Sync for Genes Phase 4 Report Identifies Areas for Improvement

Farma Darya

In a report following Phase 4 of the Sync for Genes project, an expert panel described challenges identified and five recommendations that could advance the Sync for Genes program through future phases.

The Sync for Genes program, launched in 2017 by the Office of the National Coordinator for Health Information Technology (ONC) initially in partnership with the National Institutes of Health, is designed to enable the sharing of standardized genomic information among laboratories, providers, patients, and researchers by advancing the development and use of industry supported genomic standards. Progress on this goal is realized through a series of phases that demonstrate how technology can address the challenges to development, implementation, and adoption of genomics standards. The work conducted in Phase 4 furthers the work of earlier phases and was designed to generate insights that will guide Phase 5.

The two Phase 4 demonstration projects centered on providing genomic information for patient care purposes through HL7 FHIR-based genomics APIs.

The first involved care for pediatric brain tumors. The Children’s Hospital of Philadelphia’s (CHOP’s) Center for Data-Driven Discovery in Biomedicine and the University of California, San Francisco (UCSF) are part the Children’s Brain Tumor Network and the Pacific Pediatric Neuro-Oncology Consortium. Existing agreements among all entities were leveraged for sharing clinical genomic testing data. The objective of this demonstration project was for genomic data, including variants, from CHOP patients with brain tumors to be mapped to FHIR and made available to the UCSF team for query and retrieval using a prototype FHIR API.

The State of Utah Newborn Screening Program (NBS) had an overarching goal of expanding screening and to improve the care of newborns at risk of developing gene-mediated diseases. The NBS participated in Sync for Genes Phase 2 to prepare methods to the transfer genomic variant results to healthcare providers. The deliverable for the Phase 2 project was a set of FHIR resources containing genomic variant results, including raw sequence data in Variant Call Format (VCF) that modeled newborns who screened positive for NBS disorders (e.g., cystic fibrosis and phenylketonuria). The Phase 4 project expanded on this work by tailoring a genomic variant report to clinical specialists to whom newborns are referred and by developing a proof-of-concept API to deliver genomic variant results to healthcare providers. Both demonstration sites provided valuable insight for future Sync for Genes demonstration projects and for the Phase 4 recommendations.

Both projects were advanced by open-source support: sandbox environments and a vcf2fhir conversion tool. The project team also learned that much of the bioinformatics workflow to do the clinical sequencing, processing, and variant calling that may be necessary is done in systems completely outside of the electronic health record. More work is needed on integrating genomic information within the clinical record.

A Technical Expert Panel (TEP) identified the following six implementation and adoption challenges:

1. Standards Development and Content. Standards are needed to support the integration and use of genomic data into both clinical and research systems. They are developed by standards development organizations (SDOs), member-supported organizations using a lengthy process that fosters consensus through formal balloting, ensures content is fit for purpose through well-formed use cases and is implementable, and assures ongoing maintenance of the standard.

2.  Implementation of Genomic Standards. The implementation of standards requires technical expertise and domain resources in both the standard development and implementation environments. Implementation, however, requires adoption by potential users to be effective within an organization and can support interoperability only when it is adopted by a community.

3.  Infrastructure to Support Genomics. The complexity of genomic data and its clinical use require specialized infrastructure. Strategies are needed to integrate, manage, and deliver genomic data, test results, and interpretations in ways that are consumable by end users, who may not be trained in genomics.

4. Utilization of Genomic Data. The value of genomic data can only be realized if they can be accessed and used effectively by different end users. Researchers utilize genomic data for discovery of disease mechanisms and treatments; clinicians to diagnosis and treat patients; and patients to understand hereditary risks, make lifestyle choices, and assist with family planning.

5. Educational Needs of Both Patients and Providers. The educational needs of both providers and patients fall into two primary categories: the need for reliable content and for systems that can effectively deliver that content. The TEP focused on delivery of content that is developed elsewhere, primarily by specialty societies, to both clinicians and patients.

6.  Policy Issues. Policies can inadvertently pose challenges to the collection and use of genomic data. For example, regulatory requirements can impose significant burden on the acquisition and exchange of genomic information, as can intellectual property rights of various proprietary systems.

The TEP also made five recommendations to inform future phases of the program:

1. Develop a set of interoperable genomic standards by convening a diverse set of stakeholders to develop and document use cases that include both the research and clinical perspectives and support harmonization of selected standards that result in a set of interoperable genomic standards.
2. Develop a publicly accessible, centrally maintained sandbox environment that includes a server, implemented genomic standards, example data sets, test scripts, and related tooling.
3. Support the implementation and adoption of genomic standards by exploring incentives that could positively influence decision-making related to the implementation and adoption of standards and by providing technical support for potential users.
4. Explore opportunities to improve the delivery of educational content that is developed and maintained by researchers and clinical experts in the field of genetics.

5. Explore opportunities to address gaps in policy.

The report notes that there is much more work to do in order to support interoperable implementation and to address the longer-term needs such as access to reliable educational materials tailored for specific users and to policies that align with the rapidly evolving field of genomics.

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