With Pilots Done, What’s Next for Sync for Genes?

Dec. 1, 2017
Sync for Genes was established to expedite the use of standards to enable patients’ ability to share their genomics information. What did pilot projects find?

There has been a noteworthy milestone in the “Sync for Genes” effort that was launched to complement the Sync for Science (S4S) project.

A quick reminder: the goal of S4S is to use HL7’s FHIR standard to allow individuals to access their health data and send it to researchers in support of the Precision Medicine Initiative (now dubbed All of Us). Backed by the Office of the National Coordinator for Health IT, Sync for Genes was established to expedite the use of standards to enable and improve patients’ ability to share their genomics information.

Now ONC has published a report based on the findings from the five Sync for Genes pilot projects.

Gil Alterovitz, Ph.D., assistant professor in the Division of Medical Sciences/Computational Health Informatics at Harvard Medical School/Boston Children’s Hospital and co-chair of HL7’s Clinical Genomics Work Group, is leading the Sync for Genes effort.

At the 2016 HL7 Genomics Policy Conference in Washington, D.C., Alterovitz gave a presentation explaining how Sync for Genes would complete the “Ring of FHIR” by enabling genomic data to be shared in the same way that SMART on FHIR apps are starting to ease the sharing of clinical data. Sync for Genes builds upon the S4S pilot program and uses the FHIR Genomics standard developed by the HL7 Clinical Genomics Work Group for reporting clinical genetic and genomic observations, (FHIR Genomics serves as the basis for the specification for the Sync for Genes data format.)

As the first step toward integrating clinical genomics into the point-of-care, Sync for Genes leverages FHIR to communicate information from clinical genomic laboratories in a format for universal use across medicine.

So what did the pilots explore and what are the next steps? Here are some highlights from the report:

FHIR Queries: FHIR’s query capability generated great interest. It was noted that FHIR implementers do not have to make all available data elements searchable. The returned results from a query and their format were of interest. Results are returned as a Bundle resource that contains a limited number of results per “page” and further results can be requested as desired. One pilot did see a need for the Bundle to contain just pointers to other resources rather than the resources themselves because of the potentially large volume of data being returned. FHIR’s search capability does not do this currently, but it is worth looking into, possibly by designing certain resource elements as references.

Value Sets: Pilot participants had interest in value sets and how to define and utilize them in FHIR. The Clinical Genomics Work Group can coordinate with future pilots/implementers to define meaningful value sets for use cases and workflows. During this pilot phase, value sets related to publication references, ancestry, and specimen type were discussed. Value sets can be specified for use within FHIR, and FHIR plans to allow value sets to be registered at the FHIR website as a way for a group to maintain a value set.

FHIR Server Functionality: The functionality of FHIR servers, in general, interested the pilots. Details related to storing data on the FHIR server were explored. For instance, the order of operations required when multiple resources reference each other can get complicated, but a resource can always be modified to reference a newly created resource.

Future Work: It is expected that the number of patient sequences done for clinical utility will likely outpace the number of sequenced for research in the coming years. Thus, standards for communicating this information from laboratories for use at point of care, and facilitating its potential secondary use for research, will become increasingly important in the years ahead.

The report suggests that a next step to facilitate real-world use case implementation is to pilot full workflows/business rules as in the HL7 Domain Analysis Model (DAM), while incorporating the findings from the pilot phase into the next round of development of Sync for Genes, FHIR Genomics, and the pilots individually. The report also notes that in some cases, workflows and business rules in any future Sync for Genes activity will need to account for the problem of patient matching. Patient matching can be an issue when transmitting or searching for data about a particular patient. Data systems in different laboratories, clinics, or repositories will assign an identifier to a patient, but often this identifier is not known to any outside system. FHIR itself defines a mechanism to perform patient matching but leaves the matching implementation details open so that any suitable specification can be used.

Another important step is facilitating EHR integration of genomic information from laboratories via FHIR. Pilots could test FHIR Genomics for Genomic Archive and Computer/Communication System integration with EHRs and/or link laboratories with cloud-based system vendors.

Yet another area that needs more work is security, the report notes. It suggests pilot testing on protected health information and guidance on CLIA/HIPAA-related issues and privacy/security via SMART on FHIR. “The privacy and security of genomic data is of vital importance,” it notes. “These have begun to be explored by a number of the pilots. Yet, additional considerations with respect to PHI and workflow integration with CLIA/HIPAA-related guidance for pilots may be beneficial for adoption.”

This is important work and a key element of a new type of healthcare — with the patient at the center — just taking shape now.

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