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

ABSTRACT: 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.

SUBMITTER: Ryu B

PROVIDER: S-EPMC7445611 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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

Ryu Borim B Shin Soo-Yong SY Baek Rong-Min RM Kim Jeong-Whun JW Heo Eunyoung E Kang Inchul I Yang Joshua SungWoo JS Yoo Sooyoung S

Journal of medical Internet research 20200810 8

<h4>Background</h4>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 clinica ...[more]

PMID: 32773368

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Project description:BackgroundElectronic health record (EHR) system users devise workarounds to cope with mismatches between workflows designed in the EHR and preferred workflows in practice. Although workarounds appear beneficial at first sight, they frequently jeopardize patient safety, the quality of care, and the efficiency of care.ObjectiveThis review aims to aid in identifying, analyzing, and resolving EHR workarounds; the Sociotechnical EHR Workaround Analysis (SEWA) framework was published in 2019. Although the framework was based on a large case study, the framework still required theoretical validation, refinement, and enrichment.MethodsA scoping literature review was performed on studies related to EHR workarounds published between 2010 and 2021 in the MEDLINE, Embase, CINAHL, Cochrane, or IEEE databases. A total of 737 studies were retrieved, of which 62 (8.4%) were included in the final analysis. Using an analytic framework, the included studies were investigated to uncover the rationales that EHR users have for workarounds, attributes characterizing workarounds, possible scopes, and types of perceived impacts of workarounds.ResultsThe SEWA framework was theoretically validated and extended based on the scoping review. Extensive support for the pre-existing rationales, attributes, possible scopes, and types of impact was found in the included studies. Moreover, 7 new rationales, 4 new attributes, and 3 new types of impact were incorporated. Similarly, the descriptions of multiple pre-existing rationales for workarounds were refined to describe each rationale more accurately.ConclusionsSEWA is now grounded in the existing body of peer-reviewed empirical evidence on EHR workarounds and, as such, provides a theoretically validated and more complete synthesis of EHR workaround rationales, attributes, possible scopes, and types of impact. The revised SEWA framework can aid researchers and practitioners in a wider range of health care settings to identify, analyze, and resolve workarounds. This will improve user-centered EHR design and redesign, ultimately leading to improved patient safety, quality of care, and efficiency of care.

Project description:ImportanceUnderstanding how the electronic health record (EHR) system changes clinician work, productivity, and well-being is critical. Little is known regarding global variation in patterns of use.ObjectiveTo provide insights into which EHR activities clinicians spend their time doing, the EHR tools they use, the system messages they receive, and the amount of time they spend using the EHR after hours.Design, setting, and participantsThis cross-sectional study analyzed the deidentified metadata of ambulatory care health systems in the US, Canada, Northern Europe, Western Europe, the Middle East, and Oceania from January 1, 2019, to August 31, 2019. All of these organizations used the EHR software from Epic Systems and represented most of Epic Systems's ambulatory customer base. The sample included all clinicians with scheduled patient appointments, such as physicians and advanced practice practitioners.ExposuresClinician EHR use was tracked by deidentified and aggregated metadata across a variety of clinical activities.Main outcomes and measuresDescriptive statistics for clinician EHR use included time spent on clinical activities, note documentation (as measured by the percentage of characters in the note generated by automated or manual data entry source), messages received, and time spent after hours.ResultsA total of 371 health systems were included in the sample, of which 348 (93.8%) were located in the US and 23 (6.2%) were located in other countries. US clinicians spent more time per day actively using the EHR compared with non-US clinicians (mean time, 90.2 minutes vs 59.1 minutes; P < .001). In addition, US clinicians vs non-US clinicians spent significantly more time performing 4 clinical activities: notes (40.7 minutes vs 30.7 minutes; P < .001), orders (19.5 minutes vs 8.75 minutes; P < .001), in-basket messages (12.5 minutes vs 4.80 minutes; P < .001), and clinical review (17.6 minutes vs 14.8 minutes; P = .01). Clinicians in the US composed more automated note text than their non-US counterparts (77.5% vs 60.8% of note text; P < .001) and received statistically significantly more messages per day (33.8 vs 12.8; P < .001). Furthermore, US clinicians used the EHR for a longer time after hours, logging in 26.5 minutes per day vs 19.5 minutes per day for non-US clinicians (P = .01). The median US clinician spent as much time actively using the EHR per day (90.1 minutes) as a non-US clinician in the 99th percentile of active EHR use time per day (90.7 minutes) in the sample. These results persisted after controlling for organizational characteristics, including structure, type, size, and daily patient volume.Conclusions and relevanceThis study found that US clinicians compared with their non-US counterparts spent substantially more time actively using the EHR for a wide range of clinical activities or tasks. This finding suggests that US clinicians have a greater EHR burden that may be associated with nontechnical factors, which policy makers and health system leaders should consider when addressing clinician wellness.

Project description:AimsUnderstanding atypical forms of diabetes (AD) may advance precision medicine, but methods to identify such patients are needed. We propose an electronic health record (EHR)-based algorithmic approach to identify patients who may have AD, specifically those with insulin-sufficient, non-metabolic diabetes, in order to improve feasibility of identifying these patients through detailed chart review.MethodsPatients with likely T2D were selected using a validated machine-learning (ML) algorithm applied to EHR data. "Typical" T2D cases were removed by excluding individuals with obesity, evidence of dyslipidemia, antibody-positive diabetes, or cystic fibrosis. To filter out likely type 1 diabetes (T1D) cases, we applied six additional "branch algorithms," relying on various clinical characteristics, which resulted in six overlapping cohorts. Diabetes type was classified by manual chart review as atypical, not atypical, or indeterminate due to missing information.ResultsOf 114,975 biobank participants, the algorithms collectively identified 119 (0.1%) potential AD cases, of which 16 (0.014%) were confirmed after expert review. The branch algorithm that excluded T1D based on outpatient insulin use had the highest percentage yield of AD (13 of 27; 48.2% yield). Together, the 16 AD cases had significantly lower BMI and higher HDL than either unselected T1D or T2D cases identified by ML algorithms (P<0.05). Compared to the ML T1D group, the AD group had a significantly higher T2D polygenic score (P<0.01) and lower hemoglobin A1c (P<0.01).ConclusionOur EHR-based algorithms followed by manual chart review identified collectively 16 individuals with AD, representing 0.22% of biobank enrollees with T2D. With a maximum yield of 48% cases after manual chart review, our algorithms have the potential to drastically improve efficiency of AD identification. Recognizing patients with AD may inform on the heterogeneity of T2D and facilitate enrollment in studies like the Rare and Atypical Diabetes Network (RADIANT).

Project description:ObjectiveData in electronic health records (EHRs) is being increasingly leveraged for secondary uses, ranging from biomedical association studies to comparative effectiveness. To perform studies at scale and transfer knowledge from one institution to another in a meaningful way, we need to harmonize the phenotypes in such systems. Traditionally, this has been accomplished through expert specification of phenotypes via standardized terminologies, such as billing codes. However, this approach may be biased by the experience and expectations of the experts, as well as the vocabulary used to describe such patients. The goal of this work is to develop a data-driven strategy to (1) infer phenotypic topics within patient populations and (2) assess the degree to which such topics facilitate a mapping across populations in disparate healthcare systems.MethodsWe adapt a generative topic modeling strategy, based on latent Dirichlet allocation, to infer phenotypic topics. We utilize a variance analysis to assess the projection of a patient population from one healthcare system onto the topics learned from another system. The consistency of learned phenotypic topics was evaluated using (1) the similarity of topics, (2) the stability of a patient population across topics, and (3) the transferability of a topic across sites. We evaluated our approaches using four months of inpatient data from two geographically distinct healthcare systems: (1) Northwestern Memorial Hospital (NMH) and (2) Vanderbilt University Medical Center (VUMC).ResultsThe method learned 25 phenotypic topics from each healthcare system. The average cosine similarity between matched topics across the two sites was 0.39, a remarkably high value given the very high dimensionality of the feature space. The average stability of VUMC and NMH patients across the topics of two sites was 0.988 and 0.812, respectively, as measured by the Pearson correlation coefficient. Also the VUMC and NMH topics have smaller variance of characterizing patient population of two sites than standard clinical terminologies (e.g., ICD9), suggesting they may be more reliably transferred across hospital systems.ConclusionsPhenotypic topics learned from EHR data can be more stable and transferable than billing codes for characterizing the general status of a patient population. This suggests that EHR-based research may be able to leverage such phenotypic topics as variables when pooling patient populations in predictive models.

Project description:BackgroundThe predominant implementation paradigm of electronic health record (EHR) systems in low- and middle-income countries (LMICs) relies on standalone system installations at facilities. This implementation approach exacerbates the digital divide, with facilities in areas with inadequate electrical and network infrastructure often left behind. Mobile health (mHealth) technologies have been implemented to extend the reach of digital health, but these systems largely add to the problem of siloed patient data, with few seamlessly interoperating with the EHR systems that are now scaled nationally in many LMICs. Robust mHealth applications that effectively extend EHR systems are needed to improve access, improve quality of care, and ameliorate the digital divide.ObjectiveWe report on the development and scaled implementation of mUzima, an mHealth extension of the most broadly deployed EHR system in LMICs (OpenMRS).MethodsThe "Guidelines for reporting of health interventions using mobile phones: mobile (mHealth) evidence reporting assessment (mERA)" checklist was employed to report on the mUzima application. The World Health Organization (WHO) Principles for Digital Development framework was used as a secondary reference framework. Details of mUzima's architecture, core features, functionalities, and its implementation status are provided to highlight elements that can be adapted in other systems.ResultsmUzima is an open-source, highly configurable Android application with robust features including offline management, deduplication, relationship management, security, cohort management, and error resolution, among many others. mUzima allows providers with lower-end Android smartphones (version 4.4 and above) who work remotely to access historical patient data, collect new data, view media, leverage decision support, conduct store-and-forward teleconsultation, and geolocate clients. The application is supported by an active community of developers and users, with feature priorities vetted by the community. mUzima has been implemented nationally in Kenya, is widely used in Rwanda, and is gaining scale in Uganda and Mozambique. It is disease-agnostic, with current use cases in HIV, cancer, chronic disease, and COVID-19 management, among other conditions. mUzima meets all WHO's Principles of Digital Development, and its scaled implementation success has led to its recognition as a digital global public good and its listing in the WHO Digital Health Atlas.ConclusionsGreater emphasis should be placed on mHealth applications that robustly extend reach of EHR systems within resource-limited settings, as opposed to siloed mHealth applications. This is particularly important given that health information exchange infrastructure is yet to mature in many LMICs. The mUzima application demonstrates how this can be done at scale, as evidenced by its adoption across multiple countries and for numerous care domains.

Dataset Information

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

Publications

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

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