Abstract
BackgroundNext-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.ObjectiveThe 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.MethodsWe 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.ResultsApproximately 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.ConclusionsThis 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.
Highlights
This study successfully demonstrated how quality information of clinical Next-generation sequencing (NGS) genomic testing can be exchanged in a standardized format
Next-generation sequencing (NGS) technology has been rapidly adopted in clinical practice, with the scope extended to early diagnosis, disease classification, and treatment planning [1,2,3]
In the dashboard user interface (UI), genomic resources in the Fast Healthcare Interoperability Resources (FHIR) server are compiled using the GET method to display the summary of data such as the total number of genomic tests and the number of tests based on the year and specimen type for the complete genomic test results
Summary
Next-generation sequencing (NGS) technology has been rapidly adopted in clinical practice, with the scope extended to early diagnosis, disease classification, and treatment planning [1,2,3]. To implement clinical NGS applications, health care providers operate their own NGS laboratories or request genomic tests to external laboratories. The NGS genomic testing reports provide information regarding genomic variations and related data. As the number of requests for NGS genomic testing increases, considerable efforts have been made to deliver the testing results clearly and unambiguously [6,7,8,9,10]. 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. Most reports provide insufficient quality information to confirm the reliability of genomic testing owing to the complexity of the NGS process
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