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CKD subpopulations defined by risk-factors: A longitudinal analysis of electronic health records.

ABSTRACT: Chronic kidney disease (CKD) is a progressive disease that evades early detection and is associated with various comorbidities. Although clinical comprehension and control of these comorbidities is crucial for CKD management, complex pathophysiological interactions and feedback loops make this a formidable task. We have developed a hybrid semimechanistic modeling methodology to investigate CKD progression. The model is represented as a system of ordinary differential equations with embedded neural networks and takes into account complex disease progression pathways, feedback loops, and effects of 53 medications to generate time trajectories of eight clinical biomarkers that capture CKD progression due to various risk factors. The model was applied to real world data of US patients with CKD to map the available longitudinal information onto a set of time-invariant patient-specific parameters with a clear biological interpretation. These parameters describing individual patients were used to segment the cohort using a clustering approach. Model-based simulations were conducted to investigate cluster-specific treatment strategies. The model was able to reliably reproduce the variability in biomarkers across the cohort. The clustering procedure segmented the cohort into five subpopulations - four with enhanced sensitivity to a specific risk factor (hypertension, hyperlipidemia, hyperglycemia, or impaired kidney) and one that is largely insensitive to any of the risk factors. Simulation studies were used to identify patient-specific strategies to restrain or prevent CKD progression through management of specific risk factors. The semimechanistic model enables identification of disease progression phenotypes using longitudinal data that aid in prioritizing treatment strategies at individual patient level.

SUBMITTER: Ramaswamy R

PROVIDER: S-EPMC8592509 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundLittle is known about risk factors for early (e.g., erythema migrans) and disseminated Lyme disease manifestations, such as arthritis, neurological complications, and carditis. No study has used both diagnoses and free text to classify Lyme disease by disease stage and manifestation.MethodsWe identified Lyme disease cases in 2012-2016 in the electronic health record (EHR) of a large, integrated health system in Pennsylvania. We developed a rule-based text-matching algorithm using regular expressions to extract clinical data from free text. Lyme disease cases were then classified by stage and manifestation using data from both diagnoses and free text. Among cases classified by stage, we evaluated individual, community, and health care variables as predictors of disseminated stage (vs. early) disease using Poisson regression models with robust errors. Final models adjusted for sociodemographic factors, receipt of Medical Assistance (i.e., Medicaid, a proxy for low socioeconomic status), primary care contact, setting of diagnosis, season of diagnosis, and urban/rural status.ResultsAmong 7310 cases of Lyme disease, we classified 62% by stage. Overall, 23% were classified using both diagnoses and text, 26% were classified using diagnoses only, and 13% were classified using text only. Among the staged diagnoses (n = 4530), 30% were disseminated stage (762 arthritis, 426 neurological manifestations, 76 carditis, 95 secondary erythema migrans, and 76 other manifestations). In adjusted models, we found that persons on Medical Assistance at least 50% of time under observation, compared to never users, had a higher risk (risk ratio [95% confidence interval]) of disseminated Lyme disease (1.20 [1.05, 1.37]). Primary care contact (0.59 [0.54, 0.64]) and diagnosis in the urgent care (0.22 [0.17, 0.29]), compared to the outpatient setting, were associated with lower risk of disseminated Lyme disease.ConclusionsThe associations between insurance payor, primary care status, and diagnostic setting with disseminated Lyme disease suggest that lower socioeconomic status and less health care access could be linked with disseminated stage Lyme disease. Intervening on these factors could reduce the individual and health care burden of disseminated Lyme disease. Our findings demonstrate the value of both diagnostic and narrative text data to identify Lyme disease manifestations in the EHR.

Project description:BackgroundElectronic health records (EHRs) provide rich data on many domains not routinely available in other data, as such, they are a promising source to study changes in health outcomes using longitudinal study designs (eg, cohort studies, natural experiments, etc.). Yet, patient attrition rates in these data are unknown.ObjectiveThe objective of this study was to estimate overall and among adults with diabetes or hypertension: (1) patient attrition over a 3-year period at community health centers; and (2) the likelihood that patients with Medicaid permanently switched their source of primary care.Research designA retrospective cohort study of 2012-2017 data from the Accelerating Data Value Across a National Community Health Center Network (ADVANCE) Clinical Data Research Network of community health centers were used to assess EHR data attrition. Oregon Medicaid enrollment and claims data were used to estimate the likelihood of changing the source of primary care.SubjectsA total of 827,657 patients aged 19-64 with ≥1 ambulatory visit from 76 community health center systems across 20 states. In all, 232,891 Oregon Medicaid enrollees (aged 19-64) with a gap of ≥6 months following a claim for a visit billed to a primary care source.MeasuresPercentage of patients not returning within 3 years of their qualifying visit (attrition). The probability that a patient with Medicaid permanently changed their primary care source.ResultsAttrition over the 3 years averaged 33.5%; attrition rates were lower (<25%) among patients with diabetes and/or hypertension. Among Medicaid enrollees, the percentage of provider change after a 6-month gap between visits was 12% for community health center patients compared with 39% for single-provider practice patients. Over 3 years, the likelihood of a patient changing to a new provider increased with length of time since their last visit but remained lowest among community health center patients.ConclusionThis study demonstrates the use of the EHR dataset is a reliable source of data to support longitudinal studies while highlighting variability in attrition by primary care source and chronic conditions.

Project description:Abstract Objective Hypertension has long been recognized as one of the most important predisposing factors for cardiovascular diseases and mortality. In recent years, machine learning methods have shown potential in diagnostic and predictive approaches in chronic diseases. Electronic health records (EHRs) have emerged as a reliable source of longitudinal data. The aim of this study is to predict the onset of hypertension using modern deep learning (DL) architectures, specifically long short-term memory (LSTM) networks, and longitudinal EHRs. Materials and Methods We compare this approach to the best performing models reported from previous works, particularly XGboost, applied to aggregated features. Our work is based on data from 233 895 adult patients from a large health system in the United States. We divided our population into 2 distinct longitudinal datasets based on the diagnosis date. To ensure generalization to unseen data, we trained our models on the first dataset (dataset A “train and validation”) using cross-validation, and then applied the models to a second dataset (dataset B “test”) to assess their performance. We also experimented with 2 different time-windows before the onset of hypertension and evaluated the impact on model performance. Results With the LSTM network, we were able to achieve an area under the receiver operating characteristic curve value of 0.98 in the “train and validation” dataset A and 0.94 in the “test” dataset B for a prediction time window of 1 year. Lipid disorders, type 2 diabetes, and renal disorders are found to be associated with incident hypertension. Conclusion These findings show that DL models based on temporal EHR data can improve the identification of patients at high risk of hypertension and corresponding driving factors. In the long term, this work may support identifying individuals who are at high risk for developing hypertension and facilitate earlier intervention to prevent the future development of hypertension.

Project description:Blacks/African-Americans are overrepresented in the number of COVID-19 infections, hospitalizations and deaths. Reasons for this disparity have not been well-characterized but may be due to underlying comorbidities or sociodemographic factors. To systematically determine patient characteristics associated with racial/ethnic disparities in COVID-19 outcomes. A retrospective cohort study with comparative control groups. Patients tested for COVID-19 at University of Michigan Medicine from March 10, 2020 to April 22, 2020. 5,698 tested patients and two sets of comparison groups who were not tested for COVID-19: randomly selected unmatched controls (n = 7,211) and frequency-matched controls by race, age, and sex (n = 13,351). Main Outcomes and Measures: We identified factors associated with testing and testing positive for COVID-19, being hospitalized, requiring intensive care unit (ICU) admission, and mortality (in/out-patient during the time frame). Factors included race/ethnicity, age, smoking, alcohol consumption, healthcare utilization, and residential-level socioeconomic characteristics (SES; i.e., education, unemployment, population density, and poverty rate). Medical comorbidities were defined from the International Classification of Diseases (ICD) codes, and were aggregated into a comorbidity score. Of 5,698 patients, (median age, 47 years; 38% male; mean BMI, 30.1), the majority were non-Hispanic Whites (NHW, 59.2%) and non-Hispanic Black/African-Americans (NHAA, 17.2%). Among 1,119 diagnosed, there were 41.2% NHW and 37.4% NHAA; 44.8% hospitalized, 20.6% admitted to ICU, and 3.8% died. Adjusting for age, sex, and SES, NHAA were 1.66 times more likely to be hospitalized (95% CI, 1.09-2.52; P=.02), 1.52 times more likely to enter ICU (95% CI, 0.92-2.52; P=.10). In addition to older age, male sex and obesity, high population density neighborhood (OR, 1.27 associated with one SD change [95% CI, 1.20-1.76]; P=.02) was associated with hospitalization. Pre-existing kidney disease led to 2.55 times higher risk of hospitalization (95% CI, 1.62-4.02; P<.001) in the overall population and 11.9 times higher mortality risk in NHAA (95% CI, 2.2-64.7, P=.004). Pre-existing type II diabetes/kidney diseases and living in high population density areas were associated with high risk for COVID-19 susceptibility and poor prognosis. Association of risk factors with COVID-19 outcomes differed by race. NHAA patients were disproportionately affected by obesity and kidney disease.

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CKD subpopulations defined by risk-factors: A longitudinal analysis of electronic health records.

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