Search

Purpose: The primary aim of this work was to convert the Information System for Research in Primary Care (SIDIAP) from Catalonia, Spain, to the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). Our second aim was to provide a descriptive analysis of COVID-19-related outcomes among the general population. Patients and Methods: We mapped patient-level data from SIDIAP to the OMOP CDM and we performed more than 3,400 data quality checks to assess its readiness for research. We established a general population cohort as of the 1st March 2020 and identified outpatient COVID-19 diagnoses or tested positive for, hospitalised with, admitted to intensive care units (ICU) with, died with, or vaccinated against COVID-19 up to 30th June 2022. Results: After verifying the high quality of the transformed dataset, we included 5,870,274 individuals in the general population cohort. Of those, 604,472 had either an outpatient COVID-19 diagnosis or positive test result, 58,991 had a hospitalisation, 5,642 had an ICU admission, and 11,233 died with COVID-19. A total of 4,584,515 received a COVID-19 vaccine. People who were hospitalised or died were more commonly older, male, and with more comorbidities. Those admitted to ICU with COVID-19 were generally younger and more often male than those hospitalised and those who died. Conclusion: We successfully transformed SIDIAP to the OMOP CDM. From this dataset, a general population cohort of 5.9 million individuals was identified and their COVID-19-related outcomes over time were described. The transformed SIDIAP database is a valuable resource that can enable distributed network research in COVID-19 and beyond.

BACKGROUND: We investigated whether we could use influenza data to develop prediction models for COVID-19 to increase the speed at which prediction models can reliably be developed and validated early in a pandemic. We developed COVID-19 Estimated Risk (COVER) scores that quantify a patient's risk of hospital admission with pneumonia (COVER-H), hospitalization with pneumonia requiring intensive services or death (COVER-I), or fatality (COVER-F) in the 30-days following COVID-19 diagnosis using historical data from patients with influenza or flu-like symptoms and tested this in COVID-19 patients.METHODS: We analyzed a federated network of electronic medical records and administrative claims data from 14 data sources and 6 countries containing data collected on or before 4/27/2020. We used a 2-step process to develop 3 scores using historical data from patients with influenza or flu-like symptoms any time prior to 2020. The first step was to create a data-driven model using LASSO regularized logistic regression, the covariates of which were used to develop aggregate covariates for the second step where the COVER scores were developed using a smaller set of features. These 3 COVER scores were then externally validated on patients with 1) influenza or flu-like symptoms and 2) confirmed or suspected COVID-19 diagnosis across 5 databases from South Korea, Spain, and the United States. Outcomes included i) hospitalization with pneumonia, ii) hospitalization with pneumonia requiring intensive services or death, and iii) death in the 30 days after index date.RESULTS: Overall, 44,507 COVID-19 patients were included for model validation. We identified 7 predictors (history of cancer, chronic obstructive pulmonary disease, diabetes, heart disease, hypertension, hyperlipidemia, kidney disease) which combined with age and sex discriminated which patients would experience any of our three outcomes. The models achieved good performance in influenza and COVID-19 coh

Purpose: Routinely collected real world data (RWD) have great utility in aiding the novel coronavirus disease (COVID-19) pandemic response. Here we present the international Observational Health Data Sciences and Informatics (OHDSI) Characterizing Health Associated Risks and Your Baseline Disease In SARS-COV-2 (CHARYBDIS) framework for standardisation and analysis of COVID-19 RWD. Patients and Methods: We conducted a descriptive retrospective database study using a federated network of data partners in the United States, Europe (the Netherlands, Spain, the UK, Germany, France and Italy) and Asia (South Korea and China). The study protocol and analytical package were released on 11th June 2020 and are iteratively updated via GitHub. We identified three nonmutually exclusive cohorts of 4,537,153 individuals with a clinical COVID-19 diagnosis or positive test, 886,193 hospitalized with COVID-19, and 113,627 hospitalized with COVID-19 requiring intensive services. Results: We aggregated over 22,000 unique characteristics describing patients with COVID-19. All comorbidities, symptoms, medications, and outcomes are described by cohort in aggregate counts and are readily available online. Globally, we observed similarities in the USA and Europe: More women diagnosed than men but more men hospitalized than women, most diagnosed cases between 25 and 60 years of age versus most hospitalized cases between 60 and 80 years of age. South Korea differed with more women than men hospitalized. Common comorbidities included type 2 diabetes, hypertension, chronic kidney disease and heart disease. Common presenting symptoms were dyspnea, cough and fever. Symptom data availability was more common in hospitalized cohorts than diagnosed. Conclusion: We constructed a global, multi-centre view to describe trends in COVID-19 progression, management and evolution over time. By characterising baseline variability in patients and geography, our work provides critical context that may otherwi

BackgroundWe described the demographics, cancer subtypes, comorbidities, and outcomes of patients with a history of cancer and coronavirus disease 2019 (COVID-19). Second, we compared patients hospitalized with COVID-19 to patients diagnosed with COVID-19 and patients hospitalized with influenza.MethodsWe conducted a cohort study using eight routinely collected health care databases from Spain and the United States, standardized to the Observational Medical Outcome Partnership common data model. Three cohorts of patients with a history of cancer were included: (i) diagnosed with COVID-19, (ii) hospitalized with COVID-19, and (iii) hospitalized with influenza in 2017 to 2018. Patients were followed from index date to 30 days or death. We reported demographics, cancer subtypes, comorbidities, and 30-day outcomes.ResultsWe included 366,050 and 119,597 patients diagnosed and hospitalized with COVID-19, respectively. Prostate and breast cancers were the most frequent cancers (range: 5%-18% and 1%-14% in the diagnosed cohort, respectively). Hematologic malignancies were also frequent, with non-Hodgkin's lymphoma being among the five most common cancer subtypes in the diagnosed cohort. Overall, patients were aged above 65 years and had multiple comorbidities. Occurrence of death ranged from 2% to 14% and from 6% to 26% in the diagnosed and hospitalized COVID-19 cohorts, respectively. Patients hospitalized with influenza (n = 67,743) had a similar distribution of cancer subtypes, sex, age, and comorbidities but lower occurrence of adverse events.ConclusionsPatients with a history of cancer and COVID-19 had multiple comorbidities and a high occurrence of COVID-19-related events. Hematologic malignancies were frequent.ImpactThis study provides epidemiologic characteristics that can inform clinical care and etiologic studies.

Background: SARS-CoV-2 is straining health care systems globally. The burden on hospitals during the pandemic could be reduced by implementing prediction models that can discriminate patients who require hospitalization from those who do not. The COVID-19 vulnerability (C-19) index, a model that predicts which patients will be admitted to hospital for treatment of pneumonia or pneumonia proxies, has been developed and proposed as a valuable tool for decision-making during the pandemic. However, the model is at high risk of bias according to the "prediction model risk of bias assessment" criteria, and it has not been externally validated. Objective: The aim of this study was to externally validate the C-19 index across a range of health care settings to determine how well it broadly predicts hospitalization due to pneumonia in COVID-19 cases. Methods: We followed the Observational Health Data Sciences and Informatics (OHDSI) framework for external validation to assess the reliability of the C-19 index. We evaluated the model on two different target populations, 41,381 patients who presented with SARS-CoV-2 at an outpatient or emergency department visit and 9,429,285 patients who presented with influenza or related symptoms during an outpatient or emergency department visit, to predict their risk of hospitalization with pneumonia during the following 0-30 days. In total, we validated the model across a network of 14 databases spanning the United States, Europe, Australia, and Asia. Results: The internal validation performance of the C-19 index had a C statistic of 0.73, and the calibration was not reported by the authors. When we externally validated it by transporting it to SARS-CoV-2 data, the model obtained C statistics of 0.36, 0.53 (0.473-0.584) and 0.56 (0.488-0.636) on Spanish, US, and South Korean data sets, respectively. The calibration was poor, with the model underestimating risk. When validated on 12 data sets containing influenza patients across the OH

Objective To characterise patients with and without prevalent hypertension and COVID-19 and to assess adverse outcomes in both inpatients and outpatients. Design and setting This is a retrospective cohort study using 15 healthcare databases (primary and secondary electronic healthcare records, insurance and national claims data) from the USA, Europe and South Korea, standardised to the Observational Medical Outcomes Partnership common data model. Data were gathered from 1 March to 31 October 2020. Participants Two non-mutually exclusive cohorts were defined: (1) individuals diagnosed with COVID-19 (diagnosed cohort) and (2) individuals hospitalised with COVID-19 (hospitalised cohort), and stratified by hypertension status. Follow-up was from COVID-19 diagnosis/hospitalisation to death, end of the study period or 30 days. Outcomes Demographics, comorbidities and 30-day outcomes (hospitalisation and death for the diagnosed' cohort and adverse events and death for the hospitalised' cohort) were reported. Results We identified 2 851 035 diagnosed and 563 708 hospitalised patients with COVID-19. Hypertension was more prevalent in the latter (ranging across databases from 17.4% (95% CI 17.2 to 17.6) to 61.4% (95% CI 61.0 to 61.8) and from 25.6% (95% CI 24.6 to 26.6) to 85.9% (95% CI 85.2 to 86.6)). Patients in both cohorts with hypertension were predominantly >50 years old and female. Patients with hypertension were frequently diagnosed with obesity, heart disease, dyslipidaemia and diabetes. Compared with patients without hypertension, patients with hypertension in the COVID-19 diagnosed cohort had more hospitalisations (ranging from 1.3% (95% CI 0.4 to 2.2) to 41.1% (95% CI 39.5 to 42.7) vs from 1.4% (95% CI 0.9 to 1.9) to 15.9% (95% CI 14.9 to 16.9)) and increased mortality (ranging from 0.3% (95% CI 0.1 to 0.5) to 18.5% (95% CI 15.7 to 21.3) vs from 0.2% (95% CI 0.2 to 0.2) to 11.8% (95% CI 10.8 to 12.8)). Patients in the COVID-19 hospitalised cohort with hypert

This study aimed to analyse the trajectories and mortality of multimorbidity patterns in patients aged 65 to 99 years in Catalonia (Spain). Five year (2012–2016) data of 916,619 participants from a primary care, population-based electronic health record database (Information System for Research in Primary Care, SIDIAP) were included in this retrospective cohort study. Individual longitudinal trajectories were modelled with a Hidden Markov Model across multimorbidity patterns. We computed the mortality hazard using Cox regression models to estimate survival in multimorbidity patterns. Ten multimorbidity patterns were originally identified and two more states (death and drop-outs) were subsequently added. At baseline, the most frequent cluster was the Non-Specific Pattern (42%), and the least frequent the Multisystem Pattern (1.6%). Most participants stayed in the same cluster over the 5 year follow-up period, from 92.1% in the Nervous, Musculoskeletal pattern to 59.2% in the Cardio-Circulatory and Renal pattern. The highest mortality rates were observed for patterns that included cardio-circulatory diseases: Cardio-Circulatory and Renal (37.1%); Nervous, Digestive and Circulatory (31.8%); and Cardio-Circulatory, Mental, Respiratory and Genitourinary (28.8%). This study demonstrates the feasibility of characterizing multimorbidity patterns along time. Multimorbidity trajectories were generally stable, although changes in specific multimorbidity patterns were observed. The Hidden Markov Model is useful for modelling transitions across multimorbidity patterns and mortality risk. Our findings suggest that health interventions targeting specific multimorbidity patterns may reduce mortality in patients with multimorbidity., This work was supported by a research grant from the Carlos III Institute of Health, Ministry of Economy and Competitiveness (Spain), awarded for the 2016 call under the Health Strategy Action 2013–2016, within the National Research Program oriented to Societal Challenges, within the Technical, Scientifc and Innovation Research National Plan 2013–2016 ‘[grant number PI16/00639]’, co-funded with European Union ERDF funds (European Regional Development Fund) and the Department of Health of the Catalan Government, in the call corresponding to 2017 for the granting of subsidies from the Strategic Plan for Research in Health (Pla Estratègic de Recerca i Innovació en Salut, PERIS) 2016–2020, modality research oriented to Primary care ‘[grant number SLT002/16/00058]’ and by the Catalan Government ‘[Grant Number AGAUR 2017 SGR 578]., Peer Reviewed, Postprint (published version)

A challenge to solve when analyzing multimorbidity patterns in elderly people is the management of a high number of characteristics associated with each patient. The main variables to study multimorbidity are diseases, however other variables should be considered to better classify the people included in each pattern. Age, sex, social class and medication are frequently used in the typing of each multimorbidity pattern. Subsequently the cardinality of the set of features that characterize a patient is very high and normally, the set is compressed to obtain a patient vector of new variables whose dimension is noticeably smaller than that of the initial set. To minimize the loss of information by compression, traditionally Principal Component Analysis (PCA) based projection techniques have been used, which although they are generally a good option, the projection is linear, which somehow reduces its flexibility and limits the performance. As an alternative to the PCA based techniques, in this paper, it is proposed to use autoencoders, and it is shown the improvement in the obtained multimorbidity patterns from the compressed database, when the registered data on about a million patients (5 years' follow-up) are processed. This work demonstrates that autoencoders retain a larger amount of information in each pattern and results are more consistent with clinical experience than other approaches frequently found in the literature.Clinical relevance- From an epidemiological perspective, the contribution is relevant, since it allows for a more precise analysis of multimorbidity patterns, leading to better approaches to patient health strategies., Work supported by Carlos III Institute of Health, Spanish Ministry of Economy and Competitiveness and ERDF (UE) funds under Grant PI16/00639, and in part by Catalan Government funds under Grants 2017 SGR 578 AGAUR and Strategic Plan for Research in Health PERIS grant number SLT002/16/00058, Peer Reviewed, Postprint (published version)

The aim of this study was to identify, with soft clustering methods, multimorbidity patterns in the electronic health records of a population =65 years, and to analyse such patterns in accordance with the different prevalence cut-off points applied. Fuzzy cluster analysis allows individuals to be linked simultaneously to multiple clusters and is more consistent with clinical experience than other approaches frequently found in the literature., Peer Reviewed, Postprint (published version)

The current project explores electoral data from Spanish national elections from 2000 to 2011. Using these, it is developed and tested an algorithm to predict election results with a small error. The analysed prediction is an Electoral Night Forecasting procedure, performed during the election night. Specifically, the implementation starts with the counting of the first votes and finishes with the publication of the final results. Differently from other widespread calculations, the basis of the study is not sociodemographic data. Machine Learning techniques, like clustering or PCA, are used in conjunction with electoral data from past elections and data from the current incoming votes. There are two distinguishable phases in the prediction: clustering of historical data to train the system and the prediction itself. Within the clustering phase, polling districts are grouped according to the similarity between their voting behaviour (clustering implementation depends strongly on the function chosen to calculate this similarity). Predictions of the final results are given as voting data is arriving. It is assumed that not computed polling districts have similar results to those already computed of the same cluster. With the previous assumption, predictions are improved. In addition, the error due to the bias of the early received results is reduced. The prediction model chosen to develop this approach was tested with great outcomes in the 2004 South African elections. A data study is conducted prior to the prediction, in order to find the optimal clustering type and number of clusters. Results obtained are not indicative enough to choose a good setting of the model. Consequently, the quest of the best parameters is done by the very same computation of predictions. For any tested configuration, the prediction improves the results thrown by pure counting of incoming votes. Forecasted results are studied according to the percentage of votes arrived. The study reveals tha, Aquest projecte explora les dades electorals dels comicis estatals celebrats a Espanya entre els anys 2000 i 2011. Amb elles s'elabora i testeja un algorisme de predicció de resultats electorals amb un error de predicció petit. La predicció a desenvolupar s'emmarca en l'anomenat Electoral Night Forecasting (ENF), prediccions durant la nit electoral. En concret, s'implementen durant l'escrutini, iniciant-se amb el recompte de vots de les primeres meses electorals i finalitzant amb la publicació de resultats definitius. Els còmputs a realitzar, a diferència d'altres més clàssics i coneguts, no es basen directament en dades sociodemogràfiques. Es combinen tècniques de Machine Learning, com clustering i PCA; amb dades històriques d'eleccions passades i les que s'obtenen del recompte de vots durant les eleccions actuals. Hi ha dues fases ben diferenciades per a desenvolupar la predicció: el clustering de les dades històriques, que serveix com a entrenament del sistema, i la mateixa predicció. A la fase de clustering es fan grups de meses electorals, assignant al mateix conjunt les que tenen resultats similars (aquesta agrupació dependrà en gran mesura de la funció que es fa servir per a calcular la semblança entre resultats). Tal com van arribant les dades durant l'escrutini, es van fent prediccions del resultat final. Aquestes assumeixen que els vots de les meses que encara no han finalitzat el recompte són similars a les ja escrutades del seu mateix clúster. D'aquesta manera es refina la predicció del resultat final i es redueix considerablement l'error provocat per l'arribada de meses amb patró de vot similar als primers estadis de l'escrutini. El model de predicció escollit per a realitzar aquesta aproximació es va testejar a les eleccions sud-africanes del 2004 amb bons resultats. Amb anterioritat a la fase de predicció s'estudien les dades, per a trobar el tipus de clustering i el nombre de clústers òptim a emprar. Els resultats obtinguts no són prou indicatius per, Este proyecto explora los datos electorales de los comicios estatales celebrados en España entre los años 2000 y 2011. Con ellos se elabora y testea un algoritmo de predicción de resultados electorales con un error de predicción pequeño. La predicción a desarrollar se enmarca en el llamado Electoral Night Forecasting (ENF), predicciones durante la noche electoral. En concreto, se implementan durante el escrutinio, iniciándose con el recuento de votos de las primeras mesas electorales y finalizando con la publicación de resultados definitivos. Los cómputos a realizar, a diferencia de otros más clásicos y conocidos, no se basan directamente en datos sociodemográficos. Se combinan técnicas de Machine Learning, como clustering y PCA; con datos históricos de elecciones pasadas y las que se obtienen del recuento de votos durante las elecciones actuales. Hay dos fases bien diferenciadas para desarrollar la predicción: el clustering de los datos históricos, que sirve como entrenamiento del sistema, y la misma predicción. En la fase de clustering se hacen grupos de mesas electorales, asignando al mismo conjunto las que tienen resultados similares (esta agrupación dependerá en gran medida de la función que se utiliza para calcular la semejanza entre resultados). Tal y como van llegando los datos durante el escrutinio, se van haciendo predicciones del resultado final. Éstas asumen que los votos de las mesas que aún no han finalizado el recuento son similares a las ya escrutadas de su mismo clúster. De esta manera se refina la predicción del resultado final y se reduce considerablemente el error provocado por la llegada de mesas con patrón de voto similar en los primeros estadios del escrutinio. El modelo de predicción escogido para realizar esta aproximación se implantó en las elecciones sudafricanas de 2004 con buenos resultados. Con anterioridad a la fase de predicción se estudian los datos, para encontrar el tipo de clustering y el número de clústeres óptimo a emplear. Los