Updated, um, Carlson Curve for DNA Synthesis Productivity


It seems that productivity improvements in DNA synthesis have resumed their previous pace.  As I noted in Bio-era's Genome Synthesis and Design Futures, starting in about 2002 there was a pause in productivity improvements enabled by commercially available instruments.

According to the specs and the company reps I met at iGEM 2007, a single Febit "Geniom" synthesizer can crank out about 500,000 bases a day and requires about 30 minutes of labor per run.  It looked to me like the number should be closer to 250KB per instrument per day, so I made an executive decision and allowed that the 16 synthesizers one person could run in a day could produce 2.5 megabases of single-stranded ~40-mers per day.  This in part because there is some question about the quality of the sequences produced by the particular chemistry used in the instrument.  It was asserted by the company reps that the Geniom instruments are being adopted by major gene synthesis companies as their primary source of oligos.  Note that running all those instruments would cost you up front just under US$ 5 million, without volume discounts, for 16 of the $300,000 instruments (plus some amount for infrastructure).

The quality of the DNA becomes particularly important if you are using the single-stranded oligos produced by the synthesizer to assemble a gene length construct.  To reiterate the point, the 2.5 megabases per day consists of short, single-stranded pieces.  The cost -- labor, time, and monetary -- of assembling genes is another matter entirely.  These costs are not really possible to estimate based on publicly available information, as this sort of thing is treated as secret by firms in the synthesis business.  Given that finished genes cost about 10 times as much as oligos, and that synthesis firms are probably making a decent margin on their product, the assembly process might run 5 to 8 times the cost of the oligos, but that is totally a guess.  (Here is a link to a ZIP file containing some of the graphics from the Bio-era report, including cost curves for gene and oligo synthesis.)

One final note: the Febit reps suggested they are selling instruments in part based on IP concerns of customers.  That is, a number of their customers are sufficiently concerned about releasing designs for expression chips and oligo sets -- even to contract manufacturers under confidentiality agreements -- that they are forking over $300,000 per instrument to maintain their IP security.  This is something I predicted in Genome Synthesis and Design Futures, though frankly I am surprised it is already happening.  Now we just have to wait for the first gene synthesis machine to show up on the market.  That will really change things.