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DNA Strangs in Nanopore Sensor  (Source: Nature Nanotechnology )
New method is cheaper, more accurate and needs a much smaller sample.

The study of the human genome is believed to be the key to learning more about the myriad of diseases that plague humans. The genes hold the keys to everything that makes people who they are from eye color to hair color.

DNA also holds the key to genetic diseases, and learning more about the genes that contribute to disease is part of what researchers need to unlock to be able to find cures for disease. DNA sequencing today is a time consuming and expensive process. Much of the time and expense in sequencing DNA comes from the DNA amplification process.

DNA samples have to be amplified, a process that essentially makes a copy of DNA to produce a larger sample that the sequencing methods of today can work with. Researchers at Boston University have discovered a new method that makes DNA sequencing faster and cheaper than methods used today.

The new method eliminates the need to amplify DNA, which cuts much of the cost associated with sequencing of DNA today. The new method developed by the researchers detects DNA molecules as they pass through pores 4nm wide. An electrical current at the opening of the pore is used to detect when the DNA strand is passing though.

Professor Amit Meller said, "The current study shows that we can detect a much smaller amount of DNA sample than previously reported. When people start to implement genome sequencing or genome profiling using nanopores, they could use our nanopore capture approach to greatly reduce the number of copies used in those measurements."

The team found that the longer the string of DNA, the more quickly it was able to fine the pore opening and be read. This is not what the researchers expected; a shorter strand would seemingly be easier to pass though the opening.

Meller said, "That's really surprising. You'd expect that if you have a longer 'spaghetti,' then finding the end would be much harder. At the same time this discovery means that the nanopore system is optimized for the detection of long DNA strands -- tens of thousands basepairs, or even more. This could dramatically speed future genomic sequencing by allowing analysis of a long DNA strand in one swipe, rather than having to assemble results from many short snippets."

The discovery allows researchers to boost the capture rate by orders of magnitude and reduce the size of the sample needed from about 1 billion molecules to only 100,000. A Stanford University professor who mapped his own genome in a week believes that sequencing tests need to get to the $1,500 range per test to be useful in medicine today.



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More Cheaper!!
By davebeneteau on 12/21/2009 11:36:59 AM , Rating: 4
"New method is more cheaper, more accurate and needs much smaller sample."

I love more cheaper! just saying.... lol




RE: More Cheaper!!
By davebeneteau on 12/21/2009 11:40:26 AM , Rating: 2
awwww, he fixed it.


RE: More Cheaper!!
By Smartless on 12/21/2009 1:42:26 PM , Rating: 3
That's okay.
quote:
...more quickly it was able to fine the pore opening...


I thought I was reading an article about the EU again.


RE: More Cheaper!!
By DFranch on 12/21/2009 12:04:50 PM , Rating: 4
I believe proper English is "more cheaperer". :)


RE: More Cheaper!!
By MozeeToby on 12/21/2009 12:43:34 PM , Rating: 2
Most Cheaperest?


RE: More Cheaper!!
By scrapsma54 on 12/21/2009 1:33:39 PM , Rating: 2
how about dem Dna Strangs?


RE: More Cheaper!!
By messyunkempt on 12/21/2009 6:23:31 PM , Rating: 2
It's not his fault he can not speak good not like what we do ;)


Good and Evil.
By Mitch101 on 12/21/09, Rating: 0
RE: Good and Evil.
By kaoken on 12/21/09, Rating: 0
RE: Good and Evil.
By lightfoot on 12/21/2009 6:22:30 PM , Rating: 3
Risk based pricing is still allowed - they won't be able to deny you coverage, but they will be able to charge you more.


RE: Good and Evil.
By geddarkstorm on 12/21/2009 1:50:11 PM , Rating: 3
Fortunately, your DNA sequence itself is only a small part of the picture. You have epigenetics in the form of DNA methylation, histone modifications, RNA modifications and half-lives, small non-coding regulatory RNAs, genetic changes due to damage over time, protein post-transcriptional modifications, and gene promoter regulation by self re-enforcing or environment sensing protein transcription factor pathways (things like the circadian clock, NFkB immune modulator, Myc, Jun/Stat, etc, and whose activity is controlled by your environment). Genes also cross talk to determine the amount and timing of a gene that is produced, which is just as important as what is produced.

None of this information exists within the DNA code by itself what so ever; and some of it, like DNA methylation and heterochromatin, is even random to an extent and placed down during early embryogenesis differently for each emerging tissue.

Heck, we have over 100 well characterized cases of epigenetics changing the phenotype of offspring and being inherited for several generations irregardless of genotype.

So.. just looking at your genes is not enough to know anything about how you work; it can at most give probabilities of what /could/ happen if you are exposed to this or that in specific times/concentrations/ways. Only in extreme cases, such as gene mutations that are dominant like Huntington's disease, will looking at your DNA directly catch anything for sure.


RE: Good and Evil.
By Etsp on 12/21/2009 8:52:18 PM , Rating: 3
You know, that comment was really informative and intelligent. But... irregardless is a double negative, and most linguists agree that it isn't proper English... I believe the term you were looking for is "regardless".

Don't you hate it when there's nothing to attack in your comments so someone has to nitpick about the grammar instead? I apologize, it's just I cringe when I see that word.


RE: Good and Evil.
By Fritzr on 12/22/09, Rating: 0
RE: Good and Evil.
By JonnyDough on 12/22/2009 4:13:23 AM , Rating: 2
I agree with what you said. :)

The OP is right, humans and earthworms share similar DNA. There are many many many other factors, including those that are environmental that put you at risk. Take Alzheimer for example. It seems we are still unsure as to whether it is caused by aluminum salts in our antiperspirants, or by genetics. Parkinson's is another fine example of something we really don't know too much about yet.


RE: Good and Evil.
By daemonios on 12/22/2009 7:09:46 AM , Rating: 3
Sorry to butt in, I think you've got that one wrong. Irregardless is listed as incorrect (check out http://en.wikipedia.org/wiki/Irregardless).

Etymologically, regardless means "without regard", therefore "regardless of genotype" --> without regard to genotype. Irregardless adds a negative prefix (usually im- or in-, as in impossible, invisible). So by saying irregardless you'd be saying *not without regard*, which in context does not make sense.

I think your confussion comes from "irrespective", which means more or less the same thing as "regardless".


RE: Good and Evil.
By Chemical Chris on 12/22/2009 12:19:01 AM , Rating: 3
quote:
until the company that provides it sells our info to the insurance companies who will use it to determine if you get insurance or dropped from coverage

Or you could move to one of the countries that provides universal health care (take a look, its most of them). Without trying to turn this overtly political, I will simply say that it truly saddens me to see such a potentially great country so far behind when it comes to the basic human rights of its citizens (you get sick, you should get help, its a social requirement from a social species, social != evil....its true)

ChemC


Interesting development
By slash196 on 12/21/2009 11:43:31 AM , Rating: 1
It would certainly be a massive relief of posterior pain to eliminate PCR reactions or at least reduce their necessity. Since about 90 percent of genetic research is doing PCRs and running gels, if you can streamline that you've done a lot to streamline the process.

Of course, I'd have to see this in practice to know exactly how effective it is.




RE: Interesting development
By bighairycamel on 12/21/2009 1:43:05 PM , Rating: 2
Amplication won't be going away anytime soon. Even if this method takes off, you still need around 100k+ copies of the target sequence. You can do a quantification analysis, but that still requires PCR. Or you could use the same instrumentation and amplify a million copies instead and gain the peace of mind that you have enough sample to run the sequencing analysis.


RE: Interesting development
By geddarkstorm on 12/21/2009 1:54:16 PM , Rating: 2
There's also signal to noise to worry about, so amplification is rather important. PCR is pretty dang easy though :P. Where this method takes off is that it can read really long strands of DNA fast and accurately, which current sequencing methods cannot do. Generally, one can only sequence up to 1kb of DNA at a time, and one has to do multiple "walks" across a larger piece of DNA via PCR. And /that/ is where the system will be awesomely stream lined - if one can do just a single "full molecule" amplification and be able to read the entire thing accurately in one shot.

That would save on a LOT of money and time.


Silicone
By rlthomas on 12/21/2009 8:13:47 PM , Rating: 2
Breakthrough must be due to nanopore material and "Silicone" chip...




Why so surprised?
By Graviton on 12/21/2009 10:04:30 PM , Rating: 2
In my experience, long ones always find the holes easier.




Fining pores?
By DeepBlue1975 on 12/22/2009 9:20:37 AM , Rating: 2
quote:


The team found that the longer the string of DNA, the more quickly it was able to fine the pore opening and be read.

quote:


So, when you give a fine to a pore, it opens and lets itself be read. Interesting.




Cool article but
By wgbutler on 12/21/09, Rating: -1
RE: Cool article but
By geddarkstorm on 12/21/2009 1:54:50 PM , Rating: 5
Um.. this has nothing to do with ANY of that. So please, stop trolling.


RE: Cool article but
By JonnyDough on 12/22/2009 11:30:18 AM , Rating: 1
Yeah, and the only reason we're angry anyway is because religion is one of the main causes of war. We're about to go to war over it!


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