publication date: Jun. 6, 2016
Biden Designates NCI’s Genomic Data Commons
As Foundation of Cancer Moonshot
By Matthew Bin Han Ong
CHICAGO—Vice President Joe Biden June 6 announced the NCI Genomic Data Commons as part of the National Cancer Moonshot Initiative.
The GDC, a $20 million portal that consolidates NCI’s diverse datasets, contains genomic sequences and analyses of tumors, as well as clinical data on enrollment and treatment.
Biden’s announcement—hours before his address at the 2016 annual meeting of the American Society of Clinical Oncology in Chicago—establishes NCI as the leader in a high-stakes debate over who gets to set standards for how health records data should be aggregated and organized (The Cancer Letter, June 3).
While work on the GDC began over two years ago, the initiative is being launched at a time when leading non-profit oncology groups and Big Data enterprises are vying to solve interoperability problems in conducting research and providing clinical guidance, thereby assuming the leading role in Biden’s moonshot. (The Cancer Letter, April 29).
“This is good news in the fight against cancer,” Biden said in the announcement June 6. “With the launch of this new national resource, anyone can freely access raw genomic and clinical data for 12,000 patients—with more records to follow.
“Increasing the pool of researchers who can access data and decreasing the time it takes for them to review and find new patterns in that data is critical to speeding up development of lifesaving treatments for patients.”
The GDC continues the administration’s legacy on opening up data, particularly to support health, the White House said in a fact sheet published June 6.
“This launch marks progress on both the Cancer Moonshot and the President’s Precision Medicine Initiative, which are aimed at enabling individualized care through effective prevention, diagnosis, and therapies,” the White House said. “Today, in support of making research data freely accessible, the Vice President will visit the University of Chicago to mark the public release of NCI’s GDC, a first-of-its-kind public data platform for storing, analyzing, and sharing genomic and associated clinical data on cancer.”
Funded through the Precision Medicine Initiative, the GDC is a subcontract awarded by the NCI’s principal contractor, Leidos Biomedical Research Inc. Leidos also runs the institute’s Frederick National Laboratory for Cancer Research.
Robert Grossman, chief research informatics officer and professor of medicine at the University of Chicago, is leading the project. Grossman recruited the Ontario Institute for Cancer Research to build the GDC’s user interface.
Initially, the GDC will house data from Cancer Genome Characterization Initiative, The Cancer Genome Atlas, Therapeutically Applicable Research to Generate Effective Treatment (TARGET), and The Cancer Cell Line Encyclopedia.
“It’s our hope that Genomic Data Commons will prove pivotal in advancing precision medicine where physicians attempt to tailor therapies to specific characteristics of a particular patient’s cancer,” Biden said at the ASCO annual meeting.“Our aim, the aim of Genomic Data Commons, is for researchers to have information at their fingertips about the relationship between abnormalities and mutations of genes and clinical outcomes.”
Biden’s remarks at ASCO are posted here.
The GDC is a “foundational element” in building a knowledge network for cancer, said NCI Acting Director Doug Lowy and Warren Kibbe, NCI acting deputy director and director of the NCI Center for Biomedical Informatics and Information Technology.
“We want to emphasize that the GDC is the result of a very complex undertaking that has involved years of trial, and sometimes error, to reach fruition,” Lowy and Kibbe wrote in a blog post published June 6 on Medium. “We needed to find a unified, workable data sharing platform that would encompass aspects of basic scientific discovery, molecular characterization of the disease, and clinical discovery, from decades of trials and research studies conducted by cancer researchers throughout the world, into one network that can be used by researchers everywhere.
“The GDC will provide a powerful tool for discovery using cancer genomic and clinical data,” Lowy and Kibbe said. “Once a genomic and clinical dataset has been submitted to the GDC, it’s then available to cancer investigators to identify what genes or other factors are driving a cancer, to determine indicators of a positive therapeutic pathway, and then to design clinical trials involving patients with similar genetic abnormalities so that there can be proof of benefit for any proposed therapy.
“Smarter, faster, bigger may sound reductive for such a complex system, but that’s truly what we are aiming for, and why, as the Vice President noted, the GDC is an integral part of the Cancer Moonshot.”
As a practical matter, it’s unlikely that the moonshot or Biden’s endorsement of the GDC would prevent for-profit and nonprofit groups in oncology from continuing their work.
“The hope is that the GDC will form the basis for a comprehensive knowledge system for cancer,” NCI said in a statement June 6. “GDC researchers will be able to integrate genetic and clinical data, such as cancer imaging and histological data, with information on the molecular profiles of tumors as well as treatment response. From this perspective, the GDC would become an important resource for generating potentially actionable and life-changing information that ultimately could be used by doctors and their patients.”
Merck, Bayer Join ASCO’s TAPUR
Biden’s announcement comes over a week after a roundtable discussion at Memorial Sloan Kettering Cancer Center, where he urged leading oncology bioinformatics organizations to collaborate.
“You’re all doing the same thing!” Biden said at the May 26 MSKCC event, specifically referring to ASCO’s CancerLinQ, M2Gen’s ORIEN, and the American Association for Cancer Research’s Project GENIE.
This wasn’t the first time the vice president expressed frustration on the issue. In February, Biden said his role is to help “negotiate some of the transitions that have to take place.” (The Cancer Letter, Feb. 12).
“I listened to them,” Biden said at a Duke University panel Feb. 10. “They’re all doing the same thing. They’re all about to spend hundreds of millions of dollars, well over $1 billion, for them to have their own data collection.
“I understand the way the system is built, and there’s nothing wrong with it, the profit motive is there.”
Though the moonshot comes with uncertain and relatively modest funding—and in the waning weeks of the Obama administration—it has the potential to set standards in bioinformatics and keep data in the public domain.
“With the GDC, NCI has made a major commitment to maintaining long-term storage of cancer genomic data and providing researchers with free access to these data,” NCI’s Lowy said in a statement June 6. “Importantly, the explanatory power of data in the GDC will grow over time as data from more patients are included, and ultimately the GDC will accelerate our efforts in precision medicine.”
It remains to be seen how the moonshot would advance common language and standards in oncology bioinformatics through NCI, said Jonathan Hirsch, founder and president of Syapse, a company that integrates oncology data from EHRs with genomic data.
“We applaud the launch of GDC, which liberates research genomics data generated over the last decade at NCI that had previously been difficult to access and in many different formats,” Hirsch said to The Cancer Letter. “One of the key questions that GDC will need to address is data standards for genomics, and how this research effort will help advance clinical cancer data-sharing efforts.”
On June 2, Syapse launched the Oncology Precision Network, which enables interoperability between 79 hospitals and 800 clinics across 11 states, Hirsch said. Stanford Cancer Institute, Intermountain Healthcare and Providence Health and Services jointly announced the network, which currently has 100,000 patients.
In a related development, ASCO June 6 announced a collaboration with Merck and Bayer, who will provide study drugs at no cost to patients enrolled in the Targeted Agent and Profiling Utilization Registry (TAPUR). Merck and Bayer join six other companies—Astellas, AstraZeneca, Bristol-Myers Squibb, Eli Lilly and Co., Genentech, and Pfizer—in ASCO’s first-ever clinical trial.
Since opening on March 14, 16 participants have enrolled and are receiving study treatment, and 31 more have provided consent and are in, or have completed, the screening process. The companies will provide 17 drugs that yield 15 different targeted therapy options (some of the drugs are used in combination) for participants with advanced solid tumors, multiple myeloma, or B cell non-Hodgkin lymphoma. According to ASCO, the trial is designed to include additional drugs and companies as the trial continues.
TAPUR uses the Syapse Precision Medicine Platform to automate the study workflow, including patient registration, eligibility assessment, providing TAPUR study drug options based on genomic data, drug ordering, data collection, and facilitation of the study’s Molecular Tumor Board review process.