Entire genome on the cheap

STANFORD (US)—Sequencing the human genome is a relative bargain these days, as a bioengineering professor recently proved when he mapped his entire genome for less than $50,000 with a team of just two other people.

“This is the first demonstration that you don’t need a genome center to sequence a human genome,” says Stephen Quake, professor of bioengineering at Stanford University. “It’s really democratizing the fruits of the genome revolution and saying that anybody can play in this game.”

Early efforts to map the human genome in 2001 cost hundreds of millions of dollars and involved more than 250 people. Just last year, the lowest reported cost was $250,000, and genome sequencing still required almost 200 people.

Reducing costs is critical because the more examples scientists have of the whole human genetic code, the more they can discern about how specific genes and mutations result in the traits that make us all different, the diseases that plague us, and our response to medicines.

As that understanding increases and costs drop, doctors could then sequence their patients’ genomes and provide “personalized medicine” in which prevention and treatment of disease would be informed by the patient’s exact genetic profile.

“This can now be done in one lab, with one machine, at a modest cost,” says Quake. “It’s going to unleash an enormous amount of creativity and really broaden the field.”

Quake’s genome, one of less than a dozen sequenced so far, is now available to researchers worldwide. Quake’s colleagues at Stanford’s School of Medicine have been looking through it and sometimes examining Quake himself, mining the data for interesting connections between what they can observe about him, his DNA, and his family history.

“Some of the doctors are starting to poke and prod me to see how they can couple my genome with medicine,” he adds.

To sequence his genome, Quake’s team used a commercially available, refrigerator-sized instrument called the Helicos Biosciences SMS Heliscope. Quake pioneered the underlying technology in 2003. While many techniques require generating thousands of copies of a subject’s DNA, the single molecule technique does not, reducing the cost and effort involved.

Overall, the genome is 95 percent complete, a rate comparable with other sequenced genomes, the team found. In a paper published online Aug. 9 by Nature Biotechnology, the authors are careful to note that all genome-sequencing technologies, including the one they’ve demonstrated, have produced incomplete approximations of the actual genome. Still, it is enough to help produce genuine insights about a person’s traits and health.

Stanford University news: http://news.stanford.edu

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