Despite its novel technology, Helicos still has some hurdles to overcome. The technology hasn’t yet demonstrated clear advantages over the most sophisticated sequencing machines currently in use. “Single-molecule sequencing has lots of benefits, but it’s very hard from an optics standpoint to detect a single molecule on a piece of DNA,” says Mardis. Because of this, the Helicos machine is much more expensive than the alternatives.
“We’re still a little underwhelmed,” says George Weinstock, associate director of the Genome Sequencing Center at Washington University. “Right now, I would say it’s a wash, in terms of time and cost. I would say they’re a couple of years out from having an impact.”
Still, the advance is “a pretty big accomplishment,” says Jeff Schloss, director of the Genome Technology Program at the National Human Genome Research Institute in Bethesda, MD. “It’s important to get these results in the peer-reviewed literature.” Some scientists have criticized a series of impressive but unpublished sequencing claims, saying it’s too difficult to evaluate them without having detailed information on the methodology.
Helicos is soon likely to face another slew of competitors. Development of so-called “third generation” sequencing technologies is already under way–these systems aim to sequence a single molecule of DNA in real time, boosting speed and reducing the amount and cost of chemicals used in the process.
Helicos is also moving forward rapidly. The technology used in the Science paper has already been replaced in the company’s commercial device, improving on some faults described in the paper, such as difficulty reading certain repetitive sequences.Says Timothy Harris, senior director of research at Helicos and lead author on the paper, “Things change faster than you can publish them.”