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Kerchberger VE, Peterson JF, Wei WQ. Scanning the medical phenome to identify new diagnoses after recovery from COVID-19 in a US cohort. J Am Med Inform Assoc 2023; 30:233-244. [PMID: 36005898 PMCID: PMC9452157 DOI: 10.1093/jamia/ocac159] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/29/2022] [Accepted: 08/23/2022] [Indexed: 01/20/2023] Open
Abstract
OBJECTIVE COVID-19 survivors are at risk for long-term health effects, but assessing the sequelae of COVID-19 at large scales is challenging. High-throughput methods to efficiently identify new medical problems arising after acute medical events using the electronic health record (EHR) could improve surveillance for long-term consequences of acute medical problems like COVID-19. MATERIALS AND METHODS We augmented an existing high-throughput phenotyping method (PheWAS) to identify new diagnoses occurring after an acute temporal event in the EHR. We then used the temporal-informed phenotypes to assess development of new medical problems among COVID-19 survivors enrolled in an EHR cohort of adults tested for COVID-19 at Vanderbilt University Medical Center. RESULTS The study cohort included 186 105 adults tested for COVID-19 from March 5, 2020 to November 1, 2021; of which 30 088 (16.2%) tested positive. Median follow-up after testing was 412 days (IQR 274-528). Our temporal-informed phenotyping was able to distinguish phenotype chapters based on chronicity of their constituent diagnoses. PheWAS with temporal-informed phenotypes identified increased risk for 43 diagnoses among COVID-19 survivors during outpatient follow-up, including multiple new respiratory, cardiovascular, neurological, and pregnancy-related conditions. Findings were robust to sensitivity analyses, and several phenotypic associations were supported by changes in outpatient vital signs or laboratory tests from the pretesting to postrecovery period. CONCLUSION Temporal-informed PheWAS identified new diagnoses affecting multiple organ systems among COVID-19 survivors. These findings can inform future efforts to enable longitudinal health surveillance for survivors of COVID-19 and other acute medical conditions using the EHR.
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Affiliation(s)
- Vern Eric Kerchberger
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Josh F Peterson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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2
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Sarri G, Bennett D, Debray T, Deruaz‐Luyet A, Soriano Gabarró M, Largent JA, Li X, Liu W, Lund JL, Moga DC, Gokhale M, Rentsch CT, Wen X, Yanover C, Ye Y, Yun H, Zullo AR, Lin KJ. ISPE-Endorsed Guidance in Using Electronic Health Records for Comparative Effectiveness Research in COVID-19: Opportunities and Trade-Offs. Clin Pharmacol Ther 2022; 112:990-999. [PMID: 35170021 PMCID: PMC9087010 DOI: 10.1002/cpt.2560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/02/2022] [Indexed: 11/08/2022]
Abstract
As the scientific research community along with healthcare professionals and decision makers around the world fight tirelessly against the coronavirus disease 2019 (COVID-19) pandemic, the need for comparative effectiveness research (CER) on preventive and therapeutic interventions for COVID-19 is immense. Randomized controlled trials markedly under-represent the frail and complex patients seen in routine care, and they do not typically have data on long-term treatment effects. The increasing availability of electronic health records (EHRs) for clinical research offers the opportunity to generate timely real-world evidence reflective of routine care for optimal management of COVID-19. However, there are many potential threats to the validity of CER based on EHR data that are not originally generated for research purposes. To ensure unbiased and robust results, we need high-quality healthcare databases, rigorous study designs, and proper implementation of appropriate statistical methods. We aimed to describe opportunities and challenges in EHR-based CER for COVID-19-related questions and to introduce best practices in pharmacoepidemiology to minimize potential biases. We structured our discussion into the following topics: (1) study population identification based on exposure status; (2) ascertainment of outcomes; (3) common biases and potential solutions; and (iv) data operational challenges specific to COVID-19 CER using EHRs. We provide structured guidance for the proper conduct and appraisal of drug and vaccine effectiveness and safety research using EHR data for the pandemic. This paper is endorsed by the International Society for Pharmacoepidemiology (ISPE).
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Affiliation(s)
| | - Dimitri Bennett
- Takeda Global Evidence and OutcomesTakeda Pharmaceuticals USA, IncCambridgeMassachusettsUSA
- Center for Clinical Epidemiology and BiostatisticsPerelman School of Medicine at the University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Thomas Debray
- Julius Center for Health Sciences and Primary CareUniversity Medical Centre UtrechtUtrechtThe Netherlands
- Smart Data Analysis and StatisticsUtrechtThe Netherlands
| | - Anouk Deruaz‐Luyet
- Global Epidemiology and Real‐World Evidence CoECorporate Medical AffairsBoehringer Ingelheim International GmbHIngelheim‐am‐RheinGermany
| | - Montse Soriano Gabarró
- Bayer Partnerships and Integrated Evidence Generation OfficeIntegrated Evidence Generation & Business InnovationMedical Affairs & PharmacovigilanceBayer AGBerlinGermany
| | | | - Xiaojuan Li
- Department of Population MedicineHarvard Medical School and Harvard Pilgrim Health Care InstituteBostonMassachusettsUSA
| | - Wei Liu
- Division of EpidemiologyOffice of Surveillance and EpidemiologyCenter for Drug Evaluation and Research, Food and Drug AdministrationSilver SpringMarylandUSA
| | - Jennifer L. Lund
- Department of EpidemiologyGillings School of Global Public HealthUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Daniela C. Moga
- Department of Pharmacy Practice and ScienceCollege of PharmacyUniversity of KentuckyLexingtonKentuckyUSA
| | - Mugdha Gokhale
- Department of EpidemiologyGillings School of Global Public HealthUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
- Department of EpidemiologyMerckWest PointPennsylvaniaUSA
| | - Christopher T. Rentsch
- Faculty of Epidemiology and Population HealthDepartment of Non‐communicable Disease EpidemiologyLondon School of Hygiene & Tropical MedicineLondonUK
- Department of Internal MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Xuerong Wen
- Health OutcomesPharmacy PracticeCollege of PharmacyUniversity of Rhode IslandKinstonRhode IslandUSA
| | | | - Yizhou Ye
- Global Epidemiology, Pharmacovigilance and Patient SafetyAbbVie IncNorth ChicagoIllinoisUSA
| | - Huifeng Yun
- Department of EpidemiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Andrew R. Zullo
- Department of Health Services, Policy, and PracticeBrown University School of Public HealthProvidenceRhode IslandUSA
- Department of EpidemiologyBrown University School of Public HealthProvidenceRhode IslandUSA
- Center of Innovation in Long‐Term Services and SupportsProvidence Veterans Affairs Medical CenterProvidenceRhode IslandUSA
- Department of PharmacyLifespan‐Rhode Island HospitalProvidenceRhode IslandUSA
| | - Kueiyu Joshua Lin
- Brigham and Women’s Hospital and Harvard Medical SchoolBostonMassachusettsUSA
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3
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Xu H, Buckeridge DL, Wang F, Tarczy-Hornoch P. Novel informatics approaches to COVID-19 Research: From methods to applications. J Biomed Inform 2022; 129:104028. [PMID: 35181495 PMCID: PMC8847074 DOI: 10.1016/j.jbi.2022.104028] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 02/10/2022] [Indexed: 10/30/2022]
Affiliation(s)
- Hua Xu
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - David L Buckeridge
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Fei Wang
- Department of Population Health Sciences, Cornell University, New York, NY, USA
| | - Peter Tarczy-Hornoch
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
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4
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Zhou L, Romero N, Martínez-Miranda J, Conejero JA, García-Gómez JM, Sáez C. Subphenotyping of COVID-19 patients at pre-admission towards anticipated severity stratification: an analysis of 778 692 Mexican patients through an age-sex unbiased meta-clustering technique. JMIR Public Health Surveill 2022; 8:e30032. [PMID: 35144239 PMCID: PMC9098229 DOI: 10.2196/30032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 01/29/2022] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
Background The COVID-19 pandemic has led to an unprecedented global health care challenge for both medical institutions and researchers. Recognizing different COVID-19 subphenotypes—the division of populations of patients into more meaningful subgroups driven by clinical features—and their severity characterization may assist clinicians during the clinical course, the vaccination process, research efforts, the surveillance system, and the allocation of limited resources. Objective We aimed to discover age-sex unbiased COVID-19 patient subphenotypes based on easily available phenotypical data before admission, such as pre-existing comorbidities, lifestyle habits, and demographic features, to study the potential early severity stratification capabilities of the discovered subgroups through characterizing their severity patterns, including prognostic, intensive care unit (ICU), and morbimortality outcomes. Methods We used the Mexican Government COVID-19 open data, including 778,692 SARS-CoV-2 population-based patient-level data as of September 2020. We applied a meta-clustering technique that consists of a 2-stage clustering approach combining dimensionality reduction (ie, principal components analysis and multiple correspondence analysis) and hierarchical clustering using the Ward minimum variance method with Euclidean squared distance. Results In the independent age-sex clustering analyses, 56 clusters supported 11 clinically distinguishable meta-clusters (MCs). MCs 1-3 showed high recovery rates (90.27%-95.22%), including healthy patients of all ages, children with comorbidities and priority in receiving medical resources (ie, higher rates of hospitalization, intubation, and ICU admission) compared with other adult subgroups that have similar conditions, and young obese smokers. MCs 4-5 showed moderate recovery rates (81.30%-82.81%), including patients with hypertension or diabetes of all ages and obese patients with pneumonia, hypertension, and diabetes. MCs 6-11 showed low recovery rates (53.96%-66.94%), including immunosuppressed patients with high comorbidity rates, patients with chronic kidney disease with a poor survival length and probability of recovery, older smokers with chronic obstructive pulmonary disease, older adults with severe diabetes and hypertension, and the oldest obese smokers with chronic obstructive pulmonary disease and mild cardiovascular disease. Group outcomes conformed to the recent literature on dedicated age-sex groups. Mexican states and several types of clinical institutions showed relevant heterogeneity regarding severity, potentially linked to socioeconomic or health inequalities. Conclusions The proposed 2-stage cluster analysis methodology produced a discriminative characterization of the sample and explainability over age and sex. These results can potentially help in understanding the clinical patient and their stratification for automated early triage before further tests and laboratory results are available and even in locations where additional tests are not available or to help decide resource allocation among vulnerable subgroups such as to prioritize vaccination or treatments.
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Affiliation(s)
- Lexin Zhou
- Biomedical Data Science Lab, Instituto Universitario de Tecnologías de la Información y Comunicaciones (ITACA), Universitat Politècnica de València (UPV), Valencia, ES
| | - Nekane Romero
- Biomedical Data Science Lab, Instituto Universitario de Tecnologías de la Información y Comunicaciones (ITACA), Universitat Politècnica de València (UPV), Valencia, ES
| | - Juan Martínez-Miranda
- CONACyT - Centro de Investigación Científica y de Educación Superior de Ensenada - CICESE-UT3, Ensenada, MX
| | - J Alberto Conejero
- Instituto Universitario de Matemática Pura y Aplicada (IUMPA), Universitat Politècnica de València, Valencia, ES
| | - Juan M García-Gómez
- Biomedical Data Science Lab, Instituto Universitario de Tecnologías de la Información y Comunicaciones (ITACA), Universitat Politècnica de València (UPV), Valencia, ES
| | - Carlos Sáez
- Biomedical Data Science Lab, Instituto Universitario de Tecnologías de la Información y Comunicaciones (ITACA), Universitat Politècnica de València (UPV), Camino de Vera s/n, Valencia 46022, España, Valencia, ES
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5
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Bejan CA, Cahill KN, Staso PJ, Choi L, Peterson JF, Phillips EJ. DrugWAS: Drug-wide Association Studies for COVID-19 Drug Repurposing. Clin Pharmacol Ther 2021; 110:1537-1546. [PMID: 34314511 PMCID: PMC8426999 DOI: 10.1002/cpt.2376] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/21/2021] [Indexed: 11/16/2022]
Abstract
This study aimed to systematically investigate if any of the available drugs in the electronic health record (EHR) can be repurposed as potential treatment for coronavirus disease 2019 (COVID-19). Based on a retrospective cohort analysis of EHR data, drug-wide association studies (DrugWAS) were performed on 9,748 patients with COVID-19 at Vanderbilt University Medical Center (VUMC). For each drug study, multivariable logistic regression with overlap weighting using propensity score was applied to estimate the effect of drug exposure on COVID-19 disease outcomes. Patient exposure to a drug between 3-months prior to the pandemic and the COVID-19 diagnosis was chosen as the exposure of interest. All-cause of death was selected as the primary outcome. Hospitalization, admission to the intensive care unit, and need for mechanical ventilation were identified as secondary outcomes. Overall, 17 drugs were significantly associated with decreased COVID-19 severity. Previous exposure to two types of 13-valent pneumococcal conjugate vaccines, PCV13 (odds ratio (OR), 0.31, 95% confidence interval (CI), 0.12-0.81 and OR, 0.33, 95% CI, 0.15-0.73), diphtheria toxoid and tetanus toxoid vaccine (OR, 0.38, 95% CI, 0.15-0.93) were significantly associated with a decreased risk of death (primary outcome). Secondary analyses identified several other significant associations showing lower risk for COVID-19 outcomes: acellular pertussis vaccine, 23-valent pneumococcal polysaccharide vaccine (PPSV23), flaxseed extract, ethinyl estradiol, estradiol, turmeric extract, ubidecarenone, azelastine, pseudoephedrine, dextromethorphan, omega-3 fatty acids, fluticasone, and ibuprofen. In conclusion, this cohort study leveraged EHR data to identify a list of drugs that could be repurposed to improve COVID-19 outcomes. Further randomized clinical trials are needed to investigate the efficacy of the proposed drugs.
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Affiliation(s)
- Cosmin A. Bejan
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Katherine N. Cahill
- Department of MedicineDivision of Allergy, Pulmonary and Critical Care MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Patrick J. Staso
- Department of MedicineDivision of Allergy, Pulmonary and Critical Care MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Leena Choi
- Department of BiostatisticsVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Josh F. Peterson
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Elizabeth J. Phillips
- Department of Pathology, Microbiology and ImmunologyVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of MedicineDivision of Infectious DiseasesVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of PharmacologyVanderbilt University Medical CenterNashvilleTennesseeUSA
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Binkheder S, Asiri MA, Altowayan KW, Alshehri TM, Alzarie MF, Aldekhyyel RN, Almaghlouth IA, Almulhem JA. Real-World Evidence of COVID-19 Patients' Data Quality in the Electronic Health Records. Healthcare (Basel) 2021; 9:1648. [PMID: 34946374 PMCID: PMC8701465 DOI: 10.3390/healthcare9121648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/18/2021] [Accepted: 11/25/2021] [Indexed: 11/19/2022] Open
Abstract
Despite the importance of electronic health records data, less attention has been given to data quality. This study aimed to evaluate the quality of COVID-19 patients' records and their readiness for secondary use. We conducted a retrospective chart review study of all COVID-19 inpatients in an academic healthcare hospital for the year 2020, which were identified using ICD-10 codes and case definition guidelines. COVID-19 signs and symptoms were higher in unstructured clinical notes than in structured coded data. COVID-19 cases were categorized as 218 (66.46%) "confirmed cases", 10 (3.05%) "probable cases", 9 (2.74%) "suspected cases", and 91 (27.74%) "no sufficient evidence". The identification of "probable cases" and "suspected cases" was more challenging than "confirmed cases" where laboratory confirmation was sufficient. The accuracy of the COVID-19 case identification was higher in laboratory tests than in ICD-10 codes. When validating using laboratory results, we found that ICD-10 codes were inaccurately assigned to 238 (72.56%) patients' records. "No sufficient evidence" records might indicate inaccurate and incomplete EHR data. Data quality evaluation should be incorporated to ensure patient safety and data readiness for secondary use research and predictive analytics. We encourage educational and training efforts to motivate healthcare providers regarding the importance of accurate documentation at the point-of-care.
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Affiliation(s)
- Samar Binkheder
- Medical Informatics and E-Learning Unit, Medical Education Department, College of Medicine, King Saud University, Riyadh 12372, Saudi Arabia; (M.A.A.); (K.W.A.); (T.M.A.); (M.F.A.); (R.N.A.); (J.A.A.)
| | - Mohammed Ahmed Asiri
- Medical Informatics and E-Learning Unit, Medical Education Department, College of Medicine, King Saud University, Riyadh 12372, Saudi Arabia; (M.A.A.); (K.W.A.); (T.M.A.); (M.F.A.); (R.N.A.); (J.A.A.)
- Department of Medicine, College of Medicine, King Saud University, Riyadh 12372, Saudi Arabia;
| | - Khaled Waleed Altowayan
- Medical Informatics and E-Learning Unit, Medical Education Department, College of Medicine, King Saud University, Riyadh 12372, Saudi Arabia; (M.A.A.); (K.W.A.); (T.M.A.); (M.F.A.); (R.N.A.); (J.A.A.)
- Department of Medicine, College of Medicine, King Saud University, Riyadh 12372, Saudi Arabia;
| | - Turki Mohammed Alshehri
- Medical Informatics and E-Learning Unit, Medical Education Department, College of Medicine, King Saud University, Riyadh 12372, Saudi Arabia; (M.A.A.); (K.W.A.); (T.M.A.); (M.F.A.); (R.N.A.); (J.A.A.)
- Department of Medicine, College of Medicine, King Saud University, Riyadh 12372, Saudi Arabia;
| | - Mashhour Faleh Alzarie
- Medical Informatics and E-Learning Unit, Medical Education Department, College of Medicine, King Saud University, Riyadh 12372, Saudi Arabia; (M.A.A.); (K.W.A.); (T.M.A.); (M.F.A.); (R.N.A.); (J.A.A.)
- Department of Medicine, College of Medicine, King Saud University, Riyadh 12372, Saudi Arabia;
| | - Raniah N. Aldekhyyel
- Medical Informatics and E-Learning Unit, Medical Education Department, College of Medicine, King Saud University, Riyadh 12372, Saudi Arabia; (M.A.A.); (K.W.A.); (T.M.A.); (M.F.A.); (R.N.A.); (J.A.A.)
| | - Ibrahim A. Almaghlouth
- Department of Medicine, College of Medicine, King Saud University, Riyadh 12372, Saudi Arabia;
| | - Jwaher A. Almulhem
- Medical Informatics and E-Learning Unit, Medical Education Department, College of Medicine, King Saud University, Riyadh 12372, Saudi Arabia; (M.A.A.); (K.W.A.); (T.M.A.); (M.F.A.); (R.N.A.); (J.A.A.)
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Brown JS, Bastarache L, Weiner MG. Aggregating Electronic Health Record Data for COVID-19 Research-Caveat Emptor. JAMA Netw Open 2021; 4:e2117175. [PMID: 34255055 DOI: 10.1001/jamanetworkopen.2021.17175] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jeffrey S Brown
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Mark G Weiner
- Department of Population Health Sciences, Weill Cornell Medicine, New York, New York
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