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UCSC Researchers Introduce Cancer Genomics Browser

NEW YORK (GenomeWeb News) – American scientists have developed a new online resource, dubbed the Cancer Genomics Browser, for visualizing and analyzing data related to studies of cancer genomes.

A team of researchers at the University of California at Santa Cruz Center for Biomolecular Science and Engineering developed the browser, which they tested in collaboration with investigators across the US. The team described the new browser in the April issue of Nature Methods.

"We've built the cancer browser so that researchers can upload their data and use a variety of software tools to visualize and interpret their results," co-senior author David Haussler, a biomolecular science and engineering researcher at UCSC, said in a statement.

The browser includes web-based tools to help identify cancer-related genetic patterns from large clinical and genetic studies. That, in turn, is intended to improve cancer treatment and diagnosis. For instance, researchers are using large-scale genetic studies to look for potential biomarkers that can help predict cancer treatment outcomes. Genome sequencing and analysis are also being employed to understand the molecular basis of various cancers.

The new browser helps researchers assess the results of such studies, displaying data as heatmaps representing important variables. And since genomic and clinical data are displayed beside one another, the browser is designed to help researchers integrate data from both types of studies. Statistical tools are included for users interested in doing quantitative analyses.

"What is amazing about the browser is that it allows us to combine complex molecular data and clinical observations, and provides insight into how we can truly improve treatment and outcomes," co-author Laura Esserman, a surgery and radiology professor at the University of California at San Francisco, said in a statement.

Esserman, along with co-author and Boston University researcher Marc Lenburg, who are participating in the I-SPY Trial, a multi-institution collaboration looking for biomarkers for predicting effective advanced breast cancer treatments, test drove the browser as Haussler's team developed it.

The Cancer Genomics Browser, an extension of the UCSC Genome Browser, contains publicly available data regarding cancer genomics. It is also being used by some groups involved in clinical trials to confidentially assess prepublication data.

Developers used prepublication data from the I-SPY Trial as well as the Cancer Genome Atlas while developing the browser. The team is also working with the International Cancer Genome Consortium.

The researchers noted that the browser may eventually have applications for assessing other diseases as well. "As genome-side high-throughput data become more available, we expect such tools to be increasingly important in disease research," they concluded.

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