Accepted for/Published in: JMIR Medical Informatics
Date Submitted: May 15, 2019
Open Peer Review Period: May 21, 2019 - Jul 16, 2019
Date Accepted: Feb 7, 2020
(closed for review but you can still tweet)
NGS-based Cancer Panel Data Conversion using International Standard to implement Clinical NGS Research System: Single Institute Study
ABSTRACT
Background:
The analytical capacity and speed of next generation sequencing (NGS) technology has been improved. Lots of genetic variants correlating with various diseases have been discovered based on 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 standardized, clinical decision support systems have not been fully utilized. In addition, integrating genomic data with clinical data for translational research remains a significant hurdle.
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:
The authors applied the recently published ISO/TS 20428 standard to 367 clinical sequencing reports generated by panel (91 genes) sequencing in EHR and implemented a Clinical NGS Research System (CNRS) by extending the clinical data warehouse to integrate the necessary clinical data for each patient and developed a user interface including clinical research portal, and an e-CRF (electronic-Case Report Form).
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 EHR such as diagnosis, operation, or death information. This system can support development of cohort or case-control datasets as well.
Conclusions:
The standardized clinical sequencing data could be further applied to translational research, not only for clinical practice.
Citation
Request queued. Please wait while the file is being generated. It may take some time.
Copyright
© The authors. All rights reserved. This is a privileged document currently under peer-review/community review (or an accepted/rejected manuscript). Authors have provided JMIR Publications with an exclusive license to publish this preprint on it's website for review and ahead-of-print citation purposes only. While the final peer-reviewed paper may be licensed under a cc-by license on publication, at this stage authors and publisher expressively prohibit redistribution of this draft paper other than for review purposes.