New software platform bridges gap in precision medicine for cancer

University of California at San Francisco (UCSF) 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, personalised 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,'' says 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, says 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 realised without a software platform that brings genomics to the point of care,'' says 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 paediatric 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 Tumour Board, which can recommend customised treatment plans for each patient.

The Tumour 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 says 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 targetted 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 Tumour 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 says 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 Tumour 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 says.

''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 targetted therapy as a first-line treatment,'' McCaleb says. ''And that would be truly powerful.''

Robert Nussbaum, MD, the Holly Smith Distinguished Professor in Science and Medicine and GMI director, says, ''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.''