New Software Platform Bridges Gap in Precision Medicine for Cancer

Cloud-Based System Seamlessly Integrates ‘Actionable’ Genomic Insights into Electronic Medical Record

By Pete Farley

UC San Francisco has unveiled a new cloud-based software platform that significantly advances precision medicine for cancer. Built in partnership with Palo Alto-based company Syapse, the new platform seamlessly unites genomic testing and analysis, personalized treatment regimens, and clinical and outcomes data, crucially integrating all of these features directly into UCSF’s Electronic Medical Record (EMR) system.

The project was a collaborative venture of UCSF’s Genomic Medicine Initiative (GMI) and the UCSF Helen Diller Family Comprehensive Cancer Center.

“Many major medical institutions, including UCSF, have long had the science and the technology to generate genomic test results,” said Kristen McCaleb, PhD, program manager for the GMI. “The problem we’ve had is a lack of IT infrastructure to return those results to the clinicians who order the tests in a clearly actionable format. This new platform creates a doctor-friendly report that physicians can use to put genomics into the context of a patient’s clinical history, to receive guidance based on our institution’s best practices, to query for additional information—including outcomes of prior UCSF patients—and, ultimately, to provide better care for their patients.”

Jonathan Hirsch, Syapse president and founder, said that tight integration with APeX, UCSF’s Epic-based EMR, makes the new platform uniquely powerful. “Genomics has the potential to dramatically improve patient care in oncology, but the full promise of precision medicine cannot be realized without a software platform that brings genomics to the point of care,” said Hirsch. “It is critical that genomic data be integrated with the patient’s medical history and presented to the clinician within the workflow of their EMR.”

Beginning in the spring of 2015, UCSF oncologists will be able to use the new system to order the “UCSF 500,” a panel of more than 500 gene mutations that have been implicated in a range of cancers, with tools built directly into their adult and pediatric patients’ EMRs. When UCSF 500 test results are available, they will automatically appear in a Syapse-powered window in the EMR, and from there, physicians will be able to trigger consultation by a newly formed Molecular Tumor Board, which can recommend customized treatment plans for each patient.

The Tumor Board’s recommendations are recorded in Syapse alongside the physician’s decisions, and the patient’s clinical course will be continuously tracked, with the resulting information, including clinical notes and summaries, displayed to the physician in an easy-to-understand graphical format in the EMR.

Hirsch said that the assembly of the UCSF 500 wouldn’t have been possible without the energetic involvement of UCSF’s medical oncologists. “The clinicians at UCSF have been highly involved in defining what ‘actionability’ truly is—knowing which genomic alterations in which cancer types can be best treated with targeted therapies. They’re sitting down and doing the hard work of creating a cancer genomics knowledge-base, which has allowed Syapse to design automated clinical decision support that reflects UCSF’s leading oncology care.”

Because the Syapse system is cloud-based, implemented on Amazon Web Services (AWS), physicians and members of the Molecular Tumor Board can query a patient’s test results in real time against the latest entries in UCSF’s knowledge-base, which also draws from public genetics, oncology, and clinical trial databases, as well as the current scientific literature. Hirsch said AWS was selected for its robust security, support for medical privacy-law compliance, scalability, and stability.

A de-identified version of each patient’s clinical history from APeX and information on how patients respond to treatments is simultaneously added to a dedicated clinical research knowledge-base within Syapse, so future recommendations of the Molecular Tumor Board for any patient’s case will always be informed by the latest clinical experience. Because APeX is based on Epic, a widely used EMR system, the new platform is easily scalable, and could easily capture clinical data from many medical centers in a consistent, easily accessible form, Hirsch said.

“Our top priority is benefitting our patients today, but if we can begin to collect and leverage the knowledge we gain from each positive patient outcome, and combine our experience with that of others doing similar work worldwide, future patients may be able to sidestep conventional therapies and go directly to the best targeted therapy as a first-line treatment,” McCaleb said. “And that would be truly powerful.”

Robert Nussbaum, MD, the Holly Smith Distinguished Professor in Science and Medicine and GMI director, said, “This collaboration is just one example of what the GMI is doing to bring genomics to bear on clinical medicine. The partnership is the product of a large multidisciplinary team of oncologists, molecular pathologists, and IT specialists. We are excited with the results and look forward to using it to improve the care of our patients.”

UCSF is the nation's leading university exclusively focused on health. Now celebrating the 150th anniversary of its founding as a medical college, UCSF is dedicated to transforming health worldwide through advanced biomedical research, graduate-level education in the life sciences and health professions, and excellence in patient care. It includes top-ranked graduate schools of dentistry, medicine, nursing and pharmacy; a graduate division with world-renowned programs in the biological sciences, a preeminent biomedical research enterprise and top-tier hospitals, UCSF Medical Center and UCSF Benioff Children's Hospitals.