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Building bridges across electronic health record systems through inferred phenotypic topics.

ABSTRACT: OBJECTIVE:Data 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. METHODS:We 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). RESULTS:The 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. CONCLUSIONS:Phenotypic 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.

SUBMITTER: Chen Y

PROVIDER: S-EPMC4464930 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature

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Building bridges across electronic health record systems through inferred phenotypic topics.

Chen You Y Ghosh Joydeep J Bejan Cosmin Adrian CA Bejan Cosmin Adrian CA Gunter Carl A CA Gupta Siddharth S Kho Abel A Liebovitz David D Sun Jimeng J Denny Joshua J Malin Bradley B

Journal of biomedical informatics 20150401

<h4>Objective</h4>Data 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 appr ...[more]

PMID: 25841328

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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:ObjectiveDiscovering subphenotypes of complex diseases can help characterize disease cohorts for investigative studies aimed at developing better diagnoses and treatments. Recent advances in unsupervised machine learning on electronic health record (EHR) data have enabled researchers to discover phenotypes without input from domain experts. However, most existing studies have ignored time and modeled diseases as discrete events. Uncovering the evolution of phenotypes - how they emerge, evolve and contribute to health outcomes - is essential to define more precise phenotypes and refine the understanding of disease progression. Our objective was to assess the benefits of an unsupervised approach that incorporates time to model diseases as dynamic processes in phenotype discovery.MethodsIn this study, we applied a constrained non-negative tensor-factorization approach to characterize the complexity of cardiovascular disease (CVD) patient cohort based on longitudinal EHR data. Through tensor-factorization, we identified a set of phenotypic topics (i.e., subphenotypes) that these patients established over the 10 years prior to the diagnosis of CVD, and showed the progress pattern. For each identified subphenotype, we examined its association with the risk for adverse cardiovascular outcomes estimated by the American College of Cardiology/American Heart Association Pooled Cohort Risk Equations, a conventional CVD-risk assessment tool frequently used in clinical practice. Furthermore, we compared the subsequent myocardial infarction (MI) rates among the six most prevalent subphenotypes using survival analysis.ResultsFrom a cohort of 12,380 adult CVD individuals with 1068 unique PheCodes, we successfully identified 14 subphenotypes. Through the association analysis with estimated CVD risk for each subtype, we found some phenotypic topics such as Vitamin D deficiency and depression, Urinary infections cannot be explained by the conventional risk factors. Through a survival analysis, we found markedly different risks of subsequent MI following the diagnosis of CVD among the six most prevalent topics (p < 0.0001), indicating these topics may capture clinically meaningful subphenotypes of CVD.ConclusionThis study demonstrates the potential benefits of using tensor-decomposition to model diseases as dynamic processes from longitudinal EHR data. Our results suggest that this data-driven approach may potentially help researchers identify complex and chronic disease subphenotypes in precision medicine research.

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).

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Building bridges across electronic health record systems through inferred phenotypic topics.

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Building bridges across electronic health record systems through inferred phenotypic topics.

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