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Names: Second, Third, Next Generation or Massively Parallel
Michael Smith
Posted: Wednesday, January 26, 2011 9:06 PM
Joined: 12/2/2010
Posts: 1


Names: Second, Third, Next Generation or Massively Parallel sequencing?

Seems to me the naming convention is getting messy.  I'm not a fan of second and third generation with the newer technologies (i.e., PacBio and Ion Torrent along with nanopore) referred to as third generation.  Massive throughput increases from Illumina and Solid make them a generation increase too. The technology progression is like a cloudburst rather than a progression from one generation to another.  What should we be calling all of these new sequencing technologies?  I like massively parallel, but some are much less massively parallel than others by orders of magnitude...


Kevin Davies
Posted: Monday, January 31, 2011 3:32 PM
Joined: 12/1/2010
Posts: 1


Michael,

 

You raise an interesting question. You're right, it is getting messy, but I'm not sure that it matters. PacBio says it is definitely "3rd-Gen", though when I asked CEO Hugh Martin last year what he defined as 3rd-Gen, he said it was "everything that 2nd gen is—throughput, cost per base, etc.—with the addition of very long read lengths, extremely low reagent or consumable cost and very fast run times.” Nothing terribly conceptual there.

 

Ion Torrent not only shuns the "3rd-Gen" label, they also reject "next-gen sequencing." Last year, founder Jonathan Rothberg said: "In ‘next-gen,’ the box was the machine. But now, the substrate is the machine." If PacBio is 3rd-Gen, one could argue that nanopore sequencing, when it eventually arrives in whatever incarnation, will be "4th-gen" because it doesn't involve lasers or fluorescence. It doesn't matter much what they call it, so long as it works!

 

 


Eric Glazer
Posted: Tuesday, February 1, 2011 8:46 AM

It’s an interesting topic for discussion.  From a marketing perspective, especially marketing content like online communities or conferences, ontology is so important.   We have begun talking to folks about this exact nomenclature conundrum (2nd gen vs. 3rd gen, etc).  In general, as Kevin points out, users do not really care exactly how the technology is achieving results.  However, when referencing a novel technology like Ion Torrent’s there does seem to be merit to label it as a “next generation” technology  (in this case 3rd generation).  The reason, in my mind, is that although the technology is also massively parallel, the platform is based upon micro electronics (computer chips) which makes it fundamentally different than the traditional "2nd gen" technologies.   In addition, from a business model perspective, there are manufacturing advantages that differentiate Ion Torrent from the previous generation. Maybe “micro electronics” and "nanopore sequencing" is the "next" or "third" generation? 


 
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