Professor develops cheaper way to map DNA

Thursday, August 13, 2009

By: Melissa Chan

Stephen Quake, professor of bioengineering at Stanford University, recently developed the first commercially available human genome sequencer. At $48,000 per use, the HeliScope Single Molecule Sequencer promises to decode a complete human genome in as quickly as four weeks.

Previous methods to sequence genomes began as early as 1990 with the international Human Genome Project. Using a method created by Frederick Sanger in 1975, the team’s project mapped a full genome by 2003 at the cost of $500,000. Last year, a human genome was decoded at the cost of $250,000 with a team of 200 people.

Quake’s machine only requires a team of three and at a fraction of the price.

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

This drop in cost, time, personnel and space—the system is only about the size of a refrigerator—will allow individual laboratories to execute affordable yet large-scale experiments.

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

Quake reported his achievements on Monday in the online journal Nature Biotechnology, stating that he had sequenced his own genome with a team comprised of himself, physics graduate student Dmitry Pushkarev and Research Technical Manager Norma Neff Ph.D.

According to Puskarev, widespread genome sequencing will be useful for things such as determining the origin of a disease by mapping out the genomes of the mother, father and child.

Quake developed the technology for the sequencer and founded Helicos BioSciences Corporation in 2003 to expand and complete the process.

The innovative genetic analyzer will undoubtedly increase the number of genomes sequenced, adding important information to the entire field of study.

While he added his name to the list of eight people who have had their genomes sequenced, Quake also unearthed some important information about his own personal genetics. He discovered through his genetic makeup that he has a rare mutation variant associated with heart disease.

“We would like to find candidate things that might cause disease; we are really in the infancy right now of the field,” said Mike Cherry, associate professor in genetics.

The machine achieves the reduced cost by simplification, harnessing the power of direct DNA measurement. While previous techniques generated thousands of copies of DNA, the single molecule technique does not, thereby reducing cost and effort.

Quake’s genome sequence will be made public, as previous genome sequences have been made to speed the advances of the scientific community as a whole.

“We are about to see the floodgates opened and many human genomes sequenced,” Quake told the Stanford Report.

DNAWellnessinfo.com Resource: http://www.stanforddaily.com/cgi-bin/?p=1032403