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.'"

Comments

99.3% accurate?

[Valdrax]

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?

Re:99.3% accurate?

[imamac]

I realize that we aren't going to be trying to make a cloned copy from this data...

What makes you so sure? Who knows where this will lead?

Re:99.3% accurate?

[Maximum Prophet]

How many errors are introduced during normal human reproduction? The dogs they've cloned so far are less than 99.999% identical.

Re:99.3% accurate?

[Anonymous Coward]

It's common practice in bioinformatics to measure the same data repetitively in an effort to reduce the error. While 0.993 isn't very good, (0.993)^3 is pretty awsome. In practice, the errors might be correlated (as in a flaw in the measuring system), so the benefit of re-measuring might not be exponential...however it should be darn close.

Re:99.3% accurate?

[ccguy]

Well, depends if those 28/4000 errors are the same in each run or not.

If they can sequence the whole thing in less than 30 minutes one time with a 0.001% "read" error rate, my guess is that they can get it probabilistically near 100% correct in 2 hours or so.

By the way, what's the current error rate? Is it 0? (just asking)

Re:99.3% accurate?

[morgan_greywolf]

1 Hour Genome Sequencing: 30,000 errors or less or YOUR MONEY BACK!

Re:99.3% accurate?

[scorp1us]

There is a saying from the old sailing days. "Never set sail with two compasses". One is ok, three is better. But never two. The paralysis from not knowing which is right is far worse than being wrong and correcting later.

Re:99.3% accurate?

[shaitand]

If you were sequencing DNA and got a B then you'd seriously need to recheck the equipment (or the competence of the operator). Perhaps a T or a G, or even a C but never a B.

Re:99.3% accurate?

[fracai]

Oh well. At least it's not the first time somebody missed a point on /.

Don't you mean "Oh well. At least it's not the first time somebody missed a point on /".

Re:99.3% accurate?

[peter303]

One in 10E8 is the DNA base-pair copy error rate. Even so thats around 60 when a sperm meets egg. Another much more when there a trillion somatic cells dividing on average 50 times each in a human lifetime. The vast majority are errors are neutral, but accumulating ten or so specifically unluckly ones in a cell may be a cancer.

Re:99.3% accurate?

[Adriax]

Or you could run a parallel processing setup, 3-5 sequencing chips all given the same sample at the same time. More expensive, but you'd get that effective 100% rate in the half hour time.

$5k for a genetic sequencer that could give effectively 100% accuracy in half an hour would be pittance for pretty much every hospital in the US.
Hell, the first malpractice lawsuit it prevents (detect a disorder that would make a commonly used treatment crippling or fatal to the patient) would pay for the machine 1000 times over.

Re:99.3% accurate?

[TooMuchToDo]

Unless of course all three of your compasses are giving you different readings. In that case, you simply yell "Where the hell is my sextant."

Sub-$1000 genome sequencing

[morgan_greywolf]

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!

Re:Sub-$1000 genome sequencing

[Ethanol-fueled]

"...my plans for world domination will be comlete!"

Hopefully you'll fix that nasty intercalary deletion bug first!

Kicks ass on Moore's Law...

[djupedal]

> 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' :)

Re:error correction

[Hurricane78]

Yes. It's called "natural selection". :P