NCSA, Mayo explore techniques to visualize genetic information for clinicians | National Center for Supercomputing Applications at the University of Illinois

NCSA, Mayo explore techniques to visualize genetic information for clinicians

02.28.11 -

Biomedical researchers are generating a tremendous amount of genomic data about cancer, which has the potential to improve clinicians' ability to diagnose, treat and prevent the disease.

But in order for this complex, heterogeneous data to be useful in a clinical setting, it must be clear and easy to understand, with the relevant information drawn from the overwhelming flood. Researchers at NCSA, Mayo Clinic and the Genomic Institute of Singapore have begun a pilot project to develop an effective way to visually present genomic data to clinicians. The project is one of several being carried out by the Mayo Illinois Alliance for Technology-Based Healthcare, a joint effort launched in 2010.

"There are all sorts of ways in which visualization tools could be deployed to inform students, clinical practitioners, genetic counselors and patients about the role of genomics in health and disease," said Dr. Frank Prendergast, director of Mayo's Center for Individualized Medicine and a co-principal investigator for the pilot project. "I am especially taken with how such tools can be used to explain genomics to patients; gene sequences by themselves can be stultifyingly uninformative!"

The goal is to "bridge the gap between research and clinicians," says Michael Welge, who leads the data-intensive technologies and applications research team at NCSA. "How do you visually represent information from the research laboratory to the clinician so the clinician can use this in their workflow?"

Welge's team brings substantial data visualization expertise to the project, while the team from Singapore provides insight into the research perspective on the data and how it is currently visually represented. The clinicians from Mayo and other hospitals (including Carle Hospital in Urbana) can explain their typical workflow and how they could use genomic data in diagnosis and in formulating treatment plans.

"We're learning which information is relevant and how they make clinically relevant determinations from these data," Welge says. From all of this information, "we can start to create a process to look at visual metaphors that might satisfy the needs of the clinicians."

The plan is to have an initial prototype or mockup this spring; this will be used as the basis for follow-on proposals and research.

"This will be a highly iterative process. We won't get it right the first time," Welge cautions. He thinks a system could be ready for clinical deployment in two to five years.

While Welge's team frequently tackles data visualization challenges, the potential impact of the cancer genome project is particularly exciting. In fact, former NCSA'er Colleen Bushell, now the head of product development for spin-off company RiverGlass, returned to the center part-time specifically to work on this project.

"I really wanted to apply my skills and experience to something that would help progress the field of personalized medicine," she says.

"This field in particular gives you a chance to really make a difference," Welge says. "There might be a decision made on a therapy or understanding a predisposition to a disease that makes a big difference in someone's life."