Open source oncology software from Pitt, UPMC to speed genomic data sharing

By Mike Miliard
10:32 AM
With research institutions 'choking on data,' new precision medicine helps researchers manage large volumes.

TCGA Expedition, a new new tool developed by the University of Pittsburgh, UPMC and the Pittsburgh Supercomputing Center, can help cancer investigators wade through huge amounts of genomic data.

The open-source technology, which manages data from The Cancer Genome Atlas project, continuously downloads, processes and manages TCGA data, allowing researchers to choose specific tools as they work toward better treatments.

"Starting with TCGA, our goal is to make large data sets available to the average researcher who would not otherwise be able to access this information," said Rebecca Jacobson, MD, professor of biomedical informatics and chief information officer at Pitt's School of Medicine, in a statement.

"There's a growing understanding that further advances in health care are going to require a previously unseen level of data sharing, which will require new tools," she added. "That's particularly true in cancer research, as recognized by the major focus on data sharing in Vice President Joseph Biden's recently announced Cancer Moonshot initiative."

[Also: Vice President Biden announces vast list of federal and private-sector collaborations at Cancer Moonshot Summit]

Cancers are caused by an overgrowth of cells due to an error in DNA. By examining a cancer's complete set of DNA, or genome, researchers can gain new insights into better care plans.

The goal of TCGA - a joint effort of the National Cancer Institute and the National Human Genome Research Institute - is to collect and share genomic data from cancers with poor prognoses and the greatest impacts on public health, researchers say.

So far the initiative has profiled 33 different cancers from more than 11,000 patients; the resulting data has been used in more than 1,000 cancer studies.

"These very large data sets are incredibly hard to work with because they are enormous, not only in terms of the amount of digital storage space they need, but also in terms of the complexity of software and computational processing power that they require," said Jacobson. "Right now, our institutions are choking on data."
"This work is about enabling and speeding up science," said Adrian Lee, director of IPM and of UPCI's Women's Cancer Research Center. "Resources such as this will be key in our move to precision cancer genomic medicine."

The fact that the tool is open source and freely available means researchers hope it will be adopted far and wide in the fight against cancer.

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