Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Republic of Korea.
Smart Healthcare Research Institute, Samsung Medical Center, Seoul, Republic of Korea.
J Med Internet Res. 2021 Apr 28;23(4):e26261. doi: 10.2196/26261.
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.
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.
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.
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.
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.
下一代测序（NGS）技术已在临床实践中迅速采用，其应用范围扩展到早期诊断、疾病分类和治疗计划。随着对 NGS 基因组测试请求数量的增加，已经做出了大量努力来清晰、明确地提供测试结果。为了保证临床 NGS 基因组测试的合法性，应该在结果中包含产生基因组数据过程中的质量信息。然而，由于 NGS 过程的复杂性，大多数报告提供的质量信息不足以确认基因组测试的可靠性。
本研究旨在开发一个基于 Fast Healthcare Interoperability Resources（FHIR）的网络应用程序 NGS Quality Reporting（NGS-QR），用于报告和管理从临床 NGS 基因组测试中获得的质量信息。
我们定义了用于交换临床 NGS 基因组测试质量信息的数据元素，并对 FHIR 基因组资源进行了配置，以实现标准化格式的信息交换。然后，我们开发了基于 FHIR 的网络应用程序和 FHIR 服务器来交换质量信息，并使用 R Shiny 服务器实现了统计分析工具。
使用三星医疗中心设计的靶向测序管道 CancerSCAN 收集的大约 1000 个实验数据条目，用于使用真实数据验证 NGS-QR 应用程序的实现。用户可以共享 NGS 基因组测试的质量信息，并验证单个样本在整体分布中的质量状态。
本研究成功展示了如何以标准化格式交换临床 NGS 基因组测试的质量信息。随着临床环境中对 NGS 基因组测试的需求增加和基因组数据的积累，质量信息可以作为参考材料来提高测试质量。该应用程序还可以激励实验室进行诊断测试，以提供高质量的基因组数据。
