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Focus on the gene scene
CAMBRIDGE, Mass.—At the Broad Institute of MIT and Harvard, researchers recently made a breakthrough in the challenge of visualizing the massive amount of genomic data being generated by developing the Integrative Genomics Viewer (IGV), a visualization tool that helps users simultaneously integrate and analyze different types of genomic data. IGV also offers researchers the flexibility to zoom in on a specific genomic regions of interest or to pan out for a broad, whole-genome view.
As if that wasn't enough, it's a visualization tool for which researchers don't have to pay a dime and can be downloaded straight from the Broad's Web site.
As noted in a news release about the deal, researchers are "collecting vast amounts of diverse genomic data with ever-increasing speed, but effective ways to visualize these data in an integrated manner have lagged behind the ability to generate them."
To address this problem, Broad researchers took their cue from Google Maps, which allows people to go from a view of the world to a view of their street in a matter of a few clicks with almost no fuss. The secret? According to Jim Robinson, a senior software engineer at the Broad who co-developed IGV: Only feed the user the exact amount of information he or she is able to view on the screen at that particular moment in time.
In addition to choosing a Google Maps-like "street view" of the As, Cs, Ts, and Gs that make up the genome, researchers can also simultaneously visualize additional layers of complex information about gene expression as well as sequence alterations, or mutations in the genetic code. Other genomic details, such as copy number variation, chromatin immunoprecipation data, and epigenetic modifications, can also be viewed in IGV.
Moreover, all these data can be overlaid or superimposed to determine how changes at one level will affect another. Users can choose from a variety of display options, viewing their data as a heat map, histogram, scatter plot or other formats of their choice.
"There are other tools out there that can integrate stuff, but the unique aspect of IGV at the moment is how we handle the problem of volume by just serving up little pieces as you need them," says Robinson.
"Most visualization tools are limited in their ability to handle multiple types of genomic data and are typically 'retrofitted' to accommodate new data types as they have arisen," adds Michael Reich, director of cancer informatics development at the Broad Institute. "IGV was designed from the ground up to integrate all of these data, and to provide a strong platform for future growth and refinement."
In addition to integrating detailed, localized views of genomic data, as several other tools do—and adding the whole-genome view, which few tools offer—IGV also was designed to provide smooth zooming and panning across all resolution scales, Robinson notes.
Broad Associate Member John Rinn, an assistant professor at Harvard University and Beth Israel Deaconess Medical Center, has used a variety of visualization tools to sift through different types of genomic data and says that before IGV, he had to use three different programs to visually integrate data: "But now this one, universal browser allows me to rapidly scan the entire genome and identify promising regions, which has revolutionized my work."
Reich expects IGV to increase the flow of discovery in many areas of biomedical research, but says he is particularly excited about its potential and, in fact, its "already groundbreaking use" in ongoing studies of the cancer genome. DDN