The DNA sequencing systems on the market produce their output by synthesizing new DNA in a way that allows them to read the identity of the base that's added. There have been a few ideas floated around that involved reading the bases directly from existing molecules, but the technical challenges of doing so have kept anyone from bringing these technologies to market. Now, a company called Oxford Nanopore has announced that it will be selling a DNA-reading machine before the year is over. Not only does this represent an entirely new sequencing technology, but the systems will be sold as rack-mounted hardware that can be clustered.

The basic principle behind nanopore sequencing is pretty simple (we've got more detail if you're interested). An external voltage forces DNA molecules to snake their way through a narrow protein pore embedded in a membrane. As each base passes through, its distinct chemical properties cause changes in the voltage difference across the membrane. By tracking the local voltage changes, it's possible to identify each base as it slides through the pore.

This has some nice features; there are no enzymes or chemicals consumed as the DNA is being read, which cuts down on the cost and speeds up the reading dramatically. There's also (at least theoretically) no limit the the length of the DNA molecule that goes through the pore. If you could keep a human chromosome intact, you could potentially send the whole thing through the pore. The same system also can identify proteins and RNA, so the same hardware can be repurposed for multiple uses.

But crafting a system that matches pores to miniaturized voltage-reading hardware has turned out to be a challenge, and the speed of the system actually works to its disadvantage, making it harder to separate out the signal of each individual base.

Oxford apparently feels that it has overcome most of these problems. It's crafted a system in which a single piece of hardware can read the output of 2,000 pores simultaneously. The error rate is still substantial—according to reports, it's about four percent—but the company claims that will be reduced considerably by the time a product hits the market.

The nanopores and hardware will be sold as a removable cartridge, with each cartridge capable of processing all the samples in a standard 96-well plate. You just snap the cartridge onto a plate, and drop it into the Oxford Nanopore machines. The control software will generate sequence from a single well of the plate, until a target output is reached; it will then flush the system and move on to the next plate.

The novel thing about the hardware is that it's designed to run in parallel. Each machine is rack-mountable, and a user can set it up so that an entire rack is is working on the same sample at once (so, for example, every sample in well six could contain DNA from the same source). The whole rack would then generate sequence until the aggregate target is reached before moving on.

The ability to go massively parallel means that these machines can produce sequence at a staggering rate; Oxford is claiming that 20 of the rack units could pump out an entire human genome in 15 minutes (doing the computing to actually generate a final genome sequence would take quite a bit longer). And the costs are very competitive. Estimates are that a billion base pairs (a Gigabase) will be in the area of $30. That places a reasonable coverage of the genome at under $5,000.

Oxford clearly has the manufacturing sorted out, and it already has plans to increase the density of the nanopores on their hardware. So the question is whether it can drop the error rate and increase the length of the reads. If it can manage both of those, this technology could potentially transform genome sequencing.

In addition to the high-throughput hardware, Oxford has also announced a compact, single-use system that is actually about the size of a cell phone and plugs in to computers as a USB device. The goal for this is to provide things like rapid on-site diagnostics.