Published online 3 April 2008 | Nature | doi:10.1038/news.2008.735

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Machine is the first of a new generation to hit the market.

No need to amplify: you don't need multiple copies of bits of DNA with new sequencers. Getty

A Massachusetts company has published data from a DNA sequencer that can read individual letters from single molecules of DNA. The machine, produced by Helicos BioSciences, is the first of a new generation of devices, called single-molecule DNA sequencers, to enter the market.

Single-molecule approaches are widely regarded as the future of sequencing, because they do not require the DNA to be 'amplified' (copied into multiple, identical strands) before it is sequenced. The amplification step can introduce errors into the sequence and does not work well for some DNA fragments, making it difficult to sequence a genome’s full complement of DNA.

By avoiding these complications, single-molecule approaches may reduce the time and the cost of sequencing an individual’s genome. “They're cool,” says Edward Rubin, director of the US Department of Energy’s Joint Genome Institute, a genome-sequencing facility in Walnut Creek, California. “Eventually, single-molecule sequencing will be what we use.”

Close race

The competition in the sequencing field has been heating up this year as companies jostle to be the first, the fastest and the cheapest to sequence large amounts of DNA. Helicos will be competing with established companies such as California-based Illumina of San Diego and Applied Biosystems of Foster City. In February, Illumina claimed to have kept the costs for an entire human genome down to just US$100,000 (see Company claims to have sequenced man's genome cheaply). and a month later, Applied Biosystems stated that it had sequenced a human genome using less than $60,000 worth of reagents.

Helicos has not yet sequenced a human genome — it looked instead at the genome of a virus called M13 that infects bacteria. But it has published its initial data in a peer-reviewed journal1. The virus's genome is tiny — nearly a millionth the size of the human genome — but the firm estimates that their machine could sequence a human genome for about $72,000 in eight weeks. The machine itself will cost customers US$1.35 million, according to the company website.

Helicos’ method begins by chopping the genome into small fragments. An enzyme then attaches a short DNA tag onto the end of each fragment. The tag binds to a complementary DNA molecule attached to a platform, anchoring the DNA fragment in place. A DNA replicating enzyme is then added along with a stock of DNA 'letters' or bases carrying fluorescent labels. As the fluorescent DNA forms into strands that complement the genome fragments, a camera takes a picture of each newly added base.

This method, called ‘sequencing by synthesis’, is similar in principle to that used by other sequencers. But Helicos has adapted its method so that it can detect the light from individual letters of DNA. The other procedures require many thousands of identical genome fragments to be sequenced simultaneously to get a signal bright enough to interpret.

Bit by bit

But there is a catch: Helicos can sequence only small fragments. In today's report, the fragments carried about 30 DNA letters. That puts the machine on par with some currently used sequencers, but nevertheless limits its usefulness for sequencing large genomes. Sequenced fragments need to be pieced together by looking at overlapping regions: the smaller the fragments, the more difficult it is to assemble them.

This means that Helicos’ machine would struggle to sequence a large genome that has never been sequenced before. It could stitch together at least 85% of a person's genome, says Timothy Harris of Helicos and lead author on the paper, using the already-published human genome as a reference — more than enough of a sequencing effort to be useful for personal genomics.

Pacific Biosciences of Menlo Park, California, has said that its single-molecule sequencing machines can sequence DNA fragments of over 1,000 bases long. That data has yet to be published, however, and the company has estimated that their first machine will not hit the market until 2010.

The competition is driving the field rapidly toward the lofty goal of a $1,000 human genome sequence, which Harris thinks will be reached in less than five years. “Maybe that will be Helicos and maybe not,” he says. “There are a lot of people pushing in that direction.”