A dozen years after completion of the Human Genome Project, genomic medicine still faces a major hurdle: Turning genetic test results into concise information that a doctor and patient can act on.

A resolution to that quandary has been surprisingly elusive, but it is critical for precision medicine to fulfill its potential. Kristen McCaleb, PhD, the program manager for the UCSF Genomic Medicine Initiative, has been working with Palo Alto-based software developer Syapse Inc. to do just that.

Researchers like McCaleb can generate reports on a patient’s genomics, but it’s usually just information about what genes are there. “Clinicians need an interpretation of what that means,” McCaleb says. “Does it change a diagnosis? Or affect treatment or other procedures the patient should have?”

[[{"fid":"286","view_mode":"third","fields":{"format":"third","field_image_position[und]":"ucsf-images-wrapping-left"},"type":"media","link_text":null,"attributes":{"alt":"Screen shot of Syapse interface","height":1052,"width":1170,"class":"media-element file-third"}}]]Syapse is bridging that gap by giving clinicians a user-friendly interface that’s integrated into the UC’s APeX electronic medical records system. The Syapse software provides a knowledge base that integrates a de-identified version of each patient’s clinical history with information on the patient’s response to treatments, as well as with data from current scientific literature and from public genetics-, oncology- and clinical trial databases. The result is genomics-guided diagnosis and treatment in specialties ranging from oncology to rare diseases.

Using the cloud-based Syapse, a physician can query a patient's test results in real time and compare them against the latest entries in the knowledge base. The resulting information is displayed for the provider in an easy-to-understand graphical format, with clinical notes and summaries automatically populated in the EMR.

A key element of Syapse is that it’s set up to process test results from the UCSF 500, a collection of more than 500 gene mutations implicated in a range of cancers. Oncologists can call up the test results in Syapse to see at a glance what current or trial therapies have been effective with that tumor type and, from there, trigger a consultation by a newly formed Molecular Tumor Board, a group comprising expert physicians and researchers who can recommend customized treatment plans for each patient.

‘Omic technologies have an impact far beyond cancer care. Applications are being developed for treatment for conditions such as diabetes and infectious disease. McCaleb notes that ‘omics can be of particular help for patients who remain undiagnosed. “There are many people who’ve struggled with symptoms they’ve never been able to find a cause for,” she says. “Many causes of disease can be found by knowing the protein coding regions of the genome.”

McCaleb hopes that, eventually, the system will be able to incorporate other markers, such as metabolic and microbiome data, making ‘omics even more useful.

The partnership with Syapse, which grew out of introductions during UCSF’s 2013 OME Precision Medicine Summit, has allowed McCaleb and her Genomic Medicine Initiative team to create a truly customized software platform that benefits from both clinical and programming expertise. As such, it is one example of the value of outside collaborations and UCSF’s geographic proximity to both Silicon Valley and one of the world’s greatest biotech hubs. “We’re leading the charge and pushing boundaries,” McCaleb says, describing how such industry partnerships stretch UCSF’s capabilities. “If we’re tactical and deploy our resources well, UCSF will become the national center for ‘omic medicine.”