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

Real-Time DNA Sequencing from Single Polymerase Mo

[mapkinase]

Abstract:

We present single-molecule, real-time sequencing data obtained from a DNA polymerase performing uninterrupted template-directed synthesis using four distinguishable fluorescently labeled deoxyribonucleoside triphosphates (dNTPs). We detected the temporal order of their enzymatic incorporation into a growing DNA strand with zero-mode waveguide nanostructure arrays, which provide optical observation volume confinement and enable parallel, simultaneous detection of thousands of single-molecule sequencing reactions. Conjugation of fluorophores to the terminal phosphate moiety of the dNTPs allows continuous observation of DNA synthesis over thousands of bases without steric hindrance. The data report directly on polymerase dynamics, revealing distinct polymerization states and pause sites corresponding to DNA secondary structure. Sequence data were aligned with the known reference sequence to assay biophysical parameters of polymerization for each template position. Consensus sequences were generated from the single-molecule reads at 15-fold coverage, showing a median accuracy of 99.3%, with no systematic error beyond fluorophore-dependent error rates.

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.

Article in Science

[prograde]

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

I guess I can drop my X prize plans

[damn_registrars]

Since this technique should be a shoe-in for the Archon X Prize.

Re:99.3% accurate?

[prograde]

It's common practice in bioinformatics to measure the same data repetitively in an effort to reduce the error.

It's common practice on Slashdot to read the article before posting. From the abstract of the Science article:

Consensus sequences were generated from the single-molecule reads at 15-fold coverage, showing a median accuracy of 99.3%, with no systematic error beyond fluorophore-dependent error rates.

So that's 99.3% after averaging 15 reads. Not exactly replicating the same read 15 times..more like taking random starting points and aligning the results where they overlap, so that each base is covered in 15 different reads.

Don't get me wrong - this is really cool, and a massive speed-up over current "next-gen" sequencing. And I'm sure that it will get better.

To answer the GP - yes, this is an acceptable error rate, for now.

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.

Slashdotted: Abstract and Fulltext

[chihowa]

It looks to be inaccessible. Here are the abstract and fulltext links.

Re:99.3% accurate?

[Anonymous Coward]

If you RTFP (requires subscription), no systematic errors were detected
http://www.sciencemag.org/cgi/content/full/323/5910/133

nitpick

[Zenaku]

One base-pair does not a gene make.

New Scientist Write Up

[Fnord666]

Here is an article in New Scientist about the new process. It explains it fairly well and even defines what a ZMW is.

Re:Gattica...

[Noddegamra]

Since inosine.