Large‐scale association analyses based on observational health care databases such as electronic health records have been a topic of increasing interest in the scientific community. However, challenges due to nonprobability sampling and phenotype misclassification associated with the use of these data sources are often ignored in standard analyses. The extent of the bias introduced by ignoring these factors is not well‐characterized. In this paper, we develop an analytic framework for characterizing the bias expected in disease‐gene association studies based on electronic health records when disease status misclassification and the sampling mechanism are ignored. Through a sensitivity analysis approach, this framework can be used to obtain plausible values for parameters of interest given
Tensions in Representing Behavioral Data in an Electronic Health Record
Abstract Taking an action research approach, we engaged in fieldwork with school-based behavioral health care teams to: observe record keeping practices, design and deploy a prototype system addressing key challenges, and reflect on its use. We describe the challenges of capturing behavioral data using both paper and electronic records. Creating records of behaviors requires direct observation, and as a result the record keeping responsibility is challenging to distribute across a care team. Behavioral data on paper must be transferred and prepared for reporting, both inside the organization and to stakeholders outside of the organization. In prototyping a computerized working record, we targeted user needs for capturing details of a behavioral incident in the moment. Challenges persisted through the transition from paper to our prototype, and based on these empirical findings over two years of fieldwork, we present five tensions in representing behavioral data in an electronic health record. These tensions reflect the differences between entering behavioral data into the record for intraorganizational use versus interorganizational use.
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- Award ID(s):
- 1816319
- NSF-PAR ID:
- 10332285
- Date Published:
- Journal Name:
- Computer Supported Cooperative Work (CSCW)
- Volume:
- 30
- Issue:
- 3
- ISSN:
- 0925-9724
- Page Range / eLocation ID:
- 393 to 424
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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summary results from standard analysis. We develop an online tool for performing this sensitivity analysis. Simulations demonstrate promising properties of the proposed method. We apply our approach to study bias in disease‐gene association studies using electronic health record data from the Michigan Genomics Initiative, a longitudinal biorepository effort within The University Michigan health system. -
Background Acute respiratory failure is generally treated with invasive mechanical ventilation or noninvasive respiratory support strategies. The efficacies of the various strategies are not fully understood. There is a need for accurate therapy-based phenotyping for secondary analyses of electronic health record data to answer research questions regarding respiratory management and outcomes with each strategy. Objective The objective of this study was to address knowledge gaps related to ventilation therapy strategies across diverse patient populations by developing an algorithm for accurate identification of patients with acute respiratory failure. To accomplish this objective, our goal was to develop rule-based computable phenotypes for patients with acute respiratory failure using remotely monitored intensive care unit (tele-ICU) data. This approach permits analyses by ventilation strategy across broad patient populations of interest with the ability to sub-phenotype as research questions require. Methods Tele-ICU data from ≥200 hospitals were used to create a rule-based algorithm for phenotyping patients with acute respiratory failure, defined as an adult patient requiring invasive mechanical ventilation or a noninvasive strategy. The dataset spans a wide range of hospitals and ICU types across all US regions. Structured clinical data, including ventilation therapy start and stop times, medication records, and nurse and respiratory therapy charts, were used to define clinical phenotypes. All adult patients of any diagnoses with record of ventilation therapy were included. Patients were categorized by ventilation type, and analysis of event sequences using record timestamps defined each phenotype. Manual validation was performed on 5% of patients in each phenotype. Results We developed 7 phenotypes: (0) invasive mechanical ventilation, (1) noninvasive positive-pressure ventilation, (2) high-flow nasal insufflation, (3) noninvasive positive-pressure ventilation subsequently requiring intubation, (4) high-flow nasal insufflation subsequently requiring intubation, (5) invasive mechanical ventilation with extubation to noninvasive positive-pressure ventilation, and (6) invasive mechanical ventilation with extubation to high-flow nasal insufflation. A total of 27,734 patients met our phenotype criteria and were categorized into these ventilation subgroups. Manual validation of a random selection of 5% of records from each phenotype resulted in a total accuracy of 88% and a precision and recall of 0.8789 and 0.8785, respectively, across all phenotypes. Individual phenotype validation showed that the algorithm categorizes patients particularly well but has challenges with patients that require ≥2 management strategies. Conclusions Our proposed computable phenotyping algorithm for patients with acute respiratory failure effectively identifies patients for therapy-focused research regardless of admission diagnosis or comorbidities and allows for management strategy comparisons across populations of interest.more » « less
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Abstract Background Social and behavioral determinants of health (SBDH) are environmental and behavioral factors that often impede disease management and result in sexually transmitted infections. Despite their importance, SBDH are inconsistently documented in electronic health records (EHRs) and typically collected only in an unstructured format. Evidence suggests that structured data elements present in EHRs can contribute further to identify SBDH in the patient record. Objective Explore the automated inference of both the presence of SBDH documentation and individual SBDH risk factors in patient records. Compare the relative ability of clinical notes and structured EHR data, such as laboratory measurements and diagnoses, to support inference. Methods We attempt to infer the presence of SBDH documentation in patient records, as well as patient status of 11 SBDH, including alcohol abuse, homelessness, and sexual orientation. We compare classification performance when considering clinical notes only, structured data only, and notes and structured data together. We perform an error analysis across several SBDH risk factors. Results Classification models inferring the presence of SBDH documentation achieved good performance (F1 score: 92.7–78.7; F1 considered as the primary evaluation metric). Performance was variable for models inferring patient SBDH risk status; results ranged from F1 = 82.7 for LGBT (lesbian, gay, bisexual, and transgender) status to F1 = 28.5 for intravenous drug use. Error analysis demonstrated that lexical diversity and documentation of historical SBDH status challenge inference of patient SBDH status. Three of five classifiers inferring topic-specific SBDH documentation and 10 of 11 patient SBDH status classifiers achieved highest performance when trained using both clinical notes and structured data. Conclusion Our findings suggest that combining clinical free-text notes and structured data provide the best approach in classifying patient SBDH status. Inferring patient SBDH status is most challenging among SBDH with low prevalence and high lexical diversity.more » « less
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Abstract Objective Modern healthcare data reflect massive multi-level and multi-scale information collected over many years. The majority of the existing phenotyping algorithms use case–control definitions of disease. This paper aims to study the time to disease onset and progression and identify the time-varying risk factors that drive them. Materials and Methods We developed an algorithmic approach to phenotyping the incidence of diseases by consolidating data sources from the UK Biobank (UKB), including primary care electronic health records (EHRs). We focused on defining events, event dates, and their censoring time, including relevant terms and existing phenotypes, excluding generic, rare, or semantically distant terms, forward-mapping terminology terms, and expert review. We applied our approach to phenotyping diabetes complications, including a composite cardiovascular disease (CVD) outcome, diabetic kidney disease (DKD), and diabetic retinopathy (DR), in the UKB study. Results We identified 49 049 participants with diabetes. Among them, 1023 had type 1 diabetes (T1D), and 40 193 had type 2 diabetes (T2D). A total of 23 833 diabetes subjects had linked primary care records. There were 3237, 3113, and 4922 patients with CVD, DKD, and DR events, respectively. The risk prediction performance for each outcome was assessed, and our results are consistent with the prediction area under the ROC (receiver operating characteristic) curve (AUC) of standard risk prediction models using cohort studies. Discussion and Conclusion Our publicly available pipeline and platform enable streamlined curation of incidence events, identification of time-varying risk factors underlying disease progression, and the definition of a relevant cohort for time-to-event analyses. These important steps need to be considered simultaneously to study disease progression.more » « less
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Recent scientific and policy initiatives frame clinical settings as sites for intervening upon inequality. Electronic health records and data analytic technologies offer opportunity to record standard data on education, employment, social support, and race-ethnicity, and numerous audiences expect biomedicine to redress social determinants based on newly available data. However, little is known on how health practitioners and institutional actors view data standardization in relation to inequity. This article examines a public safety-net health system’s expansion of race, ethnicity, and language data collection, drawing on 10 months of ethnographic fieldwork and 32 qualitative interviews with providers, clinic staff, data scientists, and administrators. Findings suggest that electronic data capture institutes a decontextualized racialization within biomedicine as health practitioners and data workers rely on biological, cultural, and social justifications for collecting racial data. This demonstrates a critical paradox of stratified biomedicalization: The same data-centered interventions expected to redress injustice may ultimately reinscribe it.
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1007/s10606-021-09402-7
