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Merger of TranSmart, i2b2 Aims to Provide Informatics Boost to Precision Medicine Efforts


CHICAGO (GenomeWeb) – As genomic tools continue to make their way from the research lab into clinical practice, the recently announced merger between the TranSmart Foundation and the Informatics for Integrating Biology and the Bedside (i2b2) aims to provide researchers and clinicians with an open-source resource that could benefit precision medicine efforts.

Earlier this month, the two organizations announced their plans to combine into a single foundation focused on providing open-source biomedical software and databases for precision medicine. "We're creating an entire open-source home for people who want to bring precision medicine into clinical practice," said TranSmart Foundation CEO Keith Elliston.

I2b2 was founded in 2004 at Partners HealthCare in Boston as a National Institutes of Health-funded National Center for Biomedical Computing. It has developed a scalable computational framework to apply clinical and genomic data to drug discovery and precision medicine, initially to support patient data registries for academic researchers.

TranSmart, a data management system for translational biomedical research, came along in 2009, when Johnson & Johnson's Janssen Pharmaceuticals wanted to add more molecular data to its research. Researchers at Johnson & Johnson and Recombinant Data Corp. built TranSmart on the i2b2 platform.

According to a 2010 article in the Journal of Translational Medicine, TranSmart addressed a shortfall in i2b2: difficulty translating preclinical models into usable knowledge. Developers added access to research data — including genomic information — to clinical data present in i2b2, as well as advanced analytics and visualization features.

"The pharma teams were looking for a more deeply integrated system of all the data from the molecular biology side through to the clinical data," explained Rudy Potenzone, vice president of marketing and acting chief operating officer of TranSmart.

"The TranSmart platform offers them more accessible and improved analytics and visualization of the data.  It also provides the deeper set of genomics data in an easy-to-use interface where the clinicians can ask questions of the database without a deep knowledge of data queries and statistical analyses," Potenzone said.

In 2013, J&J spun the technology off into theTranSmart Foundation, a nonprofit public/private partnership focused on the continued development of the TranSmart technology. Participants have invested more than $100 million in the two platforms over the years, Elliston said.

The two organizations had been talking about formally getting together for close to a year and a half, according to Potenzone.

"The data model has started to get a little disconnected," Potenzone said. "There has been a call from the community for a little better coordination."

The two sets of technology had lived in different worlds for years. "Our communities are adjacent, but not really overlapping at all," Elliston said.

Separately, the two user bases did not have ready access to all relevant genomic, metabolic, and clinical data, plus analytics and visualization tools in a single place, hampering their ability to tailor treatments to specific patient populations. "That is what a combined i2b2 and tranSMART platform will accomplish," Potenzone said.

In advance of the merger, TranSmart and i2b2 have been working on greater coordination. For example, in June 2016, the TranSmart Foundation and the Harvard Medical School Department of Biomedical Informatics held a joint conference on how to coordinate application of the TranSmart platform for translational research and the i2b2 platform for clinical research. The second annual meeting is set for June 22 in Boston.

"This merger is the best thing that could happen to each community," said Paul Avillach, who runs a biomedical informatics research lab at Harvard.

Avillach noted that, unlike TranSmart, i2b2 is capable of managing longitudinal patient data. "Any deep phenotypes can be integrated in i2b2 and not in TranSmart," he said. "TranSmart has additional statistical tools to generate summary statistics, while i2b2 only aggregate counts of patients."

Avillach was one of the catalysts for the merger, combining databases from each platform in a pilot integration. He and his boss, i2b2 co-creator Isaac Kohane, have melded the latest version of i2b2 with an older release of TranSmart to build a system suitable for both translational and clinical research.

To date, researchers have created 10 registries on the integrated system, including theNational Health and Nutrition Examination Survey, theGlobal Rare Diseases Patient Registry Data Repository, and one for autism. Joining the registries takes about 30 seconds, Avillach said.

No official decision has been made yet to merge i2b2 and TranSmart onto a single platform outside of Harvard, where Avillach is running the pilot integration. A full merger of platforms is certainly is under consideration, according to Potenzone.

For now, the combined entity will be called the i2b2/TranSmart Foundation, but Elliston said there potentially could be "new branding" 18 to 24 months down the road.