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Breakthrough In Detecting DNA Mutations Could Help Treat Cancer, TB

samzenpus posted 1 year,1 day | from the narrowing-it-down dept.

Medicine 42

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."

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42 comments

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Detecting Mutation (4, Funny)

i kan reed (749298) | 1 year,1 day | (#44412709)

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

Re:Detecting Mutation (1)

aled (228417) | about a year ago | (#44438779)

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

Help help I've got rabies! (0, Offtopic)

Anonymous Coward | 1 year,1 day | (#44412739)

Yaargh help I've got foaming at the mouth rabies!

Patent (0)

EvilSS (557649) | 1 year,1 day | (#44412951)

So how long will this be under the patent lock and key before anyone can benefit from it?

Also, is the University of Washington the only university doing any research anymore? Or do they just have really good PR? Every time I see one of these stories lately, the University of Washington is involved

Re:Patent (2, Informative)

Antipater (2053064) | 1 year,1 day | (#44413035)

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 [wikipedia.org] .

Re:Patent (3, Informative)

Anonymous Coward | 1 year,1 day | (#44413275)

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.

Patents? (3, Informative)

delt0r (999393) | 1 year,1 day | (#44412965)

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

Re:Patents? (1)

Beardo the Bearded (321478) | 1 year,1 day | (#44413733)

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

Re:Patents? (1)

delt0r (999393) | 1 year,11 hours | (#44421519)

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.

Great news... (1)

Steve_Ussler (2941703) | 1 year,1 day | (#44413029)

But I certainly need help for athletes foot.

Re:Great news... (0)

Anonymous Coward | 1 year,1 day | (#44413137)

Amputation, works every time.

Just be wary of doctors charging an arm...

Re:Great news... (1)

Anonymous Coward | 1 year,1 day | (#44413225)

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

It's a press release (2, Insightful)

Anonymous Coward | 1 year,1 day | (#44413043)

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!

Re:It's a press release (0)

Anonymous Coward | 1 year,1 day | (#44413081)

the subject matter looses credibility.

Look out, it's loose! Get the tranquilizer gun, quick!

Re:It's a press release (0)

Anonymous Coward | 1 year,1 day | (#44414349)

Oops!

Sounds like BRCA1 and BRCA2 case... (1)

parkinglot777 (2563877) | 1 year,1 day | (#44413063)

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.

Re:Sounds like BRCA1 and BRCA2 case... (2)

Qzukk (229616) | 1 year,1 day | (#44413267)

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).

Re:Sounds like BRCA1 and BRCA2 case... (0)

Anonymous Coward | 1 year,1 day | (#44413357)

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.

Re:Sounds like BRCA1 and BRCA2 case... (4, Informative)

pepty (1976012) | 1 year,1 day | (#44415647)

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.

Re:Sounds like BRCA1 and BRCA2 case... (1)

TCQuad (537187) | 1 year,1 day | (#44416113)

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 [idtdna.com] . 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.

Re:Sounds like BRCA1 and BRCA2 case... (1)

pepty (1976012) | about a year ago | (#44438103)

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 ;)

Re:Sounds like BRCA1 and BRCA2 case... (0)

Anonymous Coward | 1 year,1 day | (#44413441)

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.

If they are patenting genes you are completely correct; however, if they are patenting the technique for finding these mutations then that is a completely different story. To really find out I'd have to read the TFA and pull out the context of your quote.

But Still (-1)

Anonymous Coward | 1 year,1 day | (#44413233)

isn't it easier to throw seeds on the soil, grow cannabis, harvest, grind it down to black oil and use that instead...

In any event with the TIME left on EARTH, It's much more productive for the HUMAN..

PLUS DNA requires obamacare, and IRS, and DHS, ELECTRONIC DATABASES, LOSS OF SECOND AMENDMENT, AND FOURTH, AND FIRST, AND TENTH, AND FIFTH and all that shit.. The only transparancy is your life under the Government's mother fucking microscope.

Re:But Still (-1)

Anonymous Coward | 1 year,1 day | (#44413731)

I forgot about, the Afgan heroin the troops protect. the mixing of it with crap that destroys your GUT if it's ever used as pharmaceutical, not to mention it's
a temp bandaid not even looking for a heal. Might as well be doing cocaine.
On the other hand cannabis, you can grow, grind it down to suitable substances which work for each person. Don't smoke??, then you'll be eating it somehow.

The only, and I do mean ONLY good news is that food packaging people have somehow transferred their technology to the people, and now each format can be safely handled with out spreading germs and spoiled food crap or INSECTS everywhere. The only question is what stick is stuck up USG's ass now besides a police state and stealing our money, resources, property, creativity, rights and instead putting us all on their kill lists?

535 people vs 3.2 million
Where did DHS come from?
Who did 911 really? (not that 49 dollar blue and white costco book of lies!)
Who did all of these monetary changes and financial transactions without our consent?

The thing is, is while you email them via popvox or HOW ever, even directly and they reply back with their electronic warfare template psyop talking points in reply back in your email box, you know the feedback loop is broken.

You can't protest in the streets.
You can't email them without a bunch of bull crap.
You can't have them arrested.

Now what?
They broke their oath, and DOJ don't do jack. (Eric Holder + Obama + Alexander + Clapper!?)
Martha Stewart paid for lying, why ain't Clapper (an official), in Ft Leavenworth?

And just what's up with POTUS natural born status?
I'm sorry, I DO have a problem with this!

And then there's the Zionists. Dual Citizens of Israel holding OFFICE!!!!! And TOP AGENCIES!!!!
Mossad running the show!!!!!

The US is broke and somehow Feinstein, Pelosi, Boxer, Lieberman, and on and friggin on can find money to donate to ISRAEL? Why to KILL PEOPLE?!
I was with them for YEARS, and I know better now. I never saw how insolent and insidious they have become, they swear an oath to protect the constitution, but BREAK IT WITH THEIR RELIGION! AND THEN ATTACK THE US CONSTITUTION

drain the swamp MONSTERS!

Re:But Still (0)

Anonymous Coward | 1 year,1 day | (#44413997)

Thank you for moving from your street corner to this online presence. When passing by your usual spot, I only get to hear a tiny amount of incoherent rambling, unless I miss the walk signal. As such, it takes me many trips to hear every one of your crazy, unfounded conspiracy theories. I also appreciate that online I am not at risk of getting hit by excess froth or spittle as I pass you, even though your keyboard must be much at risk. With you now having online access, you will also be able to add multiple new conspiracy theories to your repertoire- I look forward to your upcoming improved incoherent rants.

Re:But Still (0)

Anonymous Coward | 1 year,1 day | (#44414099)

oh hell that wasn't clear at all. SORRY.

I mean, they they "those people" can virus up your box with their unlimited resources, and that you should make a hard backup, or clone (if you will) of your drives as soon as possible before they get into them. ;o)

If your wondering about passwords, I would be getting them onto an encrypted container. Preferably mobile, say like keepass laying inside a puddle of mud of your choosing. that's just for the hackers. The NSA I don't have advice for. I see how over time they can make it REALLY HARD for me to change something they can't get right back into quickly. And I got to be honest, I trusted them for years and years, I always thought they would be on the up and up and trying to make things better...I still have hope that there are enough left who obey the oath they SWORE to the US CONSTITUTION and sadly the POTUS (who needs a security guard to check his credentials), to see through what's happening now. It's pretty thick, and I was snowed cause I VOTED for obama because the corporate media destroyed Ron Paul.

That's the way I see it. There's a lot more with the DSM-5 (false science) and Obamacare, the NCiS db, the Fact that the SKY isn't BLUE it's WHITE (SAG/SRM wx op's) , and the crap in our food (radiation, oil) , oceans (radiation, Oil) , the WAFFLE BOARDING of ENTIRE CITIES via weather modification ground based steering.

Banksters vs DOJ = EH, POTUS, GAX JC, fuk nevermind..

Where do you want to start that yeah, we have a problem? Executive orders, UN Treaties. Oh give me your firearms too. And Passwords.

I tell ya what, you show me where the threat is mr obama, and I'll tell you if it's okay or not, to use whatever insidious friggin secret crap (which you will either explain, or find someone FAST to explain.. " tech on them. "

I am getting old. I sure hope there are others out there like me. Otherwise I think this country and PLANET may be toast.

Re:But Still (0)

Anonymous Coward | 1 year,1 day | (#44414219)

All that spittle coming from your frosty mouth is because you are a retard. lol

Treat TB? (1)

ArcadeMan (2766669) | 1 year,1 day | (#44413351)

How do you treat a terabyte?

Re:Treat TB? (0)

Anonymous Coward | 1 year,1 day | (#44413821)

Feinstein, Pelosi, Boxer, Lieberman, and on and friggin on can find money to donate to ISRAEL? Why to KILL PEOPLE?!

VIRUS YOUR TERABYTE FOOL, MAKE IT READ ONLY QUICK

WTF? (1)

Cyberax (705495) | 1 year,1 day | (#44413533)

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.

Re:WTF? (2)

Hatta (162192) | 1 year,1 day | (#44413977)

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.

Re:WTF? (5, Informative)

Cyberax (705495) | 1 year,1 day | (#44414109)

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.

Re:WTF? (1)

Ubi_NL (313657) | 1 year,1 day | (#44415551)

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

Solution vs. Substrate-bound Hybridization (1)

Guppy (12314) | 1 year,1 day | (#44416725)

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.

Analogy: Differential Signaling (2)

Guppy (12314) | 1 year,1 day | (#44416545)

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 [wikipedia.org] -- 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.

Molecular Beacons (1)

Anonymous Coward | 1 year,1 day | (#44414271)

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

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

yous FAIL i7!! (-1)

Anonymous Coward | 1 year,1 day | (#44414403)

havei the energy and exciting;

Re:yous FAIL i7!! (0)

Anonymous Coward | 1 year,1 day | (#44414443)

BUy a lot of SILVER and SHINE it like a MIRROR and shine it back in their faces. STRAIGHT UP.

GOAT REPTILIAN ALIEN SPACE FARTS (GRASF) (-1)

Anonymous Coward | 1 year,1 day | (#44414407)

GOAT REPTILIAN ALIEN SPACE FARTS (GRASF)
DEPLOY teh 80' *120' MIRROR back in their faces

that's witchcraft bay bee

yay (1)

qwerty_forever (1612789) | 1 year,1 day | (#44414641)

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

Prevention (0)

Anonymous Coward | 1 year,1 day | (#44417351)

Try preventing cancer in the first place. Eat a little chocolate daily. Be sure it is not a 10% cocoa Hershey bar. It needs to be at least 86%. I use 100% in my sugared coffee every morning.

What about the fishes? (1)

gringer (252588) | 1 year,1 day | (#44417413)

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 [wikipedia.org] ? Or maybe something similar to SOLiD's NGS sequencing process?

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