May 31, 2014

When are we going to get a 3rd generation sequencer?

Two years ago, there were at least a dozen companies trying to develop DNA sequencing technology to rival incumbents like Illumina, Life Technologies, Roche/454, PacBio, and Complete Genomics (the latter offers sequencing as a service). What has changed since?

Despite numerous optimistic announcements by start-ups (for example, here and here and here and here and here) and investments totaling more than $400 million, there hasn't yet been any great breakthrough. The only exception is Oxford Nanopore, whose MinION sequencers seems to be close to ready for prime time.

The table below lists companies that have said they are developing sequencing technology and that have received funding according to the online database Crunchbase, which tracks that sort of thing:

Acquired by Roche

Even though that's a long list, it is not complete. Companies whose funding situation or current status are unclear and who have therefore not made it onto the list are Noblegen, Base 4 Innovation , Electron Optica, the Beijing Institute of Genomics (BIG), Electronic Biosciences, Qiagen's Intelligent Bio-systems, Reveo, and MobiousBiosytems. Doubtlessly, some of those have quietly exited the race.

Let's summarise: There are a lot of companies trying to develop the sequencer of the future, and at least some of them have received generous funding. Most have been active for at least two years, but we haven't seen any results yet, at least in the form of a sequencing machine we can buy. Clearly, 3rd generation sequencing is a though nut to crack.

I'd like to thank Keith Robison for pointing out omissions in an earlier version of this post, which I've now fixed.


  1. PacBio is a 3rd generation sequencer!

  2. Melanie is right, there may be some argument as to how to name the 4th-gen, next-next-gen, 'last-gen' (I think Genia coined that one!) but in accepted terms PacBio is definitely 3rd gen. It's not useful to be confusing.

  3. I concede that PacBio and maybe IonTorrent can be called 3rd gen, but I'd be surprised if anyone really, actually gets confused the title of my post

  4. Nice update on all of the players, but you did not mention that GnuBio was acquired by Bio-Rad.

  5. I think a clearer definition of "3rd generation sequencing" would do good here.
    For me, technical aspects are more relevant here than cost or throughput concerns. 3rd gen sequencing should enable researchers to look at DNA in a way that hasn't been possible before. More specifically, I expect a 3rd gen platform to be single molecule based and independent of amplification of the target DNA, so that issues with PCR bias and dephasing limiting read length are overcome.
    From that perspective, Ion Torrent clearly does not qualify as 3rd gen platform. Pacbio on the other hand does, and delivers to these expectations very well. Actually, to my knowledge it's currently the only true 3rd gen platform robustly and successfully working in the field.

    I'd be very interested to hear if there are other views on what should be expected from a 3rd gen platform.

  6. Hi Art, you can now add Base4 to your list!

    1. Thanks James, seems like I'll have to do an update of my list soon. QuantuMDx also has attracted additional funding since I posted the list.