Innovation often comes in unexpected ways. We posted recently about the ScalaBLAST system, able to run genome sequences in under an hour, using one of the top 50 supercomputers on the planet. An enormous leap, certainly -- 9 hours is the current sequencing standard -- but its reliance on a supercomputer puts it out of the reach of medical professionals for a few years yet, at best. But it turns out that brute force isn't the only option.
Researchers at 454 Life Sciences have developed a method of running genome sequences that takes far less time than the current standard method, at a far lower cost -- and doesn't require a supercomputer. Instead, it relies on fireflies.
The machine uses the chemistry of fireflies to generate a flash of light each time a unit of DNA is correctly analyzed. The flashes from more than a million DNA-containing wells, arrayed on a credit-card-sized plate, are monitored by a light-detecting chip, of the kind used in telescopes to detect the faintest light from distant stars. Then, they are sent to a computer that reconstructs the sequence of the genome.
The main downside to this technology is that it's currently limited to DNA fragments of about 100 base pairs in length, far short of what the traditional method can accomplish. This means that, until the technology is able to read longer segments of DNA, it will likely be limited to the sequencing of organisms with smaller or simpler genomes. This still has significant value, as the tropical disease sequencing we posted about recently can attest.
If it takes another few years for the firefly method to reach a point that allows it to reliably sequence human DNA, what we'll see is a race between that and the brute force method -- on Moore's Law-cheap desktop computers -- as a tool for the hospital. A few years after that, it'll be a tool for any doctor's office. And a few years after that, something one could even get for the home. By the 2020s, you'll be getting DNA sequencing systems as the surprise in a box of cereal.