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A Grassroots Institute


Sometimes you have to get by with a little help from your friends. Such is the case with the recently established Institute for Genomic Medicine at the University of California, San Diego, where a severely stricken state economy and limited university budget have forced the institute's executive committee to operate with the mantra that no man — or institute — is an island.

To compensate for a lack of giant startup coffers, the institute's founders have focused more on securing a brain trust from around the UCSD campus to form a strong foundation upon which to slowly build IGM. "We have had generous intellectual support from the school of medicine, and very broad-based support from the various UCSD campuses, the undergraduate biology department, and the school of engineering," says Joseph Gleeson, a professor of neurosciences and pediatrics at UCSD, and a Howard Hughes Medical Institute Investigator. "UCSD is a place that builds things from the grassroots up. We don't have someone that guides things from the top down, so we haven't identified a big source of funding to get the initiative going."

Gleeson is also a member of IGM's executive committee, which includes institute director and UCSD professor of ophthalmology and human genetics Kang Zhang, and Bruce Hamilton, director of the UCSD Genetics Training Program. Gleeson says that plans to construct a dedicated building for IGM have stalled slightly due to the poor state of the California economy. When plans are finalized, however, the group hopes to break ground by the end of this year and begin moving in by 2012 or early 2013. Currently, the researchers are still distributed across the UCSD campus. Until the institute has its own in-house sequencing and data analysis gear, members will make use of the university's Biomedical Genomics Laboratory core.

And while the institute is getting a certain amount of startup funding thanks to the powers that be at the university, when that runs out, the core membership will have to assume operational costs with shared grants and private donations.

Medical efforts

Despite a grim economic landscape, the folks behind the new institute have not been deterred in their efforts to realize the potential of genomic medicine to change the way doctors will treat patients. IGM will initially focus on various forms of cancer, AIDS, and neuropsychiatric, developmental, and eye diseases. With the UCSD Medical Center nearby and a slew of investigators taking a genomics approach to their own areas of disease research, success could be just a matter of putting all the pieces together in one location. "We have outstanding researchers in many disorders, and we're all learning about genomics on our own and applying some technologies in our own labs or maybe outside of the university," Gleeson says. "We would really like to make a central place where we could all deposit the new technologies and be able to better take advantage of them."

Its leaders hope the institute can ultimately deliver real-life solutions to common problems doctors and patients face every day. "We really want to be a part of bringing personalized medicine to the people of San Diego and [to] the national scene. …. If we could make advances in some of these targeted disease areas, we will be taken seriously by the rest of the genetics community, and that's our challenge," Gleeson says. For many involved, the establishment of IGM is seen as a coming-out party for the university as a significant genomics research site. "Unfortunately, UCSD has not really had much of a presence in genetics. With the exception of a few people who have done some important work, we haven't had a department of genetics or an institute or anything like that," Gleeson adds. "But we have certain unique strengths — a lot of our faculty is just out of their postdoc and excited to get something done."

Eventually IGM researchers would like to perform genome-scale -sequencing on every patient that comes through the doors of the Medical Center as well as the local children's hospital. Some of the key areas the institute will focus on include whole exome sequencing and copy number variation — especially as they relate to particular disease entities where UCSD has strong patient cohorts. "Our vision is we would like to perform genetic analysis on every patient ... and then we would like to work with the pharmaceutical companies to take advantage of that information in disease drug trials and by helping them look for outliers in their various clinical trials," Gleeson says.

To that end, the institute is being pitched to university scientists with relevant patient cohorts as a place where they might be able to get more out of their data. "We're trying to get all the researchers on campus who have unique patient cohorts together and say that IGM can be a place where you can bring your cohorts with your phenotypic data and think of ways you get them all genotyped with whatever platform would be most applicable, whether it's copy number variation, high-density SNP arrays, and then let's see what data falls out," he says. "Whether it's a pharmaceutical response or whatever, you can apply the richness of the genetic data to your particular problem."

Getting started

IGM is currently building itself from the ground up with a core team of members from across the university. This initial group includes several researchers from the Cellular and Molecular Medicine department as well as individual researchers with specialized skill sets, such as Trey Ideker, division chief of genetics and associate professor in the department of medicine and bioengineering at UCSD, who will lend his expertise in bioinformatics and genetic network analysis. Terry Gaasterland, professor and director of the nearby Scripps Genome Center, is now also spending a lot of time on the medical school campus helping IGM plan for its bioinformatics infrastructure.

In addition to creating synergy among resources and researchers on the UCSD campus, equally essential is the role that other institutes will play, particularly the J. Craig Venter Institute, which is right in IGM's backyard. Albert La Spada, an IGM member and genetics chief in the pediatrics department at the UCSD Medical Center, has high hopes for on-campus and off-campus collaborations. "I think at UCSD and the affiliated institutes there is incredible expertise in emerging genomics technologies, including next-generation sequencing and, perhaps most importantly, computational biology and bioinformatics," La Spada says. Breaking through bioinformatics bottlenecks will also be facilitated by resources at the San Diego Supercomputer Center and the California Institute for Telecommunications and Technology. "What is unique about UCSD is that we're positioned to leverage this type of program based upon access to those resources and infrastructure … but we're looking to partner with all types of organizations as the program grows and evolves," La Spada adds.

He is looking forward to the institute working to elucidate the mechanisms of neurological disease — his current area of focus. La Spada would really like to have a better handle on the pathways responsible for neurodegenerative processes, and it appears that for a number of these disorders, these pathways involve alterations in transcriptional function. "Being able to interrogate the transcriptome of neurons is an important and necessary approach that this institute will better allow in the future, so there are certain emerging technologies that could better position our group to have a leadership role in [that area]," La Spada says.

The Institute for Genomic Medicine
Director: Kang Zhang
Established: 2009
Size: There are currently about 16 researchers that have come aboard the institute, although this number will probably increase as more UCSD faculty start contributing to its efforts.
Funding: Initially, IGM will garner the majority of its launch funding from money allocated by UCSD's budget. Once the institute is up and running, grants and private funding from its core members will have to keep the institute afloat.
Focus: IGM is intended to be a center point for all genomics efforts on the UCSD campus. It also aims to take part in collaborations with other genomics institutes with the goal of making personalized medicine a reality.

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