Gazelles, elephants, blue whales and dodos: next-generation sequencing at the zoo

The big news today is that Life Tech, of SOLiD fame intend to acquire Ion Torrent, subject to certain technical milestones being reached. The best blog coverage is at Omics Omics and Genetic Future.

This means Illumina, Life Tech and Roche, our sequencing Big Three have all now got into bed with "next-next-generation" technology platforms. Roche have previously signed up IBM's nanopore technology and Illumina have entered into a marketing and distribution alliance with Oxford Nanopore.

What does this all mean?

Each platform holder is trying to balance their portfolio and position for the future. Roche are struggling to get much more throughput from the 454 platform and so it makes sense that they focus on the potentially superior nanopore platform. This is some way off, perhaps 5-7 years.  Roche's portfolio has got a big hole the middle right now.

Illumina are dominant but are also looking to the future. Oxford Nanopore looks like a sensible alliance, and I'd predict we'll see it hit in about 3 years time.

By snapping up Ion Torrent, Life Tech have gone for a quite different technology which looks much more likely to integrate happily into the clinical diagnostics market. As announced, Ion Torrent's closest competitor is the 454 Jr.

In fact, the Ion Torrent system is rather similar to the 454 sequencing system in many ways (not surprising as Jonathan Rothberg started 454 as well as Ion Torrent).  Ion Torrent's main advantage is price, clocking in at $50-100k for the instrument and $500 a run in consumables. It's also fast, a promised 1 hour per run (but still a day for sample prep). But this isn't single molecule and the throughput is low, clocking in at 100Mb. This is a gazelle: fast, agile, but relatively weak.

But Life Tech have also announced another in-house technology called quantum dot single-molecule sequencing (more here), and covered their bases well.

A more practical consideration is that the term "next-generation sequencing" is dead. It's all getting way too confusing. Despite my expectation that technology should progress linearly and result in steady improvements in each areas, this isn't the case. Right now you can pick and choose from a menu of options. You can have direct sequencing (single molecule), faster sequencing, faster sample prep, higher throughput, longer reads, cheaper, but you can't have it all.

Continuing the animal analogy; SOLiD and HiSeq are now looking like elephants (or rhinos, or hippos) - powerful, but slow and cumbersome.

So, where does that leave us:

Before you prompt me: where does the PacBio RS sit? Well, in view of its size - perhaps this should be the blue whale. And Helicos, alas is perhaps the dodo.