Clinical Genomic Sequencing Reports in Electronic Health Record Systems Based on International Standards: Implementation Study

HL7 FHIR-based tools and initiatives to support clinical research: a scoping review

OBJECTIVES

The HL7® fast healthcare interoperability resources (FHIR®) specification has emerged as the leading interoperability standard for the exchange of healthcare data. We conducted a scoping review to identify trends and gaps in the use of FHIR for clinical research.

MATERIALS AND METHODS

We reviewed published literature, federally funded project databases, application websites, and other sources to discover FHIR-based papers, projects, and tools (collectively, "FHIR projects") available to support clinical research activities.

RESULTS

Our search identified 203 different FHIR projects applicable to clinical research. Most were associated with preparations to conduct research, such as data mapping to and from FHIR formats (n = 66, 32.5%) and managing ontologies with FHIR (n = 30, 14.8%), or post-study data activities, such as sharing data using repositories or registries (n = 24, 11.8%), general research data sharing (n = 23, 11.3%), and management of genomic data (n = 21, 10.3%). With the exception of phenotyping (n = 19, 9.4%), fewer FHIR-based projects focused on needs within the clinical research process itself.

DISCUSSION

Funding and usage of FHIR-enabled solutions for research are expanding, but most projects appear focused on establishing data pipelines and linking clinical systems such as electronic health records, patient-facing data systems, and registries, possibly due to the relative newness of FHIR and the incentives for FHIR integration in health information systems. Fewer FHIR projects were associated with research-only activities.

CONCLUSION

The FHIR standard is becoming an essential component of the clinical research enterprise. To develop FHIR's full potential for clinical research, funding and operational stakeholders should address gaps in FHIR-based research tools and methods.

Genomic considerations for FHIR®; eMERGE implementation lessons

Structured representation of clinical genetic results is necessary for advancing precision medicine. The Electronic Medical Records and Genomics (eMERGE) Network's Phase III program initially used a commercially developed XML message format for standardized and structured representation of genetic results for electronic health record (EHR) integration. In a desire to move towards a standard representation, the network created a new standardized format based upon Health Level Seven Fast Healthcare Interoperability Resources (HL7® FHIR®), to represent clinical genomics results. These new standards improve the utility of HL7® FHIR® as an international healthcare interoperability standard for management of genetic data from patients. This work advances the establishment of standards that are being designed for broad adoption in the current health information technology landscape.

Fast Healthcare Interoperability Resources (FHIR)-Based Quality Information Exchange for Clinical Next-Generation Sequencing Genomic Testing: Implementation Study

Background

Next-generation sequencing (NGS) technology has been rapidly adopted in clinical practice, with the scope extended to early diagnosis, disease classification, and treatment planning. As the number of requests for NGS genomic testing increases, substantial efforts have been made to deliver the testing results clearly and unambiguously. For the legitimacy of clinical NGS genomic testing, quality information from the process of producing genomic data should be included within the results. However, most reports provide insufficient quality information to confirm the reliability of genomic testing owing to the complexity of the NGS process.

Objective

The goal of this study was to develop a Fast Healthcare Interoperability Resources (FHIR)–based web app, NGS Quality Reporting (NGS-QR), to report and manage the quality of the information obtained from clinical NGS genomic tests.

Methods

We defined data elements for the exchange of quality information from clinical NGS genomic tests, and profiled a FHIR genomic resource to enable information exchange in a standardized format. We then developed the FHIR-based web app and FHIR server to exchange quality information, along with statistical analysis tools implemented with the R Shiny server.

Results

Approximately 1000 experimental data entries collected from the targeted sequencing pipeline CancerSCAN designed by Samsung Medical Center were used to validate implementation of the NGS-QR app using real-world data. The user can share the quality information of NGS genomic testing and verify the quality status of individual samples in the overall distribution.

Conclusions

This study successfully demonstrated how quality information of clinical NGS genomic testing can be exchanged in a standardized format. As the demand for NGS genomic testing in clinical settings increases and genomic data accumulate, quality information can be used as reference material to improve the quality of testing. This app could also motivate laboratories to perform diagnostic tests to provide high-quality genomic data.

The 21st Century Cures Act: A Competitive Apps Market and the Risk of Innovation Blocking

The 21st Century Cures Act and the recently published "final rule" define standardized methods for obtaining electronic copies of electronic health record (EHR) data through application programming interfaces. The rule is meant to create an ecosystem of reusable, substitutable apps that can be built once but run at any hospital system "without special effort." Yet, despite numerous provisions around information blocking in the final rule, there is concern that the business practices that govern EHR vendors and health care organizations in the United States could still stifle innovation. We describe potential app ecosystems that may form. We caution that misaligned incentives may result in anticompetitive behavior and purposefully limited functionality. Closed proprietary ecosystems may result, limiting the value derived from interoperability. The 21st Century Cures Act and final rule are an exciting step in the direction of improved interoperability. However, realizing the vision of a truly interoperable app ecosystem is not predetermined.