Saturday, 18 February 2012

Oxford Nanopore megaton announcement: “Why do you need a machine?” – exclusive interview for this blog!

woke up this morning to see a whole bunch of excited tweets on Oxford Nanopore and I can totally understand why. This is the real democratization of DNA sequencing. Move over benchtop / desktop sequencers for 'laptop sequencers'!

Hmmm or a cluster of sequencers, on your compute cluster ... !

Using USB powered sequencers, and a pipette to put in the dsDNA and you might have your sequence read to FASTQ directly to your laptop. 
No known limit to read length. 
4% seq error (the good thing is that the form of error is known and therefore correctable)

Do read the url above for more info, here's the excerpted executive summary for the impatient

Executive Summary
  • Nanopore have announced a strand sequencing method, made possible by a heavily modified biological nanopore and an industrially-fabricated polymer
  • DNA passes through the nanopore and tri-nucleotides in contact with the pore are detected through electrochemistry
  • Demonstrated 2x50kb sense & anti-sense of same molecules (lambda phage) – no theoretical read length limit
  • Can sequence direct from blood without need for sample preparation
  • Two products announced:
    • MinIon – USB disposable sequencer for ~ $900 has 512 nanopores – target 150mb/hour
    • MinIon can run at 120-1000 bases/minute per pore for up to 6 hours
    • GridIon – two versions of rack-mountable sequencer with 2000 nanopores (2nd half 2012), 8000 nanopores (2013)
    • GridIons can be racked in parallel, 20 could do a whole human genome in 15 minutes
    • Each GridIon can do "tens of gigabases" over 24 hours
  • Both machines commercially available 2nd half 2012
  • Sequencing can be paused, sample recovered, replaced, started again
  • Accuracy is 96%, errors are deletions, error profile will improve through software

Check out Forbes interview with 454 / PGM inventor Jon Rothberg

"Rothberg noted that Ion Torrent’s new machine, the Proton, the company showed three completed human genomes yesterday at AGBT. More importantly, he had the machine – not a mock-up or a design – on the stage. “That’s where you need to be to ship mid-year,” he writes."

Over at Genomes Unzipped 
Oxford Nanopore CTO Clive Brown related how sequencing library prep is as simple as diluting rabbit's blood with water. Now that is impressive!

This post is getting too long because I keep updating it. 
Over at the BioITWorld, there's an interview with Clive Brown which cites other interesting info. 
First of which is the opening paragraph which is amusing in the light of ONT's rivals comments
"Clive Brown, vice president of development and informatics for Oxford Nanopore Technologies (ONT), a.k.a “the most honest guy in all of next-gen sequencing,” as dubbed by The Genome Center's David Dooling, is hoping to catch lightning in a bottle again. "

Oxford Nanopore has not yet revealed details of its future platform, but in early 2009, published a lovely paper in Nature Nanotechnology showing that its alpha-hemolysin nanopores can discriminate between the four bases of DNA (not to mention a fifth, methyl C)

Directly get methylation information from your sequencing sans complicated sample prep? That has to be another selling point. 

Not sure whether Nanopore is truly vaporware. However, gauging by the excitement over the blogosphere and the hit rates for the first to blog about it. I think Nanopore is upping the ante for the next IT sequencer. 
maybe we can only survive 2 more AGBT like this and AGBT might fizzle out as new sequencing technologies fade as our computation advances trails behind the ability to generate more data. 
Maybe you will see scientists start attending Big Data tech conferences or AGBT's  main draw will  fancy new software to assemble, align and make sense out of all the data being generated ... 

This picture tells quite a story (Wordle constructed from 3,386 tweets and retweets tagged #AGBT with @s removed).
No prizes for guessing the winner ... 

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