A Dutch research consortium led by the Center for Translational Molecular Medicine has kicked off a €16 million ($21 million) project to develop a compute infrastructure to support translational medicine in the Netherlands.
Other members of the Translational Research IT, or TraIT, initiative include the Dutch Cancer Society; the Dutch Heart Foundation; the Netherlands Federation of University Medical Centers; the Netherlands Bioinformatics Centre; the String of Pearls Initiative at Erasmus University Medical Centre; and the Netherlands eScience Center.
CTMM is a public/private initiative created to coordinate and fund multidisciplinary research projects involving Netherlands-based academia and industry. It is supported by the Dutch government, industry, and academia, as well as several research foundations.
The TraIT funding is expected to support the project's activities until 2014. The consortium will focus on developing tools that support the "translational" aspects of molecular medicine so that results can be applied to actual patient care.
The TraIT infrastructure will support CTMM projects in cardiovascular disease; cancer; neurodegenerative disease; and infection and immunity. Several of these projects are "rapidly approaching the point where large-scale clinical studies need to be performed," Peter Luijten, CTMM's chief scientific officer, said in a statement.
TraIT will enable "the standardization and sharing of data across different medical centers, research institutions, and industrial partners involved," Luitjen said.
Initially, the project will focus on integrating and querying information from CTMM's four research domains — clinical data, imaging data, biobanking, and genomics/proteomics data — with an eye toward creating a platform that enables data collection, storage, analysis, archiving, and sharing while ensuring information security.
TraIT is expected to cost between €16 million and €20 million. Half of its total budget will come from the Dutch government, 25 percent from private partners, and 25 percent from academic partners.
Single Platform, Different Uses
CTMM is currently running 21 projects in its four core research areas, many of which involve collaborators from multiple institutions. It plans to initially try out TraIT's tools in two or three projects in oncology and cardiovascular disease research, Eric Caldenhoven, CTMM's program manager for the TraIT project, told BioInform.
One of the ongoing projects that will benefit from TraIT's infrastructure is a study on colorectal cancer that aims to identify and validate biomarkers in stool DNA as well as in serum/tumor samples in order to develop genomic and proteomic tests as well as molecular MRI-based colonoscopy.
Another project, focused on prostate cancer, will look at developing and validating biomarkers to reduce over-diagnosis, over-biopsy, and over-treatment of the disease. It also aims to develop better therapy monitoring techniques for advanced cancer patients.
As a first step, TraIT applications will be set up on local servers at institutions participating in these projects to establish an environment to test out the infrastructure's data-collection abilities, Caldenhoven explained. The tools will then be moved to a central server that different sites will have access to.
Ultimately, "we will use the same infrastructure" for all the different research projects, he said. "There will be small adaptations to protocols" depending on whether the data is for oncology or cardiovascular disease, for example, "but the infrastructure [and] the approach will be the same."
The consortium intends to use existing open source and commercial resources as well as member institutions' in-house infrastructure as much as possible and will only develop new solutions for unmet needs, Caldenhoven said.
For example, it will take advantage of an IT infrastructure for biomedical research that’s been built by the Netherlands Bioinformatics Centre and the String of Pearls initiative, a collection of university medical centers in the Netherlands that is developing an infrastructure for collecting clinical data.
Additionally, TraIT will use tools that have been developed for the US National Cancer Institute's Cancer Biomedical Informatics Grid. The group also intends to partner with other European and international groups involved in similar research endeavors.
To that end it has chosen to use caBIG's tools in addition to OpenClinica, an open source clinical trials software for electronic data capture and clinical data management, Caldenhoven said, adding that the researchers will supplement these resources with their own in-house infrastructure and expertise.
For instance, caBIG has tools for biobanking and researchers associated with the String of Pearls initiative have "experience in collecting and archiving human tissues," he explained, adding that the partners are currently evaluating how best to merge the applications and the data.
Separately, the group is looking into some commercial software packages that can deliver capabilities that both caBIG and in-house infrastructure are lacking, Caldenhoven said.
He declined to mention which vendors are up for consideration for the projects because those discussions are still ongoing.
The Netherlands isn't the only EU nation to invest in an integrated platform for life science research.
The Finnish government has also committed funds to support a national project called Biomedinfra that aims to link the country's biobanking, bioinformatics, and translational research resources in addition to connecting to a larger EU effort — the European Advanced Translational Research Infrastructure in Medicine, or EATRIS — that aims to integrate resources in these three areas (BI 1/21/2011).
Caldenhoven told BioInform that TraIT's developers plan to connect its applications to initiatives like EATRIS.
He noted that many of the researchers in the Dutch initiative are also involved in that larger EU effort, which should make it possible to keep track of and synchronize their efforts with new developments in the space.
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