Cholera has killed at least 2,000 people in Haiti since October. Rapid genetic sequencing was used to identify its source. (Associated Press)Xconomy.Com / December 13, 2010
Epidemics can travel around the world in hours on airplanes. But now that DNA sequencing has gotten cheap and fast, researchers are finding ways to precisely identify the bugs in real time, find out where they came from, and fight back.
Scientists at Harvard Medical School, with the help of new sequencing machines in development at Menlo Park, Calif.-based Pacific Biosciences, were able to sequence the full genome of the deadly cholera bug that has plagued Haiti since October. The results, showing the Haitian strain originated in Southeast Asia, were published online by the New England Journal of Medicine.
PacBio made 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 gene sequencing. Its technology is supposed to be able to sequence entire genomes for as little as a few hundred dollars, in as little as 15 minutes, raising the bar in an industry led by San Diego-based Illumina and Carlsbad, Calif.-based Life Technologies.
“We hope this will be first of many papers’’ in the New England Journal, said PacBio’s chief scientific officer, Eric Schadt. “It’s a good sign the technology is maturing nicely.’’
The cholera outbreak in Haiti, confirmed Oct. 21, has made more than 90,000 people sick, killed more than 2,000, and spread to the Dominican Republic, according to a Los Angeles Times report that cited the Centers for Disease Control and Prevention.
Matt Waldor, an infectious disease specialist at Harvard Medical School, called PacBio’s chief executive, Hugh Martin, on Nov. 6, Schadt said. Waldor had heard about PacBio’s ability to sequence genomes quickly. The next day, PacBio’s executive team met and decided to act.
Waldor and colleagues grew cultures of the cholera strains of interest in their lab so there would be enough to generate DNA sequences. The samples were shipped to PacBio Nov. 10, to be run through one of the company’s prototype machines, Schadt said. Raw data came off the instrument in about 90 minutes.
The team at PacBio ultimately produced five genomes. Two were isolated from patients in Haiti, another from a recent outbreak in Bangladesh, a fourth from Peru, and the fifth from a historical reference from a 1971 outbreak in Bangladesh.
In this case, the sheer mass of data wasn’t really the problem. There are significant structural variations in different strains; such variations are hard to detect on today’s machines, Schadt said. The PacBio machine, he said, had an advantage in that it looks at much longer stretches of DNA and can piece together full genomes quickly and identify subtle variations.
The scientists were able to say the strain is from Southeast Asia, Schadt said, and get a deeper understanding of how much damage it may inflict.
One of the paper’s authors, John J. Mekalanos, is advancing a strategy to develop a vaccine that could be given across Latin America. Because of this strain’s increased pathogenicity, “the fear is it will dominate across Latin America,’’ Schadt said.
MedNetworks has significantly enhanced its brain trust as it sets out to conquer the emerging field of social networks analytics in healthcare.
The Newton start-up has created a scientific advisory board headlined by Nicholas Christakis and James Fowler, the authors of “Connected,’’ an acclaimed book on social networks.
Christakis, a physician and social scientist from Harvard University, cofounded MedNetworks, and his lab provided the core technology.
Fowler’s involvement with the company is a new development. He is a renowned professor of medical genetics and political science at the University of California San Diego whose research has explored the genetic underpinnings of certain political behavior.
Fowler is also collaborating with Facebook on projects such as how to define which people are the most influential on Facebook users’ networks.
Fowler’s expertise appears to be a perfect fit for MedNetworks. Its software is designed to help stakeholders in health care map, analyze, and activate social networks.
That would enable, say, a drug company working on a product launch to focus on doctors who have the most influence on their peers.
Or employers could use the software to optimize smoking-cessation program by focusing on employees who could influence smokers.
MedNetworks’s scientific advisory board “is something of a dream team,’’ Fowler said.
The others are:
■F. Thomas Balzer, former chief scientist of Health Market Science and the founder and chief executive of Optio Research.
■Albert-Laszlo Barabasi, director of Northeastern University’s Center for Complex Network Research.
■David Flaschen, a partner at the private equity firm Castanea Partners.
■Guido Imbens, Harvard University economics professor.
■Michael Kearns, University of Pennsylvania professor of computer and information science.
■Bruce Landon, Harvard Medical School associate professor in the department of medicine and health care policy.
■Curtis Langlotz, vice chairman for informatics at the University of Pennsylvania radiology department.
■Stanley Wasserman, Indiana University statistics professor.
Christakis, the chairman of the advisory board, spends his days as a professor of health care policy at Harvard.
Fowler said having a strong scientific advisory board is important because of the rapid pace of discoveries in social networks analysis.
Dicerna Pharmaceuticals, a Watertown developer of second-generation RNA-interference drugs, is expanding its collaboration with the Japanese drug maker Kyowa Hakko Kirin to include research on gene-silencing treatments for immunologic and inflammatory diseases.
The firms announced their original collaboration, worth up to $1.4 billion, in January to focus on treatments for cancer.
This report was compiled by the editors of Xconomy, an online news website focused on the business of technology and innovation. For more New England coverage, visit www.Xconomy.com/boston.