Biobanks and electronic medical records: enabling cost-effective research.
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ABSTRACT:
SUBMITTER: Bowton E
PROVIDER: S-EPMC4226414 | biostudies-literature | 2014 Apr
REPOSITORIES: biostudies-literature
Publications
Biobanks and electronic medical records: enabling cost-effective research.
Bowton Erica E Field Julie R JR Wang Sunny S Schildcrout Jonathan S JS Van Driest Sara L SL Delaney Jessica T JT Cowan James J Weeke Peter P Mosley Jonathan D JD Wells Quinn S QS Karnes Jason H JH Shaffer Christian C Peterson Josh F JF Denny Joshua C JC Roden Dan M DM Pulley Jill M JM
Science translational medicine 20140401 234
The use of electronic medical record data linked to biological specimens in health care settings is expected to enable cost-effective and rapid genomic analyses. Here, we present a model that highlights potential advantages for genomic discovery and describe the operational infrastructure that facilitated multiple simultaneous discovery efforts. ...[more]
Similar Datasets
Project description:electronic Medical Records & Genomics (eMERGE)
| PRJNA158491 | ENA
Project description:With increasingly ubiquitous electronic medical record (EMR) implementation accelerated by the adoption of the HITECH Act, there is much interest in the secondary use of collected data to improve outcomes and promote personalized medicine. A plethora of research has emerged using EMRs to investigate clinical research questions and assess variations in both treatments and outcomes. However, whether because of genuine complexities of modeling disease physiology or because of practical problems regarding data capture, data accuracy, and data completeness, the state of current EMR research is challenging and gives rise to concerns regarding study accuracy and reproducibility. This work explores challenges in how different experimental design decisions can influence results using a specific example of breast cancer patients undergoing excision and reconstruction surgeries from EMRs in an academic hospital and the Veterans Health Administration (VHA) We discuss emerging strategies that will mitigate these limitations, including data sharing, application of natural language processing, and improved EMR user design.
| S-EPMC5933881 | biostudies-literature
Project description:BackgroundIn South Korea, most graduated medical students undertake a 1-year internship before beginning residency and specialization. Interns usually work in a tertiary hospital and rotate between different, randomly assigned departments to be exposed to different medical specialties. Their jobs are mostly simple and repetitive but are still essential for the patient care process. However, owing to the lack of experience and overwhelming workload, interns at tertiary hospitals in South Korea are usually inefficient, often delaying the entire clinical process. Health care providers have widely adopted mobile electronic medical records (mEMRs) as they have been shown to improve workflow efficiency.ObjectiveThis study investigates the association between the frequency of mEMR usage and the clinical task completion interval time among interns in a tertiary hospital.MethodsThis mixed methods study was conducted at the Samsung Medical Center, Seoul, South Korea. Interns who worked at the Samsung Medical Center from March 2018 to February 2019 were included. The hospital electronic medical record (EMR) system known as DARWIN (Data Analysis and Research Window for Integrated kNowledge) was launched with PC and mobile. Both versions are actively used in hospitals by personnel in various positions. We collected the log data from the mEMR server and the intern clinical task time-series data from the EMR server. Interns can manage the process of identifying patients, assigning the clinical task, finishing the requested clinical intern tasks, etc, through the use of the mEMR system. We compared the clinical task completion interval among 4 groups of interns divided by the mEMR frequency quantile. Then, System Usability Score (SUS) questionnaires and semistructured interviews were conducted.ResultsThe regular mEMR users were defined as those who logged in more than once a day on average and used the mEMR until the level after login. Among a total of 87 interns, 84 used the mEMR to verify the requested clinical tasks. The most frequently used item was "Intern task list." Analysis of the 4 intern groups revealed an inverse relationship between the median time of the task completion interval and the frequency of mEMR use. Correlation analysis showed that the intern task completion time interval had a significant inverse relationship with the individual frequency of mEMR usage (coefficient=-0.27; 95% CI -0.46 to -0.04; P=.02). In the additional survey, the mean SUS value was 81.67, which supported the results of the data analysis.ConclusionsOur findings suggest that frequent mEMR use is associated with improved work efficiency in hospital interns with good usability of the mEMR. Such finding supports the idea that the use of mEMR improves the effectiveness and workflow efficiency of interns working in hospitals and, more generally, in the context of health care.
| S-EPMC7772071 | biostudies-literature
Project description:The use of electronic medical record (EMR) data is necessary to improve clinical research efficiency. However, it is not easy to identify patients who meet research eligibility criteria and collect the necessary information from EMRs because the data collection process must integrate various techniques, including the development of a data warehouse and translation of eligibility criteria into computable criteria. This research aimed to demonstrate an electronic medical records retrieval system (ERS) and an example of a hospital-based cohort study that identified both patients and exposure with an ERS. We also evaluated the feasibility and usefulness of the method. The system was developed and evaluated. In total, 800 000 cases of clinical information stored in EMRs at our hospital were used. The feasibility and usefulness of the ERS, the method to convert text from eligible criteria to computable criteria, and a confirmation method to increase research data accuracy. To comprehensively and efficiently collect information from patients participating in clinical research, we developed an ERS. To create the ERS database, we designed a multidimensional data model optimised for patient identification. We also devised practical methods to translate narrative eligibility criteria into computable parameters. We applied the system to an actual hospital-based cohort study performed at our hospital and converted the test results into computable criteria. Based on this information, we identified eligible patients and extracted data necessary for confirmation by our investigators and for statistical analyses with our ERS. We propose a pragmatic methodology to identify patients from EMRs who meet clinical research eligibility criteria. Our ERS allowed for the efficient collection of information on the eligibility of a given patient, reduced the labour required from the investigators and improved the reliability of the results.
| S-EPMC3533000 | biostudies-literature
Project description:BACKGROUND:Recent legislation in the US requires that all medical records become electronic over the next decade. In addition, ongoing developments in patient-oriented care, most notably with the advent of health social networking and personal health records, provide a plethora of new information sources for research. CONTENT:Electronic health records (EHRs) show great potential for use in observational studies to examine drug safety via pharmacovigiliance methods that can find adverse drug events as well as expand drug safety profiles. EHRs also show promise for head-to-head comparative effectiveness trials and could play a critical role in secondary and tertiary diabetes prevention efforts. A growing subset of EHRs, personal health records (PHRs), opens up the possibility of engaging patients in their care, as well as new opportunities for participatory research and personalized medicine. Organizations nationwide, from providers to employers, are already investing heavily in PHR systems. Additionally, the explosive use of online social networking sites and mobile technologies will undoubtedly play a role in future research efforts by making available a veritable flood of information, such as real-time exercise monitoring, to health researchers. SUMMARY:The future confluence of health information technologies will enable researchers and clinicians to reveal novel therapies and insights into treatments and disease management, as well as environmental and genomic interactions, at an unprecedented population scale.
| S-EPMC7534103 | biostudies-literature
Project description:BACKGROUND:Electronic medical records (EMRs) contain a wealth of information that can support data-driven decision making in health care policy design and service planning. Although research using EMRs has become increasingly prevalent, challenges such as coding inconsistency, data validity, and lack of suitable measures in important domains still hinder the progress. OBJECTIVE:The objective of this study was to design a structured way to process records in administrative EMR systems for health services research and assess validity in selected areas. METHODS:On the basis of a local hospital EMR system in Singapore, we developed a structured framework for EMR data processing, including standardization and phenotyping of diagnosis codes, construction of cohort with multilevel views, and generation of variables and proxy measures to supplement primary data. Disease complexity was estimated by Charlson Comorbidity Index (CCI) and Polypharmacy Score (PPS), whereas socioeconomic status (SES) was estimated by housing type. Validity of modified diagnosis codes and derived measures were investigated. RESULTS:Visit-level (N=7,778,761) and patient-level records (n=549,109) were generated. The International Classification of Diseases, Tenth Revision, Australian Modification (ICD-10-AM) codes were standardized to the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) with a mapping rate of 87.1%. In all, 97.4% of the ICD-9-CM codes were phenotyped successfully using Clinical Classification Software by Agency for Healthcare Research and Quality. Diagnosis codes that underwent modification (truncation or zero addition) in standardization and phenotyping procedures had the modification validated by physicians, with validity rates of more than 90%. Disease complexity measures (CCI and PPS) and SES were found to be valid and robust after a correlation analysis and a multivariate regression analysis. CCI and PPS were correlated with each other and positively correlated with health care utilization measures. Larger housing type was associated with lower government subsidies received, suggesting association with higher SES. Profile of constructed cohorts showed differences in disease prevalence, disease complexity, and health care utilization in those aged above 65 years and those aged 65 years or younger. CONCLUSIONS:The framework proposed in this study would be useful for other researchers working with EMR data for health services research. Further analyses would be needed to better understand differences observed in the cohorts.
| S-EPMC6320424 | biostudies-other
Project description:Post-market medical device surveillance is a challenge facing manufacturers, regulatory agencies, and health care providers. Electronic health records are valuable sources of real-world evidence for assessing device safety and tracking device-related patient outcomes over time. However, distilling this evidence remains challenging, as information is fractured across clinical notes and structured records. Modern machine learning methods for machine reading promise to unlock increasingly complex information from text, but face barriers due to their reliance on large and expensive hand-labeled training sets. To address these challenges, we developed and validated state-of-the-art deep learning methods that identify patient outcomes from clinical notes without requiring hand-labeled training data. Using hip replacements-one of the most common implantable devices-as a test case, our methods accurately extracted implant details and reports of complications and pain from electronic health records with up to 96.3% precision, 98.5% recall, and 97.4% F1, improved classification performance by 12.8-53.9% over rule-based methods, and detected over six times as many complication events compared to using structured data alone. Using these additional events to assess complication-free survivorship of different implant systems, we found significant variation between implants, including for risk of revision surgery, which could not be detected using coded data alone. Patients with revision surgeries had more hip pain mentions in the post-hip replacement, pre-revision period compared to patients with no evidence of revision surgery (mean hip pain mentions 4.97 vs. 3.23; t?=?5.14; p?<?0.001). Some implant models were associated with higher or lower rates of hip pain mentions. Our methods complement existing surveillance mechanisms by requiring orders of magnitude less hand-labeled training data, offering a scalable solution for national medical device surveillance using electronic health records.
| S-EPMC6761113 | biostudies-literature
Project description:Background/objectivesPragmatic trials are increasingly used to study the implementation of weight loss interventions in real-world settings. This study compared researcher-measured body weights versus electronic medical record (EMR)-derived body weights from a pragmatic trial conducted in an underserved patient population.Subjects/methodsThe PROPEL trial randomly allocated 18 clinics to usual care (UC) or to an intensive lifestyle intervention (ILI) designed to promote weight loss. Weight was measured by trained technicians at baseline and at 6, 12, 18, and 24 months. A total of 11 clinics (6 UC/5 ILI) with 577 enrolled patients also provided EMR data (n = 561), which included available body weights over the period of the trial.ResultsThe total number of assessments were 2638 and 2048 for the researcher-measured and EMR-derived body weight values, respectively. The correlation between researcher-measured and EMR-derived body weights was 0.988 (n = 1 939; p < 0.0001). The mean difference between the EMR and researcher weights (EMR-researcher) was 0.63 (2.65 SD) kg, and a Bland-Altman graph showed good agreement between the two data collection methods; the upper and lower boundaries of the 95% limits of agreement are -4.65 kg and +5.91 kg, and 71 (3.7%) of the values were outside the limits of agreement. However, at 6 months, percent weight loss in the ILI compared to the UC group was 7.3% using researcher-measured data versus 5.5% using EMR-derived data. At 24 months, the weight loss maintenance was 4.6% using the technician-measured data versus 3.5% using EMR-derived data.ConclusionAt the group level, body weight data derived from researcher assessments and an EMR showed good agreement; however, the weight loss difference between ILI and UC was blunted when using EMR data. This suggests that weight loss studies that rely on EMR data may require larger sample sizes to detect significant effects.Clinical trial registrationClinicalTrials.gov number NCT02561221.
| S-EPMC9329211 | biostudies-literature
Project description:OBJECTIVES:To assess patients' preferred method of consent for the use of information from electronic medical records for research. DESIGN:Interviews and a structured survey of patients in practices with electronic medical records. SETTING:Family practices in southern Ontario, Canada. PARTICIPANTS:123 patients: 17 were interviewed and 106 completed a survey. MAIN OUTCOME MEASURES:Patients' opinions and concerns on use of information from their medical records for research and their preferences for method of consent. RESULTS:Most interviewees were willing to allow the use of their information for research purposes, although the majority preferred that consent was sought first. The seeking of consent was considered an important element of respect for the individual. Most interviewees made little distinction between identifiable and anonymised data. Research sponsored by private insurance firms generated the greatest concern, and research sponsored by foundation the least. Sponsorship by drug companies evoked negative responses during interview and positive responses in the survey. CONCLUSIONS:Patients are willing to allow information from their medical records to be used for research, but most prefer to be asked for consent either verbally or in writing.
| S-EPMC148897 | biostudies-literature
Project description:ObjectivesElectronic health records (EHR) are commonly used for the identification of novel risk factors for disease, often referred to as an association study. A major challenge to EHR-based association studies is phenotyping error in EHR-derived outcomes. A manual chart review of phenotypes is necessary for unbiased evaluation of risk factor associations. However, this process is time-consuming and expensive. The objective of this paper is to develop an outcome-dependent sampling approach for designing manual chart review, where EHR-derived phenotypes can be used to guide the selection of charts to be reviewed in order to maximize statistical efficiency in the subsequent estimation of risk factor associations.Materials and methodsAfter applying outcome-dependent sampling, an augmented estimator can be constructed by optimally combining the chart-reviewed phenotypes from the selected patients with the error-prone EHR-derived phenotype. We conducted simulation studies to evaluate the proposed method and applied our method to data on colon cancer recurrence in a cohort of patients treated for a primary colon cancer in the Kaiser Permanente Washington (KPW) healthcare system.ResultsSimulations verify the coverage probability of the proposed method and show that, when disease prevalence is less than 30%, the proposed method has smaller variance than an existing method where the validation set for chart review is uniformly sampled. In addition, from design perspective, the proposed method is able to achieve the same statistical power with 50% fewer charts to be validated than the uniform sampling method, thus, leading to a substantial efficiency gain in chart review. These findings were also confirmed by the application of the competing methods to the KPW colon cancer data.DiscussionOur simulation studies and analysis of data from KPW demonstrate that, compared to an existing uniform sampling method, the proposed outcome-dependent method can lead to a more efficient chart review sampling design and unbiased association estimates with higher statistical efficiency.ConclusionThe proposed method not only optimally combines phenotypes from chart review with EHR-derived phenotypes but also suggests an efficient design for conducting chart review, with the goal of improving the efficiency of estimated risk factor associations using EHR data.
| S-EPMC8714286 | biostudies-literature