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Empirical assessment of alternative methods for identifying seasonality in observational healthcare data

BMC MEDICAL RESEARCH METHODOLOGY 2022年第1期22卷 1-11页

作者： Molinaro, Anthony DeFalco, Frank Janssen Res & Dev 1125 Trenton Harbourton Rd Titusville NJ 08560 USA

Background Seasonality classification is a well-known and important part of time series analysis. Understanding the seasonality of a biological event can contribute to an improved understanding of its causes and help guide appropriate responses. Observational data, however, are not comprised of biological events, but timestamped diagnosis codes the combination of which (along with additional requirements) are used as proxies for biological events. As there exist different methods for determining the seasonality of a time series, it is necessary to know if these methods exhibit concordance. In this study we seek to determine the concordance of these methods by applying them to time series derived from diagnosis codes in observational data residing in databases that vary in size, type, and provenance. Methods We compared 8 methods for determining the seasonality of a time series at three levels of significance (0.01, 0.05, and 0.1), against 10 observational health databases. We evaluated 61,467 time series at each level of significance, totaling 184,401 evaluations. Results Across all databases and levels of significance, concordance ranged from 20.2 to 40.2%. Across all databases and levels of significance, the proportion of time series classified seasonal ranged from 4.9 to 88.3%. For each database and level of significance, we computed the difference between the maximum and minimum proportion of time series classified seasonal by all methods. The median within-database difference was 54.8, 34.7, and 39.8%, for p < 0.01, 0.05, and 0.1, respectively. Conclusion Methods of binary seasonality classification when applied to time series derived from diagnosis codes in observational health data produce inconsistent results. The methods exhibit considerable discord within all databases, implying that the discord is a result of the difference between the methods themselves and not due to the choice of database. The results indicate that researchers relying on automated meth

关键词： ACHILLES ARIMA CASTOR Classification common data model Cyclical Observational data OHDSI OMOP CDM R Seasonality Time series

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allofus: an R package to facilitate use of the All of Us Researcher Workbench

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JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2024年第12期31卷 3013-3021页

作者： Smith, Louisa H. Cavanaugh, Robert Northeastern Univ Roux Inst 100 Fore St Portland ME 04101 USA Northeastern Univ Bouve Coll Hlth Sci Dept Publ Hlth & Hlth Sci Boston MA 02115 USA

Objectives Despite easy-to-use tools like the Cohort Builder, using All of Us Research Program data for complex research questions requires a relatively high level of technical expertise. We aimed to increase research and training capacity and reduce barriers to entry for the All of Us community through an R package, allofus. In this article, we describe functions that address common challenges we encountered while working with All of Us Research Program data, and we demonstrate this functionality with an example of creating a cohort of All of Us participants by synthesizing electronic health record and survey data with time *** audience All of Us Research Program data are widely available to health researchers. The allofus R package is aimed at a wide range of researchers who wish to conduct complex analyses using best practices for reproducibility and transparency, and who have a range of experience using R. Because the All of Us data are transformed into the Observational Medical Outcomes Partnership common data model (OMOP CDM), researchers familiar with existing OMOP CDM tools or who wish to conduct network studies in conjunction with other OMOP CDM data will also find value in the *** We developed an initial set of functions that solve problems we experienced across survey and electronic health record data in our own research and in mentoring student projects. The package will continue to grow and develop with the All of Us Research Program. The allofus R package can help build community research capacity by increasing access to the All of Us Research Program data, the efficiency of its use, and the rigor and reproducibility of the resulting research.

关键词： All of Us R package common data model OMOP CDM OHDSI

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Haematology Outcomes Network in Europe (HONEUR)-A collaborative, interdisciplinary platform to harness the potential of real-world data in hematology

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EUROPEAN JOURNAL OF HAEMATOLOGY 2022年第2期109卷 138-145页

作者： Bardenheuer, Kristina Van Speybroeck, Michel Hague, Clare Nikai, Enkeleida Price, Martin Janssen Pharmaceut NV Beerse Belgium

Introduction There remains a need to optimize treatments and improve outcomes among patients with hematologic malignancies. The timely synthesis and analysis of real-world data could play a key role. Objectives The Haematology Outcomes Network in Europe (HONEUR) is a federated data network (FDN) that aims to overcome the challenges of heterogenous data collected from different registries, hospitals, and other databases in different countries. It has the functionality required to analyze data from various sources in a time efficient manner, while preserving local data security and governance. With this, research studies can be performed that can increase knowledge and understanding of the management of patients with hematologic malignancies. Methods HONEUR uses the Observational Medical Outcomes Partnership (OMOP) common data model, which allows analysis scripts to be run by multiple sites using their own data, ultimately generating aggregated results. Furthermore, distributed analytics can be used to run statistical analyses across multiple sites, as if data were pooled. The external governance model ensures high-quality standards, while data ownership is retained locally. Twenty partners from nine countries are now participating, with data from more than 26 000 patients available for analysis. Research questions that can be addressed through HONEUR include assessments of natural disease history, treatment patterns, and clinical effectiveness. Conclusions The HONEUR FDN marks an important step forward in increasing the value of information routinely captured by individual hospitals, registries and other database holders, thus enabling larger-scale studies to be undertaken rapidly and efficiently.

关键词： common data model data analysis evidence generation federated data network Haematology Outcomes Network in Europe Observational Medical Outcomes Partnership real-world evidence

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Risks of complicated acute appendicitis in patients with psychiatric disorders

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BMC PSYCHIATRY 2022年第1期22卷 1-10页

作者： Kim, Junmo Yang, Chaeyoung Joo, Hyung Joon Park, Rae Woong Kim, Ga Eun Kim, Daeho Choi, Joonho Lee, Jun Ho Kim, Eunkyung Park, Seon-Cheol Kim, Kwangsoo Kim, Il Bin Seoul Natl Univ Interdisciplinary Program Bioengn Seoul South Korea Hanyang Univ Dept Psychiat Coll Med Seoul South Korea Hanyang Univ Dept Psychiat Med Ctr Seoul South Korea Korea Univ Anam Hosp Dept Internal Med Div Cardiol Seoul South Korea Korea Univ Dept Med Informat Coll Med Seoul South Korea Ajou Univ Dept Biomed Informat Sch Med Suwon South Korea Ewha Womans Univ Mokdong Hosp Dept Psychiat Coll Med Seoul South Korea Hanyang Univ Guri Hosp Dept Psychiat Guri South Korea Hanyang Univ Dept Surg Coll Med Seoul South Korea Seoul Natl Univ Hosp Transdisciplinary Dept Med & Adv Technol Seoul South Korea Seoul Natl Univ Coll Med Dept Med Seoul South Korea Korea Adv Inst Sci & Technol Grad Sch Med Sci & Engn Daejeon South Korea

Background: Acute appendicitis often presents with vague abdominal pain, which fosters diagnostic challenges to clinicians regarding early detection and proper intervention. This is even more problematic with individuals with severe psychiatric disorders who have reduced sensitivity to pain due to long-term or excessive medication use or disturbed bodily sensation perceptions. This study aimed to determine whether psychiatric disorder, psychotropic prescription, and treatment compliance increase the risks of complicated acute appendicitis. Methods: The diagnosis records of acute appendicitis from four university hospitals in Korea were investigated from 2002 to 2020. A total of 47,500 acute appendicitis-affected participants were divided into groups with complicated and uncomplicated appendicitis to determine whether any of the groups had more cases of psychiatric disorder diagnoses. Further, the ratio of complicated compared to uncomplicated appendicitis in the mentally ill group was calculated regarding psychotropic dose, prescription duration, and treatment compliance. Results: After adjusting for age and sex, presence of psychotic disorder (odds ratio [OR]: 1.951;95% confidence interval [CI]: 1.218-3.125), and bipolar disorder (OR: 2.323;95% CI: 1.194-4.520) was associated with a higher risk of having complicated appendicitis compared with absence of psychiatric disorders. Patients who are taking high-daily-dose antipsychotics, regardless of prescription duration, show high complicated appendicitis risks;High-dose antipsychotics for < 1 year (OR: 1.896, 95% CI: 1.077-3.338), high-dose antipsychotics for 1-5 years (OR: 1.930, 95% CI: 1.144-3.256). Poor psychiatric outpatient compliance was associated with a high risk of complicated appendicitis (OR: 1.664, 95% CI: 1.014-2.732). Conclusions: This study revealed a close relationship in the possibility of complicated appendicitis in patients with severe psychiatric disorders, including psychotic and bipolar disorder

关键词： Psychiatric disorder Complicated appendicitis common data model Treatment compliance

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Association Between Ursodeoxycholic Acid and Clinical Outcomesin Patients With COVID-19 Infection:Population-Based CohortStudy

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JMIR PUBLIC HEALTH AND SURVEILLANCE 2024年 10卷 e59274页

作者： Lee, Hyunjun Kim, Min Gul Yeom, Sang Woo Noh, Sang Jae Jeong, Cho Yun Kim, Minji Kang, Min Gu Ko, Ji Hoon Park, Su Cheol Kweon, Hyeok Tae Sim, Sang Il Lee, Hyun You, Yeon Seok Kim, Jong Seung Jeonbuk Natl Univ Med Sch Dept Otorhinolaryngol Head & Neck Surg Jeonju South Korea Jeonbuk Natl Univ Med Sch Dept Pharmacol Jeonju South Korea Jeonbuk Natl Univ Med Sch Dept Med Informat Jeonju South Korea Jeonbuk Natl Univ Jeonbuk Natl Univ Hosp Res Inst Clin Med Biomed Res Inst Jeonju South Korea Jeonbuk Natl Univ Hosp Big Data Ctr Jeonju South Korea Hanyang Univ Coll Med Dept Internal Med Seoul South Korea Jeonbuk Natl Univ Sch Med & Hosp Dept Med Informat Dept Otorhinolaryngol 20 Geonji Ro Jeonju 54907 Jeonbuk Do South Korea

Background: Several studies have investigated the relationship between ursodeoxycholic acid (UDCA) and COVID-19 ***, complex and conflicting results have generated confusion in the application of these results. Objective: We aimed to investigate whether the association between UDCA and COVID-19 infection can also be demonstratedthrough the analysis of a large-scale cohort. Methods: This retrospective study used local and nationwide cohorts, namely, the Jeonbuk National University Hospital intothe Observational Medical Outcomes Partnership common data model cohort (JBUH CDM) and the Korean National HealthInsurance Service claim-based database (NHIS). We investigated UDCA intake and its relationship with COVID-19 susceptibilityand severity using validated propensity score ***: Regarding COVID-19 susceptibility, the adjusted hazard ratio (aHR) value of the UDCA intake was significantlylowered to 0.71 in the case of the JBUH CDM (95% CI 0.52-0.98) and was significantly lowered to 0.93 (95% CI 0.90-0.96) inthe case of the NHIS. Regarding COVID-19 severity, the UDCA intake was found to be significantly lowered to 0.21 (95% CI0.09-0.46) in the case of JBUH CDM. Furthermore, the aHR value was significantly lowered to 0.77 in the case of NHIS (95%CI 0.62-0.95). Conclusions: Using a large-scale local and nationwide cohort, we confirmed that UDCA intake was significantly associatedwith reductions in COVID-19 susceptibility and severity. These trends remained consistent regardless of the UDCA dosage. Thissuggests the potential of UDCA as a preventive and therapeutic agent for COVID-19 infection.

关键词： Covid 19 COVID-19 ursodeoxycholic acid population-based cohort study SARS-CoV-2 Coronavirus pandemic population-based retrospective cohort study propensity score UDCA public health common data model clinical severity

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ggbio: an R package for extending the grammar of graphics for genomic data

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GENOME BIOLOGY 2012年第8期13卷 1-14页

作者： Yin, Tengfei Cook, Dianne Lawrence, Michael Iowa State Univ Dept Genet Dev & Cell Biol Ames IA 50011 USA Iowa State Univ Dept Stat Ames IA 50011 USA Genentech Inc Dept Bioinformat San Francisco CA 94080 USA

We introduce ggbio, a new methodology to visualize and explore genomics annotations and high-throughput data. The plots provide detailed views of genomic regions, summary views of sequence alignments and splicing patterns, and genome-wide overviews with karyogram, circular and grand linear layouts. The methods leverage the statistical functionality available in R, the grammar of graphics and the data handling capabilities of the Bioconductor project. The plots are specified within a modular framework that enables users to construct plots in a systematic way, and are generated directly from Bioconductor data structures. The ggbio R package is available at http://***/packages/2.11/bioc/html/***.

关键词： Genome Browser Read Alignment Genomic Viewer common data model Scalable Vector Graphic

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FOUNTAIN: a modular research platform for integrated real-world evidence generation

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BMC MEDICAL RESEARCH METHODOLOGY 2024年第1期24卷 1-10页

作者： Oberprieler, Nikolaus G. Pladevall-Vila, Manel Johannes, Catherine Layton, J. Bradley Golozar, Asieh Lavallee, Martin Liu, Fangfang Kubin, Maria Vizcaya, David Bayer AS Oslo Norway RTI Hlth Solut Barcelona Spain Henry Ford Hlth Syst Ctr Hlth Policy & Hlth Serv Res Detroit MI USA RTI Hlth Solut Waltham MA USA RTI Hlth Solut Res Triangle Pk NC USA Odysseus Inc New York NY USA Bayer AG Wuppertal Germany Bayer Pharmaceut St Joan Despi Spain

BackgroundReal-world evidence (RWE) plays a key role in regulatory and healthcare decision-making, but the potentially fragmentated nature of generated evidence may limit its utility for clinical decision-making. Heterogeneity and a lack of reproducibility in RWE resulting from inconsistent application of methodologies across data sources should be minimized through *** paper's aim is to describe and reflect upon a multidisciplinary research platform (FOUNTAIN;FinerenOne mUlti-database NeTwork for evidence generAtIoN) with coordinated studies using diverse RWE generation approaches and explore the platform's strengths and limitations. With guidance from an executive advisory committee of multidisciplinary experts and patient representatives, the goal of the FOUNTAIN platform is to harmonize RWE generation across a portfolio of research projects, including research partner collaborations and a common data model (CDM)-based program. FOUNTAIN's overarching objectives as a research platform are to establish long-term collaborations among pharmacoepidemiology research partners and experts and to integrate diverse approaches for RWE generation, including global protocol execution by research partners in local data sources and common protocol execution in multiple data sources through federated data networks, while ensuring harmonization of medical definitions, methodology, and reproducible artifacts across all studies. Specifically, the aim of the multiple studies run within the frame of FOUNTAIN is to provide insight into the real-world utilization, effectiveness, and safety of finerenone across its ***, the FOUNTAIN platform includes 9 research partner collaborations and 8 CDM-mapped data sources from 7 countries (United States, United Kingdom, China, Japan, The Netherlands, Spain, and Denmark). These databases and research partners were selected after a feasibility fit-for-purpose evaluation. Six multicountry, multidatabase

关键词： Cohort study common data model FOUNTAIN Harmonization Methodology Real-world data

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The use of electronic health records to inform cancer surveillance efforts: a scoping review and test of indicators for public health surveillance of cancer prevention and control

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BMC MEDICAL INFORMATICS AND DECISION MAKING 2022年第1期22卷 1-13页

作者： Conderino, Sarah Bendik, Stefanie Richards, Thomas B. Pulgarin, Claudia Chan, Pui Ying Townsend, Julie Lim, Sungwoo Roberts, Timothy R. Thorpe, Lorna E. NYU Grossman Sch Med Dept Populat Hlth 180 Madison Ave New York NY 10016 USA Ctr Dis Control & Prevent Div Canc Prevent & Control Atlanta GA 30333 USA New York City Dept Hlth & Mental Hyg Div Epidemiol Long Isl City NY 11101 USA NYU Grossman Sch Med Hlth Sci Lib New York NY 10016 USA

Introduction State cancer prevention and control programs rely on public health surveillance data to set objectives to improve cancer prevention and control, plan interventions, and evaluate state-level progress towards achieving those objectives. The goal of this project was to evaluate the validity of using electronic health records (EHRs) based on common data model variables to generate indicators for surveillance of cancer prevention and control for these public health programs. Methods Following the methodological guidance from the PRISMA Extension for Scoping Reviews, we conducted a literature scoping review to assess how EHRs are used to inform cancer surveillance. We then developed 26 indicators along the continuum of the cascade of care, including cancer risk factors, immunizations to prevent cancer, cancer screenings, quality of initial care after abnormal screening results, and cancer burden. Indicators were calculated within a sample of patients from the New York City (NYC) INSIGHT Clinical Research Network using common data model EHR data and were weighted to the NYC population using post-stratification. We used prevalence ratios to compare these estimates to estimates from the raw EHR of NYU Langone Health to assess quality of information within INSIGHT, and we compared estimates to results from existing surveillance sources to assess validity. Results Of the 401 identified articles, 15% had a study purpose related to surveillance. Our indicator comparisons found that INSIGHT EHR-based measures for risk factor indicators were similar to estimates from external sources. In contrast, cancer screening and vaccination indicators were substantially underestimated as compared to estimates from external sources. Cancer screenings and vaccinations were often recorded in sections of the EHR that were not captured by the common data model. INSIGHT estimates for many quality-of-care indicators were higher than those calculated using a raw EHR. Conclusion common d

关键词： Public health surveillance Public health informatics Electronic health records Early detection of cancer common data model Patient-Centered Clinical Research Network

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Impact of pitavastatin on new-onset diabetes mellitus compared to atorvastatin and rosuvastatin: a distributed network analysis of 10 real-world databases

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CARDIOVASCULAR DIABETOLOGY 2022年第1期21卷 1-14页

作者： Seo, Won-Woo Seo, Seung In Kim, Yerim Yoo, Jong Jin Shin, Woon Geon Kim, Jinseob You, Seng Chan Park, Rae Woong Park, Young Min Kim, Kyung-Jin Rhee, Sang Youl Park, Meeyoung Jin, Eun-Sun Kim, Sung Eun Hallym Univ Dept Internal Med Kangdong Sacred Heart Hosp Coll Med 150 Seongan Ro Seoul 05355 South Korea Hallym Univ Inst Liver & Digest Dis Chunchon South Korea Hallym Univ Kangdong Sacred Heart Hosp Dept Neurol Coll Med Seoul South Korea Seoul Natl Univ Dept Epidemiol Sch Publ Hlth Seoul South Korea Yonsei Univ Coll Med Dept Biomed Syst Informat Seoul South Korea Ajou Univ Dept Biomed Informat Suwon South Korea Natl Hlth Insurance Serv Ilsan Hosp Dept Family Med Goyang South Korea Ewha Womans Univ Med Ctr Dept Internal Med Sch Med Seoul South Korea Kyung Hee Univ Dept Endocrinol & Metab Sch Med Seoul South Korea Pusan Natl Univ Hosp Biomed Res Inst Busan South Korea Kyung Hee Univ Kyung Hee Univ Hosp Gangdong Cardiovasc Ctr Seoul South Korea

Background Statin treatment increases the risk of new-onset diabetes mellitus (NODM);however, data directly comparing the risk of NODM among individual statins is limited. We compared the risk of NODM between patients using pitavastatin and atorvastatin or rosuvastatin using reliable, large-scale data. Methods data of electronic health records from ten hospitals converted to the Observational Medical Outcomes Partnership common data model (n = 14,605,368 patients) were used to identify new users of pitavastatin, atorvastatin, or rosuvastatin (atorvastatin + rosuvastatin) for >= 180 days without a previous history of diabetes or HbA1c level >= 5.7%. We conducted a cohort study using Cox regression analysis to examine the hazard ratio (HR) of NODM after propensity score matching (PSM) and then performed an aggregate meta-analysis of the HR. Results After 1:2 PSM, 10,238 new pitavastatin users (15,998 person-years of follow-up) and 18,605 atorvastatin + rosuvastatin users (33,477 person-years of follow-up) were pooled from 10 databases. The meta-analysis of the HRs demonstrated that pitavastatin resulted in a significantly reduced risk of NODM than atorvastatin + rosuvastatin (HR 0.72;95% CI 0.59-0.87). In sub-analysis, pitavastatin was associated with a lower risk of NODM than atorvastatin or rosuvastatin after 1:1 PSM (HR 0.69;CI 0.54-0.88 and HR 0.74;CI 0.55-0.99, respectively). A consistently low risk of NODM in pitavastatin users was observed when compared with low-to-moderate-intensity atorvastatin + rosuvastatin users (HR 0.78;CI 0.62-0.98). Conclusions In this retrospective, multicenter active-comparator, new-user, cohort study, pitavastatin reduced the risk of NODM compared with atorvastatin or rosuvastatin.

关键词： Diabetes mellitus Pitavastatin Statin common data model

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The US Food and Drug Administration's Sentinel Initiative: Expanding the horizons of medical product safety

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PHARMACOEPIDEMIOLOGY AND DRUG SAFETY 2012年第S1期21卷 9-11页

作者： Robb, Melissa A. Racoosin, Judith A. Sherman, Rachel E. Gross, Thomas P. Ball, Robert Reichman, Marsha E. Midthun, Karen Woodcock, Janet US FDA Off Med Policy Ctr Drug Evaluat & Res Silver Spring MD 20993 USA US FDA Off Surveillance & Biometr Ctr Devices & Radiol Hlth Silver Spring MD 20993 USA US FDA Off Biostat & Epidemiol Ctr Biol Evaluat & Res Rockville MD 20852 USA US FDA Off Surveillance & Epidemiol Ctr Drug Evaluat & Res Silver Spring MD 20993 USA

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