PacBio, Harvard Use Fast Gene Sequencer to Crack DNA Code of Haitian Cholera Strain

Xconomy San Francisco — 

Epidemics can travel around the world in a matter of hours on airplanes, killing people before anyone really knows what hit them. But now that DNA sequencing has gotten so cheap and so fast, researchers are finding ways to precisely identify the bugs in real-time to find out where they came from, and how to best fight back.

The latest evidence is emerging from a team of scientists at Harvard Medical School, who, with the help of new sequencing machines in development at Menlo Park, CA-based Pacific Biosciences (NASDAQ: PACB), were able to sequence the full genome of the deadly cholera bug that has plagued Haiti since October. The results, which show the Haitian strain originated not in nearby Caribbean waters but in Southeast Asia, are being published today online in the New England Journal of Medicine.

PacBio made financial news in October when it raised $200 million in its initial public offering, which it hopes to use to capture a slice of the growing market for fast/cheap gene sequencing. The company has been generating buzz in scientific circles for its new technology that is supposed to be able to sequence entire genomes for as little as a few hundred dollars and in as little as 15 minutes—raising the bar ever higher in a sequencing industry currently led by San Diego-based Illumina (NASDAQ: ILMN) and Carlsbad, CA-based Life Technologies (NASDAQ: LIFE). But today’s publication marks the first time that the capability of the PacBio’s machine has been featured in the world’s leading medical journal for playing a role in addressing an ongoing global health concern.

“We hope this will be first of many papers,” in the New England Journal, says PacBio’s chief scientific officer, Eric Schadt. “It’s a good sign the technology is maturing nicely.”

The outbreak of cholera was confirmed in Haiti on October 21, providing an urgent new challenge for infectious disease experts. The epidemic has made more than 90,000 people sick, killed more than 2,000 people, and spread all over Haiti and into the Dominican Republic, according to a report yesterday in the Los Angeles Times, which cited figures from the U.S. Centers for Disease Control and Prevention.

Eric Schadt

Eric Schadt

Matt Waldor, an infectious disease specialist at Harvard Medical School and a Howard Hughes Medical Institute investigator, called up PacBio CEO Hugh Martin on November 6, Schadt says. Waldor didn’t have a prior relationship with the company, but had heard about the PacBio machine’s ability to sequence entire genomes of organism very quickly, and asked Martin about whether this was a task for the company’s new machine. The next day, a Sunday, the PacBio executive team got together for a “pow-wow” as Schadt says, and moved on a dime. “We decided to definitely do it,” Schadt says. “It was right in the sights of what we thought the machine was good at.”

The next day, Waldor and colleagues grew cultures of the cholera bacterial strains of interest in their lab so there would be enough of a sample to generate DNA sequences from. The samples were shipped to the PacBio headquarters in California on November 10, where they could be run through one of the company’s prototype machines, Schadt says. Raw sequence information came off the instrument in about 90 minutes, Schadt says.

The team at PacBio ultimately produced five genomes in total. Two were isolated from individual patients in Haiti, another was from a recent outbreak in Bangladesh, a fourth was from Peru, and the fifth was from a historical reference from a 1971 outbreak in Bangladesh, Schadt says.

The actual genomes themselves weren’t that big. While a human genome has … Next Page »

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