Monday, February 20, 2012

AGBT: digesting diposable MinIONs in diaspora

Despite my current ranking of 15th in Biostar, myriad page views of my BAS™ post (albeit mostly misdirected perverts), and positive response for my celebrated campaign against more microarray papers, for some reason I was not "comped" an all-expenses paid trip as honorary blog journalist to this year's Advances in Biology and Genome Technology, which is kind of like CES for sequencing people, except AGBT is still worth attending. Normally the oversight would not bother me, as bioinformatics itself is not the focus of this meeting, but the flood of #AGBT tweets would not let me forget this fact and I was forced to stew and blog in envy.

The first game changing disruptive revolutionary thing from England since 1964

Even from my distant perch it was obvious all the scientific presentations at AGBT were overshadowed by a 17-minute showstopping demo from Clive Brown of Oxford Nanopore, a company that by all appearances would either die, focus on some minor stuff, or bring it. They chose the third option, and in so doing boosted the "Clive index" to unprecedented levels. OxN's recent decision to enlist famed geneticist and serial startup advisor George Church struck me as a huge gamble, as the string of Route 128 flameouts touting his name lead me to assume long ago that Church had stowed away some cursed Tiki idol in his luggage like Bobby in that episode of the Brady Bunch. However, after reading up on OxN, I had to admit I was just bitter about Dr. Church's refusal to invest in my chain of Polonator-based paternity testing clinics, Yo Po'lonatizz!™

Two new sequencer platforms were announced:
A MinION. Forget to hit eject before removing this
and you will instantly lose $900.
  • The MinION, a $900 "disposable" USB drive which detects minute changes in voltage incurred by the passage of DNA through a robust and delicious lipid bilayer. Finally a device capable of sequencing filthy rabbit blood right on the spot!
  • The GridION system, a scalable rackmounted sequencer, which despite some lack of pricing clarity, should produce an actual $1000 15-minute human genome by 2013.
These exotic machines must be truly game-changing because they made properly expanding Albert Vilella's NGS sequencer spreadsheet quite difficult. The MinION, in particular, could be viewed as a free device with $900 of consumables. This effectively lowers the bar to getting high-throughput sequence in the doctor's office to a 100% unamortized billable transaction. These things also claim fucking unlimited read lengths.

Expression microarrays, SAGE, 454, ABI SOLiD, and now Pacific Biosciences have all left bad tastes of uncertainty and dissatisfaction in the mouths of scientists. It is easy to disappoint people on a grand scale with a $700,000 machine, but $900 worth of chemicals in a USB drive is a different animal, and it seems likely this invention will find a following if it even delivers on a fraction of what it promises.

The GridION - put it in a rack or right on the floor.
Good information on this sequencer-on-a-stick is to be found at Nick Loman's blogGenomes Unzipped, and official press releases. An excellent discussion of the nanopores themselves can be found at Omically Speaking.

More cringeworthy marketing from the West coast

The Oxford Nanopore machines are so jaw-dropping, in fact, that Jonathan Rothberg is already crying vaporware. His complaints do seem warranted, given disappointments from past year's announcements and the lack of publicly available sequence from these devices.

Unfortunately Ion Torrent has spent all of its goodwill on an inane and hamfisted advertising war against Illumina's MiSeq, an intentionally crippled opponent. Seemingly orchestrated by castoffs from the Celebrity Apprentice, this assault began with cringe-inducing derivations of Apple commercials, and has expanded to include a sort of "feature combover." Through some convoluted logic involving consensus, a professional whiteboard artist attempts to convince the public how the homopolymer error rate is actually lower using Ion Torrent PGM than MiSeq. This is the sequencing equivalent of having your mom try to convince you two apples is better than one devil dog, or some such utter nonsense.

My response was predictably measured and cerebral:
This is not the first time I have tweet-confronted Ion Torrent over its odious approach. All this is rather unnecessary because overall, and despite the homopolymer issues, the utility of the PGM has been more or less within expectations. The MiSeq is also exactly within expectations, since it is basically a transparent, measly 1/50th slice of a HiSeq. The same cannot really be said for the RS, whose error rate is clearly far above what was expected at the outset. So if anyone requires an aggressive smokescreen-type marketing campaign (or a new machine) it is Pacific Biosciences.


  1. Lol!! So the trick is to use big-ass or penis in your blog posts to draw a bit of extra attention?

  2. pretty much. you wouldn't believe the kind of sick stuff people search for.

  3. My 2013 AGBT coverage is at