Wednesday, April 30, 2008

Gene Sequencing for the Masses

Continued from page 1

By Emily Singer

While the scientists don't yet have the final figures on the Polonator's accuracy and throughput, they expect that it will sequence 10 billion base pairs in a single 80-hour run, a capacity equal to or greater than that of currently available technologies. Harvard and MIT's jointly run Broad Institute for genomic medicine, in Cambridge, MA, and the Max Planck Institute, in Germany, have already purchased devices at the $150,000 sticker price, and the machines should be delivered within the next week or two. General availability is expected by mid- to late May.

Despite almost no marketing, the Polonator has already created a buzz in the research community. McCarthy brought a prototype to a sequencing conference in Florida earlier this year and says that people were lined up to see it until the early hours of the morning. Last week, scientists at a genome-sequencing conference in San Diego, where McCarthy gave his first public presentation on the technology, found the concept intriguing. One of those in attendance was Vladimir Benes, head of the genomics core facility at the European Molecular Biology Laboratory, in Heidelberg, Germany. "It's definitely in the spirit of George Church to make technology as accessible as possible and let the community do what they like," Benes said at the time.

Patrice Milos, chief scientific officer at Helicos BioSciences, a company based in Cambridge, MA, that has just released its own sequencing machine, had a more muted reaction. "As with any technology, it's seeing what they can deliver that matters," Milos said.

The Polonator embodies an open-source philosophy. It was designed so that users can tinker with it in any way they wish. All the parts can be swapped out, and scientists can use enzymes and chemicals other than those sold by Danaher for the sequencing process. Church and others are already working on alternative chemical processes that could make the instrument more efficient. "The fact that it's open source is great," says Andrew Barry, supervisor of process development at the Broad Institute. "It's going to be a community-driven instrument."

Church believes that sequencing will ultimately be a more effective personalized-medicine tool than the microarray technologies currently on the market. (Several companies now offer chips studded with small pieces of DNA that can be used to detect specific genetic variations linked to disease.) By looking at the entire genome, sequencing is able to identify mutations that microarrays cannot. "Sequencing is turning out to be as cost effective at most things as chips are now," Church says. "And you can do things with sequencing you can't do with chips."