Background Clinical sequencing data should be shared in order to achieve the sufficient scale and diversity required to provide strong evidence for improving patient care. A distributed research network allows researchers to share this evidence rather than the patient-level data across centers, thereby avoiding privacy issues. The Observational Medical Outcomes Partnership (OMOP) common data model (CDM) used in distributed research networks has low coverage of sequencing data and does not reflect the latest trends of precision medicine. Objective The aim of this study was to develop and evaluate the feasibility of a genomic CDM (G-CDM), as an extension of the OMOP-CDM, for application of genomic data in clinical practice. Methods Existing genomic data models and sequencing reports were reviewed to extend the OMOP-CDM to cover genomic data. The Human Genome Organisation Gene Nomenclature Committee and Human Genome Variation Society nomenclature were adopted to standardize the terminology in the model. Sequencing data of 114 and 1060 patients with lung cancer were obtained from the Ajou University School of Medicine database of Ajou University Hospital and The Cancer Genome Atlas, respectively, which were transformed to a format appropriate for the G-CDM. The data were compared with respect to gene name, variant type, and actionable mutations. Results The G-CDM was extended into four tables linked to tables of the OMOP-CDM. Upon comparison with The Cancer Genome Atlas data, a clinically actionable mutation, p.Leu858Arg, in the EGFR gene was 6.64 times more frequent in the Ajou University School of Medicine database, while the p.Gly12Xaa mutation in the KRAS gene was 2.02 times more frequent in The Cancer Genome Atlas dataset. The data-exploring tool GeneProfiler was further developed to conduct descriptive analyses automatically using the G-CDM, which provides the proportions of genes, variant types, and actionable mutations. GeneProfiler also allows for querying the specific gene name and Human Genome Variation Society nomenclature to calculate the proportion of patients with a given mutation. Conclusions We developed the G-CDM for effective integration of genomic data with standardized clinical data, allowing for data sharing across institutes. The feasibility of the G-CDM was validated by assessing the differences in data characteristics between two different genomic databases through the proposed data-exploring tool GeneProfiler. The G-CDM may facilitate analyses of interoperating clinical and genomic datasets across multiple institutions, minimizing privacy issues and enabling researchers to better understand the characteristics of patients and promote personalized medicine in clinical practice.
This cohort study investigates differences in dual combination therapy use for hypertension in 8 countries and territories by country and patient demographic group.
Background Myocardial injury after noncardiac surgery (MINS) is associated with increased postoperative mortality, but the relevant perioperative factors that contribute to the mortality of patients with MINS have not been fully evaluated. Objective To establish a comprehensive body of knowledge relating to patients with MINS, we researched the best performing predictive model based on machine learning algorithms. Methods Using clinical data from 7629 patients with MINS from the clinical data warehouse, we evaluated 8 machine learning algorithms for accuracy, precision, recall, F1 score, area under the receiver operating characteristic (AUROC) curve, and area under the precision-recall curve to investigate the best model for predicting mortality. Feature importance and Shapley Additive Explanations values were analyzed to explain the role of each clinical factor in patients with MINS. Results Extreme gradient boosting outperformed the other models. The model showed an AUROC of 0.923 (95% CI 0.916-0.930). The AUROC of the model did not decrease in the test data set (0.894, 95% CI 0.86-0.922; P=.06). Antiplatelet drugs prescription, elevated C-reactive protein level, and beta blocker prescription were associated with reduced 30-day mortality. Conclusions Predicting the mortality of patients with MINS was shown to be feasible using machine learning. By analyzing the impact of predictors, markers that should be cautiously monitored by clinicians may be identified.
Myocardial injury after non-cardiac surgery (MINS) is strongly associated with postoperative outcomes. We developed a prediction model for MINS and have provided it online. Between January 2010 and June 2019, a total of 6811 patients underwent non-cardiac surgery with normal preoperative level of cardiac troponin (cTn). We used machine learning techniques with an extreme gradient boosting algorithm to evaluate the effects of variables on MINS development. We generated two prediction models based on the top 12 and 6 variables. MINS was observed in 1499 (22.0%) patients. The top 12 variables in descending order according to the effects on MINS are preoperative cTn level, intraoperative inotropic drug infusion, operation duration, emergency operation, operation type, age, high-risk surgery, body mass index, chronic kidney disease, coronary artery disease, intraoperative red blood cell transfusion, and current alcoholic use. The prediction models are available at https://sjshin.shinyapps.io/mins_occur_prediction/. The estimated thresholds were 0.47 in 12-variable models and 0.53 in 6-variable models. The areas under the receiver operating characteristic curves are 0.78 (95% confidence interval [CI] 0.77–0.78) and 0.77 (95% CI 0.77–0.78), respectively, with an accuracy of 0.97 for both models. Using machine learning techniques, we demonstrated prediction models for MINS. These models require further verification in other populations.
BACKGROUND Myocardial injury after noncardiac surgery (MINS) is associated with increased postoperative mortality, but the relevant perioperative factors that contribute to the mortality of patients with MINS have not been fully evaluated. OBJECTIVE To establish a comprehensive body of knowledge relating to patients with MINS, we researched the best performing predictive model based on machine learning algorithms. METHODS Using clinical data for 7,629 patients with MINS from the Clinical Data Warehouse, we evaluated eight machine learning algorithms for accuracy, precision, recall, F1 score, AUROC (area under the receiver operating characteristic) curve, and area under the precision-recall curve to investigate the best model for predicting mortality. Feature importance and SHapley Additive exPlanations value were analyzed to explain the role of each clinical factor in patients with MINS. RESULTS Extreme gradient boosting outperformed the other models. The model showed AUROC of 0.923 (95% confidence interval (CI): 0.916–0.930). The AUROC of the model was not decreased in the test dataset (0.894, 95% CI: 0.86–0.922) (P =.06). Antiplatelet drugs prescription, elevated C-reactive protein level, and beta blocker prescription were associated with reduced 30-day mortality. CONCLUSIONS Predicting mortality of patients with MINS was shown to be feasible using machine learning. By analyzing the impact of predictors, markers that should be cautiously monitored by clinicians may be identified.
Studies have reported conflicting results on the association between the use of renin-angiotensin-aldosterone system (RAAS) inhibitors and cancer development. We compared the incidence of cancer between patients using RAAS inhibitors and other antihypertensive drugs. This retrospective observational cohort study used data from seven hospitals in Korea that were converted for use in the Observational Medical Outcomes Partnership Common Data Model. A total of 166,071 patients on antihypertensive therapy across the databases of the seven hospitals were divided into two groups according to the use of RAAS inhibitors. The primary outcome was the occurrence of cancer. A total of 166,071 patients across the databases of the seven hospitals was included in the final analysis; 26,650 (16%) were in the RAAS inhibitors group and 139,421 (84%) in the other antihypertensive drugs group. The meta-analysis of the whole cohort showed a lower incidence of cancer occurrence in the RAAS inhibitor group (9.90 vs. 13.28 per 1000 person years; HR, 0.81; 95% confidence interval [CI], 0.75–0.88). After propensity-score matching, the RAAS inhibitor group consistently showed a lower incidence of cancer (9.90 vs. 13.28 per 1000 person years; HR, 0.86; 95% CI, 0.81–0.91). The patients using RAAS inhibitors showed a lower incidence of cancer compared with those using other antihypertensive drugs. These findings support the association between the use of RAAS inhibitors and cancer occurrence.
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