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New Method To Revolutionize DNA Sequencing
An anonymous reader writes "A new method of DNA sequencing published this week in Science identifies incorporation of single bases by fluorescence. This has been shown to increase read lengths from 20 bases (454 sequencing) to >4000 bases, with a 99.3% accuracy. Single molecule reading can reduce costs and increase the rate at which reads can be performed. 'So far, the team has built a chip housing 3000 ZMWs [waveguides], which the company hopes will hit the market in 2010. By 2013, it aims to squeeze a million ZMWs [waveguides] onto a single chip and observe DNA being assembled in each simultaneously. Company founder Stephen Turner estimates that such a chip would be able to sequence an entire human genome in under half an hour to 99.999 per cent accuracy for under $1000.'"
That's, what, 28 incorrect base pairs out of 4000? I'm not a biologist, but is this considered an acceptable error rate? Even the hopes of 99.999% accuracy seems really awful when there are about 3 billion base pairs in a human genome.
I realize that we aren't going to be trying to make a cloned copy from this data, but what uses is this "good enough" for?
If it's for-profit but free, you're not the customer -- you're the product (e.g., the Slashdot Beta's "audience").
Sub-$1000 genome sequencing will put the creation of 'designer' kids into the realm of the affordable for much of the middle class. Scary stuff. Now we just need to combine that with cheap and reliable cloning techniques and my plans for world domination will be comlete!
My blog
Abstract:
I do not believe in karma. "Funny"=-6. Do good and forbid evil. Yours, Oft-Offtopic Flamebaiting Troll.
> Company founder Stephen Turner estimates that such a chip would be able to sequence an entire human genome in under half an hour to 99.999 per cent accuracy for under $1000.
:)
I think this qualifies as a true 'technological singularity'
Is there not some form of error-correction in the sequence itself that could be exploited ?
Something like the error correction on an audio compact disk ?
Nullius in verba
I assume that the hardware at Science can withstand a slashdotting better than the crappy blog linked in the summary:
http://www.sciencemag.org/cgi/content/abstract/323/5910/133
Since this technique should be a shoe-in for the Archon X Prize.
Damn_registrars has no butt-hole. Damn_registrars has no use for a butt-hole.
Using 454 sequencing you get average read lenghts of ~400-500 bp
I suspect someone had confused 454 with the other popular next-gen sequencing technique from Illumina, which does give very short reads.
Read lenghts around 20 bp would be pretty much useless. At least for de novo sequencing..
Not necessarily. If you can drive the cost/base down far enough, you can make short reads worthwhile if you use a shotgun approach and try for large-scale coverage. Especially if you can produce the short reads at a lower rate of time/base.
Damn_registrars has no butt-hole. Damn_registrars has no use for a butt-hole.
It looks to be inaccessible. Here are the abstract and fulltext links.
If you want a vision of the future, imagine a youtube comments section scrolling - forever.
Gattaca was supposed to show us a dark future. It was supposed to be a cautionary tale. The message was, "if your DNA isn't good enough, you'll have to make do banging Uma Thermon - poor you."
I don't think the producers thought their cunning plan all the way through.
This is entirely reasonable and desirable if you replace "spider-thing" with "cancer" or "aids," or even "common cold." Gene sequencing your disease and taking the right medicine for what you *actually* have - instead of today's educated guesswork - will be a HUGE advance. Thousands die every year because they have to guess a year in advance which flu strains will be prevalent and usually guess wrong.
The use of short reads for de novo assembly only makes sense if you want a rough draft of a genome, not the complete thing. There are way too many transposable elements, repeats, variation, etc. to accurately reconstruct even a bacterial genome with short reads. Nowadays, people don't even bother trying to piece it all together. They get down to a few dozen large fragments and say "good enough". It just costs too much to get the last 1-2% with a random sequencing approach.
One base-pair does not a gene make.
If fate makes you a motorcycle, you become a motorcycle.
Although humans differ from one another in about 0.1% base pairs for a total of 3 million, the number of difference that describe human variability may be vastly smaller than this. First you discard non-coding DNA which gets you done to 30,000.
Except that when our differences are so small, the non-coding regions are even more important. They control what genes are active and to what degree. That's nearly as important as the genes themselves.
Genes are only part of the puzzle. You need to know what to do with them, and non-coding regions provide some of that along with the cellular machinery.
Scientists used to call them "junk" DNA where junk == "I can't figure it out". Why would cells spend all that energy maintaining something useless? Not very likely.
I don't know, but it works for me.
Company founder Stephen Turner estimates that such a chip would be able to sequence an entire human genome in under half an hour to 99.999 per cent accuracy for under $1000
Does that mean that the chip costs $1000 or that each human genome processed costs $1000?
error's
That character you're using... I don't think it means what you think it means...
You must be new here. You see, here on teh interweb, many of us are terribly afraid of word's ending in "s" - Plural's, possessive's, contraction's with the word "is", and occasionally even name's. The apostrophe is a polite way of warning the general reading public that an "s" is approaching so that we can brace ourselve's accordingly.
He's getting rather old, but he's a good mouse.
Here is an article in New Scientist about the new process. It explains it fairly well and even defines what a ZMW is.
'The tyrant will always find pretext for his tyranny.' - Aesop's Fables
Many people seem concerned about the reading error rate. However, as it's been pointed out, it should be easy enough to read a DNA sequence multiple times (or read the whole genome multiple times) to decrease the error rate significantly. If you have one chip that can read the entire human genome in 30 mins, you can have the same chip read it twice in an hour, or four chips reading four copies in 30 mins.
Furthermore, if you're using a technique like this to map a person's genome, you can be clever about it. Base pairs code genes, which is something you can take into account. For example, if you're reading the eye color gene, and your machine somehow consistently makes mistakes in that area, you can compare your reads to the few possible known eye color genes, and pick the most likely based on the genetic sequences of the entire gene.
In medicine, the cost of a study, as well as its reliability, availability, and predictive value, enters into the decisions made in clinical management.
Real applications of this, however, include looking for gene sequences in adults which predispose them to diseases (e.g. breast cancer) and then providing counseling and monitoring commensurate with that risk, a far less expensive effort than monitoring everyone for the same disease, even if they aren't at risk. Also, one could use this on embryonic cells obtained through amniocentesis to screen for hereditary diseases is families where there are risk factors.
Since inosine.
Considering current sequencing technology generates terabytes of data per day (see the Sanger center), then wouldn't it be efficient to maximize the amount of information per pixel (i.e. per byte)? This method is actually is much worse (orders of magnitude) than the current method. There are many other problems with what they do, but hopefully the cash infusion can last them another 2 years until the write a paper like this. BTW, the say that appropriate camera tech. will be available in 2-5 years, but they're ready now! They might be buying time...