The browser was developed by a team of scientists at UCSC's Center for Biomolecular Science and Engineering (CBSE), an interdisciplinary center housed in the Baskin School of Engineering and directed by Haussler. Ting Wang, a Helen Hay Whitney postdoctoral fellow, came up with the initial design of the browser and coordinated the team's efforts. The first three authors of the paper--postdoctoral researcher Jingchun Zhu and graduate students Zachary Sanborn and Stephen Benz--did much of the work involved in building the browser, with help from CBSE research scientist James Kent and others.
The public browser site (http://genome-cancer.ucsc.edu) hosts a growing body of publicly available cancer genomic data, and the browser is also being used on confidential, prepublication data by several groups involved in clinical trials and cancer genomics research, Wang said.
The Cancer Genomics Browser is a natural extension of the UCSC Genome Browser, a widely used platform for accessing and visualizing genomic data. Created by Kent as a tool for exploring the human genome, the UCSC Genome Browser now averages one million page requests every week. It displays data and annotations in linear tracks that parallel the DNA sequences of the dozens of genomes in the browser.
But this type of display doesn't work well with clinical data from large numbers of patients. And clinical databases don't handle genomic data very well. The Cancer Genomics Browser is able to integrate these different types of data into a single interactive display.
"Large clinical trials that include detailed molecular profiling of patient samples generate a really big mountain of data. Actually, it is more like several big mountains of data," Lenburg said. "The browser creates a way of organizing all this data, and all these different types of data, into a single unified picture."
The Cancer Genomics Browser
|Contact: Tim Stephens|
University of California - Santa Cruz