National Institutes of Health renews contract with La Jolla Institute to continue its role as host/developer of the Immune Epitope Database (IEDB)


The National Institutes of Health (NIH) has awarded a $22 million, seven-year contract renewal to the La Jolla Institute to continue its role as host and developer of the Immune Epitope Database (IEDB), the world’s largest collection of scientific data on how the immune system responds to a wide range of diseases.

The database, launched in 2006, was designed and developed by the La Jolla Institute under a multi-million dollar competitive contract from the National Institute for Allergy and Infectious Diseases (NIAID), part of the NIH. The seven-year renewal, also supported by NIAID, will maintain the La Jolla Institute at the IEDB’s helm through 2019.

“We see this contract renewal as a vote of confidence from the National Institutes of Health for our nine-year stewardship of the IEDB since its inception in 2003,” said Alessandro Sette, Ph.D., IEDB co-lead investigator. “Further, we are thrilled that the NIH’s decision will allow us to fulfill our vision to take the database’s analytical capabilities to the next level. This will enhance our own efforts, and those of researchers around the world, who are working aggressively to combat a broad spectrum of diseases heavily influenced by the immune system.”

A resource freely available to researchers worldwide, the database contains information on thousands of epitopes, which are small pieces of a molecule that trigger an immune response. Such information is vitally important to researchers attempting to design new and better vaccines against infectious diseases such as tuberculosis or treatments for allergic diseases, asthma and autoimmune disorders, such as type 1-diabetes, rheumatoid arthritis or multiple sclerosis. The database is located at

“People might wonder why information on an infectious agent, such as tuberculosis, and a case of asthma, belong in the same database,” said Stephen Wilson, Ph.D., the IEDB’s deputy principal investigator. “But at the atomic level, the small cellular pieces that the immune system is reacting to, whether it be tuberculosis bacteria, substances such as pollen that cause asthma or allergies or self proteins in autoimmune diseases such as multiple sclerosis, are all epitopes.”

Indeed, the database is the first in the world to bring together data on a diverse mix of immune-mediated diseases under a single “roof.” Initiated in the midst of post-9/11 bioterrorism concerns, the database originally focused on infectious diseases. However, the team began adding epitope data on autoimmune and other immune-mediated diseases over the last few years and the database now contains information on a broad spectrum of disorders, said Bjoern Peters, Ph.D., a bioinformatics expert and the IEDB’s co-lead investigator.

Dr. Peters said the data collection and input phase, completed in 2011, was massive and involved years of painstaking work by a team of Ph.D.s reading and culling information from more than 13,000 epitope-related research papers dating back to 1952. The database now classifies nearly 100,000 epitopes and over half a million experimental data points, curated from all published data on the subject to date.

The ability of epitopes to solicit a strong reaction from the immune system makes them extremely useful in therapeutic development, added Dr. Peters. When designing a vaccine, an epitope that solicits a strong immune attack against a virus is a good candidate for building a vaccine. With an autoimmune disease, blocking the epitope that triggers the unwanted immune system attack becomes desirable.

“This vast collection is a clear reminder of the immune system’s importance in so many diseases,” said Dr. Sette. “On one hand, the immune system protects us from infection, but it can also cause diseases like asthma or autoimmunity. Bringing together all this data in a single resource will allow researchers from different disciplines to draw analogies and pinpoint differences between diseases that, on the surface, are so different, but deep down share the link to immune recognition of miniscule molecules, the epitopes.”

With the data compilation complete, Dr. Peters said the next phase is extrapolating the most important information. “Now that we have this huge wealth of knowledge, our mission going forward is creating new ways and tools for aggregating the data in the most useful and meaningful ways possible,” he said. “Previous iterations of the database contained analysis tools, but the completed data compilation allows us to look at the big picture dating back to when scientists first began collecting epitope data.”

Dr. Wilson said significant insights are already beginning to emerge. “All of these scientists for all these years have been building a data set,” he said. “Now that we put all that data together, you can see key information that was there all along, but hidden in mounds of data. It might be that a person’s epitope discovery in 1997 is the most important regarding a particular virus, but you don’t realize it until you look at the data over time and see it repeated.”

Dr. Peters, agreed noting “patterns are turning up that will enable the scientific community to separate out the most meaningful therapeutic or vaccine candidates.”

For example, he cited information on the hepatitis C virus. “Through various scientific studies, 3,301 hepatitis C viral epitopes have been identified as triggers of the immune system,” he said. “Once all this data was compiled and analyzed, we saw a strong pattern emerge. The same region of the HCV virus comes up again and again. This tells us that epitopes in this area will likely make good candidates for developing a vaccine, because they cause the immune system to launch a strong attack against the virus.”

The IEDB contract renewal to the La Jolla Institute is funded by NIAID under contract HHSN272201200010C.

To learn more about the Institute’s work, visit