Stanford University engineer Stephen Quake has added his name to the growing list of people who have had their individual genomes sequenced.

Quake did it using a machine made by a company he co-founded, Helicos Biosciences of Cambridge, Mass. J. Craig Venter was the first scientist to sequence his own genome; six other individual human genomes have been published and others have been sequenced by private companies.

Quake describes his achievement in a paper in Nature Biotechnology, in which he reports that he sequenced his genome with the help of two other scientists and read out 90 percent of his genome, or 2.5 billion base pairs. Quake estimated that it cost $48,000, not including the cost of the sequencing machine itself, which approaches nearly $1 million. Stanford University purchased a Helicos sequencing machine last year at an undisclosed price.

Quake told the New York Times that the $48,000 price tag “will democratize access to the fruits of the genome revolution.” The price is the same as that currently quoted by the company Illumina, headquartered in San Diego, California.

But Quake’s technology is different from Illumina’s, and from every other company’s that has previously sequenced a human genome. Helicos uses so-called “single molecule” technology, meaning the DNA is analyzed without first being amplified. Scientists are excited about single-molecule sequencing because it could usher in an era of faster, cheaper and more accurate DNA sequencing, sometimes called “third generation” sequencing.

Quake and Helicos are touting the paper as a resurrection of sorts for Helicos, which stumbled after its initial public offering in 2007 due to technical glitches and the high price of its machine. Helicos CEO Steve Lombardi told Bio-IT World that Quake’s paper is “the first large statement from someone other than the company that the technology works. That’s a really important thing for us.” Yet it should be noted that Quake is not an impartial observer, as he holds shares in and consults for Helicos.

Some scientists unaffiliated with Helicos were more tepid about Quake’s paper. Clive Brown, vice president of informatics and IT at Oxford Nanopore Technologies of Oxford, UK – one of Helicos’s competitors in the third-generation sequencing race – told Bio-IT World that “Helicos deserves some kudos,” then added, “[T]hey’ve made it work about as good as it can work with single-molecule fluorescence and the camera they have.”

The Associated Press reported that Richard Gibbs, director of the Human Genome Sequencing Center at the Baylor College of Medicine in Houston, called Quake’s results impressive, but warned that accuracy will become more imperative as speed increases.

And as Daniel MacArthur, a blogger and postdoctoral researcher at Wellcome Trust Sanger Institute in Cambridge, UK, wrote, the error rate given in Quake’s paper is higher than those seen with current, so-called “second generation,” technologies.

“This paper sets the bar pretty low for other third-generation sequencing contenders: it appears that formal entry into the human genome sequencing race merely requires generating a genome sequence of the standard that second-generation sequencers were achieving in early 2008, at the same price that they’re charging right now. That’s a fairly uninspiring goal,” MacArthur wrote on his blog, Genetic Future.