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Dana-Farber and the cBioPortal for Cancer Genomics

  • Analysis of EGFR network in lung adenocarcinoma

    The increasingly useful and influential cBioPortal for Cancer Genomics provides a Web-based resource for Dana-Farber and other researchers to explore, visualize, analyze, and share multidimensional cancer genomics data sets from thousands of patients worldwide.

    The cBioPortal converts molecular profiling data from cancer tissues and cell lines into highly accessible genetic, epigenetic, gene expression, and proteomic events, for an unprecedented — and ever growing — level of interaction, collaboration, and data availability among investigators.

    Using the cBioPortal, researchers across the globe can study and share trends in the mutations of various cancer types, with an eye toward new treatments and clinical trials. Originally designed as part of the National Cancer Institute's Cancer Genome Atlas (TCGA), the cBioPortal is now used by tens of thousands of researchers. The tool is also installed at Dana-Farber and dozens of other national and international academic centers, as well as several pharmaceutical and biotech firms.

    cBioPortal opens the door to faster genomic progress

    cBioPortal Hackathon presentation

    "The cBioPortal helps researchers understand the molecular landscape of different cancer types," explains Ethan Cerami, PhD, director and lead scientist of Dana-Farber's Knowledge Systems Group. "Certain mutations may be common in one cancer type, where there is a therapy approved, and you may see the same mutation in another cancer where the therapy has not yet been approved."

    "Anybody can download our code for free, modify it, and send it back to us," says Cerami, of the open-sourced system. "By collaborating with other centers, we can gain their expertise and grow the system far faster than we ever could ourselves."

    cBioPortal at Dana-Farber

    cBioPortal Hackathon participants

    In addition to the shared cBioPortal system, research institutions like Dana-Farber are adapting the tool to create genomic information systems that contains their own patients' data, for the use of their own researchers. At Dana-Farber, the cBioPortal includes statistics from the Institute's Profile project — one of the nation's leading precision cancer medicine initiatives — sharing genomic data from nearly 7,000 Dana-Farber patients. Using the cBioPortal tool, our researchers, biologists, and clinicians can access and manipulate data through easy-to-understand visualizations and analysis tools.

    "The cBioPortal tool has been a fantastic addition to the resources available at Dana-Farber for evaluation of tumor genomics," says Amanda Redig, MD, PhD, an Oncology fellow with the Institute's Thoracic Oncology group. "It is simple to use and extremely helpful in ongoing efforts to evaluate more complex genomic changes within patients distinguished by the presence or absence of specific mutations."

    Learn about Dana-Farber's cBio Center, headed by Chris Sander, PhD, co-founder of the computational biology field.

    Hacking our way to discoveries in cancer genomics

    Oncoprint of genomic alterations in lung adenocarcinoma, showing mutations and copy number alterations for EGFR, KRAS and NF1

    During a recent "hackathon" hosted by Dana-Farber at our Boston campus, representatives from four cancer research institutions brainstormed and developed new features for the cBioPortal. In addition to Dana-Farber's Ethan Cerami, PhD, James Lindsay, PhD, and Priti Kumari, the event drew collaborators from Memorial Sloan Kettering Cancer Center (MSK); Toronto's Princess Margaret Cancer Centre; and The Hyve, a Dutch open-source bioinformatics company.

    Hackathon attendees collaborated in developing process improvements to the cBioPortal, including:

    • Data validation
    • New visualization features
    • Better performance