Next-Generation Sequencing-Based Cancer Panel Data Conversion Using International Standards to Implement a Clinical Next-Generation Sequencing Research System: Single-Institution Study.

ABSTRACT: BACKGROUND:The analytical capacity and speed of next-generation sequencing (NGS) technology have been improved. Many genetic variants associated with various diseases have been discovered using NGS. Therefore, applying NGS to clinical practice results in precision or personalized medicine. However, as clinical sequencing reports in electronic health records (EHRs) are not structured according to recommended standards, clinical decision support systems have not been fully utilized. In addition, integrating genomic data with clinical data for translational research remains a great challenge. OBJECTIVE:To apply international standards to clinical sequencing reports and to develop a clinical research information system to integrate standardized genomic data with clinical data. METHODS:We applied the recently published ISO/TS 20428 standard to 367 clinical sequencing reports generated by panel (91 genes) sequencing in EHRs and implemented a clinical NGS research system by extending the clinical data warehouse to integrate the necessary clinical data for each patient. We also developed a user interface with a clinical research portal and an NGS result viewer. RESULTS:A single clinical sequencing report with 28 items was restructured into four database tables and 49 entities. As a result, 367 patients' clinical sequencing data were connected with clinical data in EHRs, such as diagnosis, surgery, and death information. This system can support the development of cohort or case-control datasets as well. CONCLUSIONS:The standardized clinical sequencing data are not only for clinical practice and could be further applied to translational research.

SUBMITTER: Park P 

PROVIDER: S-EPMC7210491 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature