Building on big data, UPenn and UGA awarded $23.4 million pathogen genomics database contract

Kissinger, Jessica wires.env-h

December 18, 2014

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    Jessica Kissinger, a professor of genetics in the Franklin College of Arts and Sciences and director of the Institute of Bioinformatics, has become a resource for helping colleagues use their data more effectively. (Credit: Robert Newcomb/UGA)

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Athens, Ga. - A genome database team led by University of Pennsylvania and University of Georgia scientists has been awarded a new contract from the National Institutes of Allergy and Infectious Disease worth $4.3 million in 2014-2015. Assuming annual renewal, this five-year award is expected to total $23.4 million.

The team has been responsible for developing genome database resources for microbial pathogens, including the parasites responsible for malaria, sleeping sickness, toxoplasmosis and many other important diseases.

The new contract ensures work will continue on the Eukaryotic Pathogen Genomics Database—known as EuPathDB—to provide the global scientific community with free access to a wealth of genomic data related to microbial pathogens important to human health and biosecurity. EuPathDB expedites biomedical research in the lab, field and clinic, enabling the development of innovative diagnostics, therapies and vaccines.

Each month, EuPathDB receives over 6.5 million hits from 13,000 unique visitors in more than 100 countries, including areas where tropical diseases such as malaria are endemic. India is now the second largest user of its plasmodium genome database, and over 5 percent of users hail from Africa. The overall project employs 28 people on four continents.

EuPathDB is jointly directed by principal investigators David S. Roos, the E. Otis Kendall Professor of Biology in Penn's School of Arts and Sciences, and Jessica C. Kissinger, professor of genetics and director of the UGA Institute of Bioinformatics. Christian Stoeckert of Penn's Perelman School of Medicine is a co-investigator.

One of four pathogen bioinformatics resource centers supported by the National Institutes of Health, EuPathDB is responsible for disease-causing eukaryotes, which are organisms that possess a membrane-bound nucleus. Other centers support data on viruses, bacteria and insect vectors of disease.

"This database has expedited research in many ways," said Kissinger, a member of the UGA Center for Tropical and Emerging Global Diseases. "Vaccine scientists frequently want to examine how proteins have changed over time to identify those with signatures indicating that they provoke the human immune system. Those studying a specific antigen may wish to examine its structure and diversity in order to prioritize those regions that might be most promising and relatively unlikely to develop resistance."

Since its prototype was launched in 1999, the EuPathDB family of databases has become increasingly complex and increasingly valuable as a resource for researchers around the world. In total, the databases comprise about 9 terabytes of data and have been cited more than 8,000 times in the scientific literature.

"The costs and time required for genome sequencing have plummeted in the past 10 years thanks to advances in technology," Kissinger said. "Organizing this data, maintaining it in a way that is accessible and easy to use for researchers around the world, 24 hours a day, is our great challenge-and one that presents exciting opportunities for funders and other philanthropic organizations that support pathogen research."

The latest contract is the third time that NIH has awarded support to EuPathDB, building on previous contracts issued in 2004 and 2009 as well as prior grant funding from the NIH and the Burroughs Wellcome Fund. Affiliated projects have also been supported by the Wellcome Trust, the Bill and Melinda Gates Foundation, the Sloan Foundation, the World Health Organization, the U.S. Department of Agriculture, the Brazilian government and other organizations.

"The sophistication of the questions people can ask continues to increase," Roos said in a press release from UPenn. "As we move to the next phase of this project, our job is to ensure that this resource remains dynamic, taking into account how people interact with the data in ways that can have a real impact on global health."

 

Filed under: Medical Science, Health Sciences, Infectious Diseases

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