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Objective: Lung cancer is the most common cause of cancer-related death in the USA. While most patients are diagnosed following symptomatic presentation, no studies have compared symptoms and physical examination signs at or prior to diagnosis from electronic health records (EHRs) in the USA. We aimed to identify symptoms and signs in patients prior to diagnosis in EHR data., Design: Case-control study., Setting: Ambulatory care clinics at a large tertiary care academic health centre in the USA., Participants, Outcomes: We studied 698 primary lung cancer cases in adults diagnosed between 1 January 2012 and 31 December 2019, and 6841 controls matched by age, sex, smoking status and type of clinic. Coded and free-text data from the EHR were extracted from 2 years prior to diagnosis date for cases and index date for controls. Univariate and multivariable conditional logistic regression were used to identify symptoms and signs associated with lung cancer at time of diagnosis, and 1, 3, 6 and 12 months before the diagnosis/index dates., Results: Eleven symptoms and signs recorded during the study period were associated with a significantly higher chance of being a lung cancer case in multivariable analyses. Of these, seven were significantly associated with lung cancer 6 months prior to diagnosis: haemoptysis (OR 3.2, 95% CI 1.9 to 5.3), cough (OR 3.1, 95% CI 2.4 to 4.0), chest crackles or wheeze (OR 3.1, 95% CI 2.3 to 4.1), bone pain (OR 2.7, 95% CI 2.1 to 3.6), back pain (OR 2.5, 95% CI 1.9 to 3.2), weight loss (OR 2.1, 95% CI 1.5 to 2.8) and fatigue (OR 1.6, 95% CI 1.3 to 2.1)., Conclusions: Patients diagnosed with lung cancer appear to have symptoms and signs recorded in the EHR that distinguish them from similar matched patients in ambulatory care, often 6 months or more before diagnosis. These findings suggest opportunities to improve the diagnostic process for lung cancer., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY. Published by BMJ.)

We use prescription of statin medications and prescription of warfarin to explore the capacity of electronic health record data to (1) describe cohorts of patients prescribed these medications and (2) identify cohorts of patients with evidence of adverse events related to prescription of these medications. This study was conducted in the WWAMI region Practice and Research Network (WPRN)., a network of primary care practices across Washington, Wyoming, Alaska, Montana and Idaho DataQUEST, an electronic data-sharing infrastructure. We used electronic health record data to describe cohorts of patients prescribed statin or warfarin medications and reported the proportions of patients with adverse events. Among the 35,445 active patients, 1745 received at least one statin prescription and 301 received at least one warfarin prescription. Only 3 percent of statin patients had evidence of myopathy; 51 patients (17% of those prescribed warfarin) had a bleeding complication. Primary-care electronic health record data can effectively be used to identify patients prescribed specific medications and patients potentially experiencing medication adverse events.

Objective: To provide an open source, interoperable, and scalable data quality assessment tool for evaluation and visualization of completeness and conformance in electronic health record (EHR) data repositories., Materials and Methods: This article describes the tool's design and architecture and gives an overview of its outputs using a sample dataset of 200 000 randomly selected patient records with an encounter since January 1, 2010, extracted from the Research Patient Data Registry (RPDR) at Partners HealthCare. All the code and instructions to run the tool and interpret its results are provided in the Supplementary Appendix., Results: DQe-c produces a web-based report that summarizes data completeness and conformance in a given EHR data repository through descriptive graphics and tables. Results from running the tool on the sample RPDR data are organized into 4 sections: load and test details, completeness test, data model conformance test, and test of missingness in key clinical indicators., Discussion: Open science, interoperability across major clinical informatics platforms, and scalability to large databases are key design considerations for DQe-c. Iterative implementation of the tool across different institutions directed us to improve the scalability and interoperability of the tool and find ways to facilitate local setup., Conclusion: EHR data quality assessment has been hampered by implementation of ad hoc processes. The architecture and implementation of DQe-c offer valuable insights for developing reproducible and scalable data science tools to assess, manage, and process data in clinical data repositories., (© The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association.)

Pragmatic clinical trials (PCTs) are research investigations embedded in health care settings designed to increase the efficiency of research and its relevance to clinical practice. The Health Care Systems Research Collaboratory, initiated by the National Institutes of Health Common Fund in 2010, is a pioneering cooperative aimed at identifying and overcoming operational challenges to pragmatic research. Drawing from our experience, we present 4 broad categories of informatics-related challenges: (1) using clinical data for research, (2) integrating data from heterogeneous systems, (3) using electronic health records to support intervention delivery or health system change, and (4) assessing and improving data capture to define study populations and outcomes. These challenges impact the validity, reliability, and integrity of PCTs. Achieving the full potential of PCTs and a learning health system will require meaningful partnerships between health system leadership and operations, and federally driven standards and policies to ensure that future electronic health record systems have the flexibility to support research., (© The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Objective: Building federated data sharing architectures requires supporting a range of data owners, effective and validated semantic alignment between data resources, and consistent focus on end-users. Establishing these resources requires development methodologies that support internal validation of data extraction and translation processes, sustaining meaningful partnerships, and delivering clear and measurable system utility. We describe findings from two federated data sharing case examples that detail critical factors, shared outcomes, and production environment results., Methods: Two federated data sharing pilot architectures developed to support network-based research associated with the University of Washington's Institute of Translational Health Sciences provided the basis for the findings. A spiral model for implementation and evaluation was used to structure iterations of development and support knowledge share between the two network development teams, which cross collaborated to support and manage common stages., Results: We found that using a spiral model of software development and multiple cycles of iteration was effective in achieving early network design goals. Both networks required time and resource intensive efforts to establish a trusted environment to create the data sharing architectures. Both networks were challenged by the need for adaptive use cases to define and test utility., Conclusion: An iterative cyclical model of development provided a process for developing trust with data partners and refining the design, and supported measureable success in the development of new federated data sharing architectures., (Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.)

ObjectiveBuilding federated data sharing architectures requires supporting a range of data owners, effective and validated semantic alignment between data resources, and consistent focus on end-users. Establishing these resources requires development methodologies that support internal validation of data extraction and translation processes, sustaining meaningful partnerships, and delivering clear and measurable system utility. We describe findings from two federated data sharing case examples that detail critical factors, shared outcomes, and production environment results.MethodsTwo federated data sharing pilot architectures developed to support network-based research associated with the University of Washington's Institute of Translational Health Sciences provided the basis for the findings. A spiral model for implementation and evaluation was used to structure iterations of development and support knowledge share between the two network development teams, which cross collaborated to support and manage common stages.ResultsWe found that using a spiral model of software development and multiple cycles of iteration was effective in achieving early network design goals. Both networks required time and resource intensive efforts to establish a trusted environment to create the data sharing architectures. Both networks were challenged by the need for adaptive use cases to define and test utility.ConclusionAn iterative cyclical model of development provided a process for developing trust with data partners and refining the design, and supported measureable success in the development of new federated data sharing architectures.

Data variability is a commonly observed phenomenon in Electronic Health Records (EHR) data networks. A common question asked in scientific investigations of EHR data is whether the cross-site and -time variability reflects an underlying data quality error at one or more contributing sites versus actual differences driven by various idiosyncrasies in the healthcare settings. Although research analysts and data scientists have commonly used various statistical methods to detect and account for variability in analytic datasets, self service tools to facilitate exploring cross-organizational variability in EHR data warehouses are lacking and could benefit from meaningful data visualizations. DQe-v, an interactive, database-agnostic tool for visually exploring variability in EHR data provides such a solution. DQe-v is built on an open source platform, R statistical software, with annotated scripts and a readme document that makes it fully reproducible. To illustrate and describe functionality of DQe-v, we describe the DQe-v's readme document which includes a complete guide to installation, running the program, and interpretation of the outputs. We also provide annotated R scripts and an example dataset as supplemental materials. DQe-v offers a self service tool to visually explore data variability within EHR datasets irrespective of the data model. GitHub and CIELO offer hosting and distribution of the tool and can facilitate collaboration across any interested community of users as we target improving usability, efficiency, and interoperability. [ABSTRACT FROM AUTHOR]

Context: The widespread adoption of electronic health records (EHRs) offers significant opportunities to conduct research with clinical data from patients outside traditional academic research settings. Because EHRs are designed primarily for clinical care and billing, significant challenges are inherent in the use of EHR data for clinical and translational research. Efficient processes are needed for translational researchers to overcome these challenges. The Data QUEST Coordinating Center (DQCC), which oversees Data QUEST - a primary care EHR data sharing infrastructure - created processes that that guide EHR data extraction for clinical and translational research across these diverse practices. We describe these processes and their application in a case example. Case Description: The DQCC process for developing EHR data extractions not only supports researchers access to EHR data, but supports this access for the purpose of answering scientific questions. This process requires complex coordination across multiple domains, including: 1) understanding the context of EHR data; 2) creating and maintaining a governance structure to support exchange of EHR data; and 3) defining data parameters that are used in order to extract data from the EHR.1,2,3,4We use the Northwest-Alaska Pharmacogenomics Research Network (NWA-PGRN) as a case example that focuses on pharmacogenomic discovery and clinical applications to describe the DQCC process. The NWA-PGRN collaborates with Data QUEST to explore ways to leverage primary care EHR data to support pharmacogenomics research. Findings: Preliminary analysis on the case example shows that initial decisions about how researchers define the study population can influence study outcomes. Major Themes and Conclusions: The experience of the DQCC demonstrates that Coordinating Centers provide expertise in helping researchers understand the context of EHR data, create and maintain governance structures, and guide the definition of parameters for data extractions. This expertise is critical to support research with EHR data. Replication of these strategies through Coordinating Centers may lead to more efficient translational research. Investigators must also consider the impact of initial decisions in defining study groups that may potentially affect outcomes. Acknowledgements We acknowledge the Northwest Alaska Pharmacogenomics Research Network group for supporting the infrastructure and data collection, and Imara West for her assistance in data cleaning and analysis. This project was funded by the National Institute of General Medical Science (U01 GM092676) and the National Center for Advancing Translational Sciences of the National Institutes of Health (UL1TR000423). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health [ABSTRACT FROM AUTHOR]