's no genes to patent here, only a technique for identifying differences between strands of DNA and an artificially-created reference strand that's engineered to glow fluorescently.

      Think of it as an efficient diff method for DNA that doesn't involve computationally-complex gene sequencing.

      FTA:

      The probe is engineered to emit a fluorescent glow if there’s a perfect match between it and the target. If it doesn’t illuminate, that means the strands didn’t match and there was in fact a mutation in the target strand of DNA..

      So the technique will be limited to a single probe in each reaction. This could be great when all you want to check for is the presence of one or two specific mutations, but in most situations there are many different mutations that could be causing the same effect. You would have to run dozens of tests using this method to get that information. I don't see this as displacing methods that use arrays of DNA probes attached to chips: those let you check for hundreds of mutations or hundreds of species of pathogens all at the same time, but it might improve array techniques if these probes still work well when placed on arrays.

    3. Re:Sounds like BRCA1 and BRCA2 case... by TCQuad · · Score: 1

      I don't have access (I miss being able to read every paper I wanted when I was in college...), but that's not necessarily true. Multiplex qPCR (TaqMan, not SYBR) can use a number of different probes with a number of different, uniquely fluorescing fluorophores. Depending on how their method works, you may be able to adapt the protocol to accommodate these additional options. You're still looking at a small number of probes (probably ~5 before the peak overlap becomes too significant), but it's not necessarily "1".

      Honestly, though, I'd flip the protocol from how it's laid out in the press release since false negatives could be deadly if you're looking at resistance mutations. Put in three non-WT versions, assay lights up if it's mutant. If you don't care about which mutation, they can share the same fluorophore. Or three non-WT and one WT with a different fluorophore so you always get a positive if the assay went correctly and a negative if there's an unexpected mutation in a different region of the sequence.

    4. Re:Sounds like BRCA1 and BRCA2 case... by pepty · · Score: 1

      Actually I was thinking about having probes at several different wavelengths in the same sample - I was just to dense to realize that multiplexing would still work with the signal = no mutation, no signal = mutation format. Maybe that will be another paper/press release, one where they aren't focusing on low implementation costs (fixed wavelength fluorometer = $$, scanning fluorometer = $$$$)

      I'm guessing their assay depends on quenching; if they had a choice they probably would have preferred a signal = positive, no signal = negative format in part for the reason you just gave. But FRET is tetchy and expensive. That will be the third paper ;)

  7. Re:Patent by Anonymous Coward · · Score: 3, Informative

    That decision prevented naturally-occurring gene sequences from being patented. The "just uses DNA" solution from TFA uses DNA that has been engineered to "emit a fluorescent glow."

    Being entirely non-natural, it would be eligible for patent protection.

  8. Treat TB? by ArcadeMan · · Score: 1

    How do you treat a terabyte?

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  9. WTF? by Cyberax · · Score: 1

    The article blurb is a total POS. We can detect single nucleotide polymorphisms easily, using any sequencing technology or genotyping systems. I don't even see anything novel in the article, because scientists used similar technologies for AGES.

    1. Re:WTF? by Hatta · · Score: 2

      Sequencing involves in vitro DNA synthesis. It sounds to me like they are doing nothing more than solution hybridization. e.g. denature your sample, apply it to membrane with a probe on it, and let the strands anneal to the probe. Then they get a fluorescent signal if the strands anneal properly.

      My question is how they get the hybridization so specific that a single base pair difference will cause a measurable difference in hybridization. If it's as easy as they make it sound, they do this without highly controlled temperatures and buffers.

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    2. Re:WTF? by Cyberax · · Score: 5, Informative

      I'm reading the paper - they found a clever way to make sure that DNA doesn't hybridize across the SNP. That ensures that in an equilibrium solution it'll be present at much smaller concentration than a fully-hybridized DNA. That is really a neat trick, but hardly a groundbreaking achievement that will revolutionize everything.

    3. Re:WTF? by Ubi_NL · · Score: 1

      Indeed. Affymetrix used this 20 years go and pretty much stopped using it because it was unreliable...

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  10. Molecular Beacons by Anonymous Coward · · Score: 1

    Sounds like they have reinvented "Molecular Beacons" ....

    I somehow knew this before reading the article. Yay PhD!

  11. yay by qwerty_forever · · Score: 1

    breakthrough # 2,343,345,448. take that, cancer!

  12. Analogy: Differential Signaling by Guppy · · Score: 2

    Typically, hybridization probes rely on match/mismatch similarities between one target strand, and the probe strand; when the difference is a single base pair, your signal/noise ratio can be pretty poor. But while performance is typically poorer than PCR-based assays, they can be faster and easier to run, requiring less sophisticated equipment.

    This new technique uses a mechanism that simultaneously evaluates both strands of the target at once (by passing through a cross-shaped intermediate complex). Basically, it's like differential signaling -- a single-point mutation on a dsDNA segment actually produces two detectable and complementary changes, one on each strand.

    This is simplifying a bit (leaving out parts like the intermediate step used to generate toe-holds for the multi-way interaction) but that's the best computer analogy I can think of for a Slashdot explanation. It's nothing world-breaking, but it looks something with practical impact, giving a nice boost to a very widely deployed molecular diagnostic technique.

  13. Solution vs. Substrate-bound Hybridization by Guppy · · Score: 1

    That ensures that in an equilibrium solution it'll be present at much smaller concentration than a fully-hybridized DNA

    That's actually one part of the new technique that is a problem -- it's a solution-based reaction. They may or may not be able to tether it to a solid substrate and still have it work (which would be a requirement for implementation in a practical DNA micro-array). I don't have access to the full paper at this moment, so I don't know if the issue was addressed or not.

  14. What about the fishes? by gringer · · Score: 1

    The testing probes are designed to bind with a sequence of DNA that is suspected of having a mutation.... The probe is engineered to emit a fluorescent glow if there’s a perfect match between it and the target.

    So it's a highly specific FISH? Or maybe something similar to SOLiD's NGS sequencing process?

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