The Human Genome Project completed its first draft in 2000 after 10 years' work. Now a Californian company has unveiled details of a technique that it says could sequence a person's entire genome in half an hour, for under $1000.

Sequencing is the process of working out the order in which nucleotide bases appear in a strand of DNA. Until recently, this was only possible for short portions of DNA, so the most common technique involved chopping DNA into short strands, working out the sequence in each and then stitching the data together to recreate the complete genome. This process has to be repeated many times with overlapping strands of DNA to get an accurate map, which is one reason it takes so long.

A more promising approach is to watch a molecule of double-stranded DNA being constructed from a single strand in real time. The trouble is that this occurs on such a small scale that it has been impossible to see. Now a team at Pacific BioSciences in Menlo Park, California, says it has worked out how this can be done (Science, DOI: link).

DNA is assembled by an enzyme called DNA polymerase. This takes a single strand of DNA and adds the appropriate nucleotide bases to form a double strand. The new technique involves attaching a different coloured fluorescent dye to each of the four types of nucleotide and watching these flash as they are incorporated into the strand (see diagram). The sequence of coloured flashes in this molecular fireworks display indicates the order in which the nucleotides appear.
The 30-minute genome
© UnknownThe 30-minute genome.

The technique relies on two breakthroughs. First, the team developed a hollow metal cylinder 20 nanometres wide in which the DNA and the polymerase sit, known as a zero-mode waveguide (ZMW). In here, the flashes can be seen directly because the small size of the ZMW significantly reduces the amount of background light, which would otherwise overwhelm the flashes.

The second is a new way to attach the dye to a nucleotide. Instead of being attached to the part that gets incorporated into the DNA strand, as happens now, the dye is linked to a part of the nucleotide that gets discarded after the reaction. That allows the DNA to be built without adding a huge number of fluorescent tags.

So far, the team has built a chip housing 3000 ZMWs, which the company hopes will hit the market in 2010. By 2013, it aims to squeeze a million ZMWs onto a single chip and observe DNA being assembled in each simultaneously. Company founder Stephen Turner estimates that such a chip would be able to sequence an entire human genome in under half an hour to 99.999 per cent accuracy for under $1000.

Michael Metzker from the Baylor College of Medicine in Houston, Texas, is less confident, saying: "Their projection appears very optimistic."