scholarly journals Clinical Genomic Sequencing Reports in Electronic Health Record Systems Based on International Standards: Implementation Study

10.2196/15040 ◽  
2020 ◽  
Vol 22 (8) ◽  
pp. e15040 ◽  
Author(s):  
Borim Ryu ◽  
Soo-Yong Shin ◽  
Rong-Min Baek ◽  
Jeong-Whun Kim ◽  
Eunyoung Heo ◽  
...  
Keyword(s):  
Electronic Health Record ◽  
Technical Specification ◽  
Genomic Data ◽  
International Standards ◽  
Practical Implementation ◽  
Genomic Sequencing ◽  
Health Record ◽  
Sequencing Data ◽  
Genomic Test ◽  
Electronic Health

Background To implement standardized machine-processable clinical sequencing reports in an electronic health record (EHR) system, the International Organization for Standardization Technical Specification (ISO/TS) 20428 international standard was proposed for a structured template. However, there are no standard implementation guidelines for data items from the proposed standard at the clinical site and no guidelines or references for implementing gene sequencing data results for clinical use. This is a significant challenge for implementation and application of these standards at individual sites. Objective This study examines the field utilization of genetic test reports by designing the Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) for genomic data elements based on the ISO/TS 20428 standard published as the standard for genomic test reports. The goal of this pilot is to facilitate the reporting and viewing of genomic data for clinical applications. FHIR Genomics resources predominantly focus on transmitting or representing sequencing data, which is of less clinical value. Methods In this study, we describe the practical implementation of ISO/TS 20428 using HL7 FHIR Genomics implementation guidance to efficiently deliver the required genomic sequencing results to clinicians through an EHR system. Results We successfully administered a structured genomic sequencing report in a tertiary hospital in Korea based on international standards. In total, 90 FHIR resources were used. Among 41 resources for the required fields, 26 were reused and 15 were extended. For the optional fields, 28 were reused and 21 were extended. Conclusions To share and apply genomic sequencing data in both clinical practice and translational research, it is essential to identify the applicability of the standard-based information system in a practical setting. This prototyping work shows that reporting data from clinical genomics sequencing can be effectively implemented into an EHR system using the existing ISO/TS 20428 standard and FHIR resources.

scholarly journals Clinical Genomic Sequencing Reports in Electronic Health Record Systems Based on International Standards: Implementation Study (Preprint)

2019 ◽  
Author(s):  
Borim Ryu ◽  
Soo-Yong Shin ◽  
Rong-Min Baek ◽  
Jeong-Whun Kim ◽  
Eunyoung Heo ◽  
...  
Keyword(s):  
Electronic Health Record ◽  
Technical Specification ◽  
Genomic Data ◽  
International Standards ◽  
Practical Implementation ◽  
Genomic Sequencing ◽  
Health Record ◽  
Sequencing Data ◽  
Genomic Test ◽  
Electronic Health

BACKGROUND To implement standardized machine-processable clinical sequencing reports in an electronic health record (EHR) system, the International Organization for Standardization Technical Specification (ISO/TS) 20428 international standard was proposed for a structured template. However, there are no standard implementation guidelines for data items from the proposed standard at the clinical site and no guidelines or references for implementing gene sequencing data results for clinical use. This is a significant challenge for implementation and application of these standards at individual sites. OBJECTIVE This study examines the field utilization of genetic test reports by designing the Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) for genomic data elements based on the ISO/TS 20428 standard published as the standard for genomic test reports. The goal of this pilot is to facilitate the reporting and viewing of genomic data for clinical applications. FHIR Genomics resources predominantly focus on transmitting or representing sequencing data, which is of less clinical value. METHODS In this study, we describe the practical implementation of ISO/TS 20428 using HL7 FHIR Genomics implementation guidance to efficiently deliver the required genomic sequencing results to clinicians through an EHR system. RESULTS We successfully administered a structured genomic sequencing report in a tertiary hospital in Korea based on international standards. In total, 90 FHIR resources were used. Among 41 resources for the required fields, 26 were reused and 15 were extended. For the optional fields, 28 were reused and 21 were extended. CONCLUSIONS To share and apply genomic sequencing data in both clinical practice and translational research, it is essential to identify the applicability of the standard-based information system in a practical setting. This prototyping work shows that reporting data from clinical genomics sequencing can be effectively implemented into an EHR system using the existing ISO/TS 20428 standard and FHIR resources.

Genomic Data in the Electronic Health Record

2019 ◽  
Vol 2 (1) ◽  
pp. 21-33 ◽  
Author(s):  
Nephi A. Walton ◽  
Darren K. Johnson ◽  
Thomas N. Person ◽  
Srikar Chamala
Keyword(s):  
Electronic Health Record ◽  
Genomic Data ◽  
Health Record ◽  
Electronic Health

scholarly journals Practical challenges in integrating genomic data into the electronic health record

2013 ◽  
Vol 15 (10) ◽  
pp. 772-778 ◽  
Author(s):  
Abel N. Kho ◽  
Luke V. Rasmussen ◽  
John J. Connolly ◽  
Peggy L. Peissig ◽  
Justin Starren ◽  
...  
Keyword(s):  
Electronic Health Record ◽  
Genomic Data ◽  
Health Record ◽  
Electronic Health

scholarly journals Real-world integration of genomic data into the electronic health record: the PennChart Genomics Initiative

2020 ◽  
Author(s):  
Kelsey S. Lau-Min ◽  
Stephanie Byers Asher ◽  
Jessica Chen ◽  
Susan M. Domchek ◽  
Michael Feldman ◽  
...  
Keyword(s):  
Electronic Health Record ◽  
Real World ◽  
Genomic Data ◽  
Health Record ◽  
Electronic Health

scholarly journals An ancillary genomics system to support the return of pharmacogenomic results

2019 ◽  
Vol 26 (4) ◽  
pp. 306-310 ◽  
Author(s):  
Luke V Rasmussen ◽  
Maureen E Smith ◽  
Federico Almaraz ◽  
Stephen D Persell ◽  
Laura J Rasmussen-Torvik ◽  
...  
Keyword(s):  
Decision Support ◽  
Electronic Health Record ◽  
Clinical Decision Support ◽  
Clinical Decision ◽  
Health Record ◽  
Test Results ◽  
Actionable Knowledge ◽  
Genomic Test ◽  
Electronic Health ◽  
To Receive

AbstractExisting approaches to managing genetic and genomic test results from external laboratories typically include filing of text reports within the electronic health record, making them unavailable in many cases for clinical decision support. Even when structured computable results are available, the lack of adopted standards requires considerations for processing the results into actionable knowledge, in addition to storage and management of the data. Here, we describe the design and implementation of an ancillary genomics system used to receive and process heterogeneous results from external laboratories, which returns a descriptive phenotype to the electronic health record in support of pharmacogenetic clinical decision support.

scholarly journals Comprehensive Characterization of COVID-19 Patients with Repeatedly Positive SARS-CoV-2 Tests Using a Large U.S. Electronic Health Record Database

2021 ◽  
Author(s):  
Xiao Dong ◽  
Yujia Zhou ◽  
Xiao-ou Shu ◽  
Elmer V. Bernstam ◽  
Rebecca Stern ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Electronic Health Record ◽  
Health Record ◽  
Health Consequences ◽  
Sequencing Data ◽  
Testing Data ◽  
Electronic Health ◽  
Comprehensive Characterization

The comprehensive characterization of clinical and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing data for patients with repeatedly positive SARS-CoV-2 tests can help prioritize suspected cases of reinfection for investigation in the absence of sequencing data and for continued surveillance of the potential long-term health consequences of SARS-CoV-2 infection.

scholarly journals Pilot Implementation of Clinical Genomic Data into the Native Electronic Health Record: Challenges of Scalability

ACI Open ◽  
2020 ◽  
Vol 04 (02) ◽  
pp. e162-e166
Author(s):  
Nephi A. Walton ◽  
Darren K. Johnson ◽  
Thomas N. Person ◽  
Jonathon C. Reynolds ◽  
Marc S. Williams
Keyword(s):  
Electronic Health Record ◽  
Large Scale ◽  
Best Practice ◽  
Genomic Data ◽  
Information Resources ◽  
Health Record ◽  
Adoption And Implementation ◽  
Electronic Health ◽  
Pilot Implementation ◽  
Process Solutions

Background Recently, electronic health record (EHR) vendors have allowed for the storage of discrete genomic data within the EHR. With this new capability there remain many challenges related to adoption and implementation. Geisinger has genomic data available for approximately 145,000 patients. With the goal of integrating genetic data into the EHR for the entire sequenced population, we performed a pilot study on a subpopulation to assess the plausibility of large-scale deployment. Objectives Methods Discrete genomic variants were imported into the EHR. Maintenance guidelines and information resources were developed for each genetic condition and best practice alerts were built for pharmacogenomic variants. Weekly calls were held to address barriers to implementation. A list of challenges was maintained throughout the process. Solutions were proposed and categorized into short-term and long-term solutions. Results Challenges were identified and solutions proposed for five discrete areas: Conclusion Scaling the use of genomic data in the EHR requires the engagement of hospitals, open standards communities, laboratories, EHR vendors, and genomic information resources.

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