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

Abstract

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.

Designing Interoperable Health Care Services Based on Fast Healthcare Interoperability Resources: Literature Review

“…Table 1 lists the typical profile definitions and the corresponding FHIR foundational resources discussed in the reviewed articles. As shown, these articles cover a wide range of categories, including genomics [10][11][12][13][14], imaging [15][16][17], cancer [18][19][20], diabetes [21,22], COVID-19 [23,24], infections [25], electrocardiography [26], screening [27], and allergy [28].…”

Fast Healthcare Interoperability Resources for Inpatient Deterioration Detection With Time-Series Vital Signs: Design and Implementation Study

“…The implementation guide is a collection of rules applied by FHIR resources [15] that requires a clear explanation of how to solve a particular problem. In the relevant studies on FHIR [16][17][18], each paper develops and discusses a single customized resource profile on a mobile device. Although FHIR can effectively and rapidly improve health care information system interoperability, it still has not proposed an implementation guide for the machine learning application in FHIR implementation guide registry.…”

“…Despite the result that indicated that FHIR can improve the interoperability of health care information systems [26][27][28], existing studies have only developed the resource and profiles. Seong et al [16] demonstrated how quality information regarding clinical next-generation sequencing genomic testing can be exchanged in a standardized format by profiling an FHIR genomic resource and developing an FHIR-based web application that exchanges quality information. Based on the human-centered design methodology, Park et al [17] developed a worker-centered personal health record (PHR) app for occupational health.…”