Health administrative data enrichment using cohort information: Comparative evaluation of methods by simulation and application to real data.
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ABSTRACT:
SUBMITTER: Silenou BC
PROVIDER: S-EPMC6354983 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND:Joint modelling of longitudinal and time-to-event data is often preferred over separate longitudinal or time-to-event analyses as it can account for study dropout, error in longitudinally measured covariates, and correlation between longitudinal and time-to-event outcomes. The joint modelling literature focuses mainly on the analysis of single studies with no methods currently available for the meta-analysis of joint model estimates from multiple studies. METHODS:We propose a 2-stage method for meta-analysis of joint model estimates. These methods are applied to the INDANA dataset to combine joint model estimates of systolic blood pressure with time to death, time to myocardial infarction, and time to stroke. Results are compared to meta-analyses of separate longitudinal or time-to-event models. A simulation study is conducted to contrast separate versus joint analyses over a range of scenarios. RESULTS:Using the real dataset, similar results were obtained by using the separate and joint analyses. However, the simulation study indicated a benefit of use of joint rather than separate methods in a meta-analytic setting where association exists between the longitudinal and time-to-event outcomes. CONCLUSIONS:Where evidence of association between longitudinal and time-to-event outcomes exists, results from joint models over standalone analyses should be pooled in 2-stage meta-analyses.
| S-EPMC5887954 | biostudies-literature
Project description:BackgroundJoint modeling of longitudinal and time-to-event data is often advantageous over separate longitudinal or time-to-event analyses as it can account for study dropout, error in longitudinally measured covariates, and correlation between longitudinal and time-to-event outcomes. The current literature on joint modeling focuses mainly on the analysis of single studies with a lack of methods available for the meta-analysis of joint data from multiple studies.MethodsWe investigate a variety of one-stage methods for the meta-analysis of joint longitudinal and time-to-event outcome data. These methods are applied to the INDANA dataset to investigate longitudinally measured systolic blood pressure, with each of time to death, time to myocardial infarction, and time to stroke. Results are compared to separate longitudinal or time-to-event meta-analyses. A simulation study is conducted to contrast separate versus joint analyses over a range of scenarios.ResultsThe performance of the examined one-stage joint meta-analytic models varied. Models that accounted for between study heterogeneity performed better than models that ignored it. Of the examined methods to account for between study heterogeneity, under the examined association structure, fixed effect approaches appeared preferable, whereas methods involving a baseline hazard stratified by study were least time intensive.ConclusionsOne-stage joint meta-analytic models that accounted for between study heterogeneity using a mix of fixed effects or a stratified baseline hazard were reliable; however, models examined that included study level random effects in the association structure were less reliable.
| S-EPMC6492085 | biostudies-literature
Project description:ObjectiveThis research proposes a model-based method to facilitate the selection of disease case definitions from validation studies for administrative health data. The method is demonstrated for a rheumatoid arthritis (RA) validation study.Study design and settingData were from 148 definitions to ascertain cases of RA in hospital, physician and prescription medication administrative data. We considered: (A) separate univariate models for sensitivity and specificity, (B) univariate model for Youden's summary index and (C) bivariate (ie, joint) mixed-effects model for sensitivity and specificity. Model covariates included the number of diagnoses in physician, hospital and emergency department records, physician diagnosis observation time, duration of time between physician diagnoses and number of RA-related prescription medication records.ResultsThe most common case definition attributes were: 1+ hospital diagnosis (65%), 2+ physician diagnoses (43%), 1+ specialist physician diagnosis (51%) and 2+ years of physician diagnosis observation time (27%). Statistically significant improvements in sensitivity and/or specificity for separate univariate models were associated with (all p values <0.01): 2+ and 3+ physician diagnoses, unlimited physician diagnosis observation time, 1+ specialist physician diagnosis and 1+ RA-related prescription medication records (65+ years only). The bivariate model produced similar results. Youden's index was associated with these same case definition criteria, except for the length of the physician diagnosis observation time.ConclusionA model-based method provides valuable empirical evidence to aid in selecting a definition(s) for ascertaining diagnosed disease cases from administrative health data. The choice between univariate and bivariate models depends on the goals of the validation study and number of case definitions.
| S-EPMC5726099 | biostudies-literature
Project description:BackgroundThe analysis of high-throughput gene expression data with respect to sets of genes rather than individual genes has many advantages. A variety of methods have been developed for assessing the enrichment of sets of genes with respect to differential expression. In this paper we provide a comparative study of four of these methods: Fisher's exact test, Gene Set Enrichment Analysis (GSEA), Random-Sets (RS), and Gene List Analysis with Prediction Accuracy (GLAPA). The first three methods use associative statistics, while the fourth uses predictive statistics. We first compare all four methods on simulated data sets to verify that Fisher's exact test is markedly worse than the other three approaches. We then validate the other three methods on seven real data sets with known genetic perturbations and then compare the methods on two cancer data sets where our a priori knowledge is limited.ResultsThe simulation study highlights that none of the three method outperforms all others consistently. GSEA and RS are able to detect weak signals of deregulation and they perform differently when genes in a gene set are both differentially up and down regulated. GLAPA is more conservative and large differences between the two phenotypes are required to allow the method to detect differential deregulation in gene sets. This is due to the fact that the enrichment statistic in GLAPA is prediction error which is a stronger criteria than classical two sample statistic as used in RS and GSEA. This was reflected in the analysis on real data sets as GSEA and RS were seen to be significant for particular gene sets while GLAPA was not, suggesting a small effect size. We find that the rank of gene set enrichment induced by GLAPA is more similar to RS than GSEA. More importantly, the rankings of the three methods share significant overlap.ConclusionThe three methods considered in our study recover relevant gene sets known to be deregulated in the experimental conditions and pathologies analyzed. There are differences between the three methods and GSEA seems to be more consistent in finding enriched gene sets, although no method uniformly dominates over all data sets. Our analysis highlights the deep difference existing between associative and predictive methods for detecting enrichment and the use of both to better interpret results of pathway analysis. We close with suggestions for users of gene set methods.
| S-EPMC2746222 | biostudies-literature
Project description:The circRNAs sequencing results vary due to the different enrichment methods and their performance is needed to systematic comparison. This study investigated the effects of different circRNA enrichment methods on sequencing results, including abundance and species of circRNAs, as well as the sensitivity and precision. This experiment was carried out by following four common circRNA enrichment methods: including ribosomal RNA depletion (rRNA-), polyadenylation and poly (A+) RNA depletion followed by RNase R treatment (polyA+RNase R), rRNA-+polyA+RNase R and polyA+RNase R+ rRNA-. The results showed that polyA+RNase R+ rRNA - enrichment method obtained more circRNA number, higher sensitivity and abundance among them; polyA+RNase R method obtained higher precision. The linear RNAs can be thoroughly removed in all enrichment methods except rRNA depletion method. Overall, our results helps researchers to quickly selection a circRNA enrichment of suitable for own study among many enrichment methods, and it provides a benchmark framework for future improvements circRNA enrichment methods.[Figure: see text].
| S-EPMC8786342 | biostudies-literature
Project description:BackgroundConstruction of co-occurrence networks in metagenomic data often employs correlation to infer pairwise relationships between microbes. However, biological systems are complex and often display qualities non-linear in nature. Therefore, the reliance on correlation alone may overlook important relationships and fail to capture the full breadth of intricacies presented in underlying interaction networks. It is of interest to incorporate metrics that are not only robust in detecting linear relationships, but non-linear ones as well.ResultsIn this paper, we explore the use of various mutual information (MI) estimation approaches for quantifying pairwise relationships in biological data and compare their performances against two traditional measures-Pearson's correlation coefficient, r, and Spearman's rank correlation coefficient, ρ. Metrics are tested on both simulated data designed to mimic pairwise relationships that may be found in ecological systems and real data from a previous study on C. diff infection. The results demonstrate that, in the case of asymmetric relationships, mutual information estimators can provide better detection ability than Pearson's or Spearman's correlation coefficients. Specifically, we find that these estimators have elevated performances in the detection of exploitative relationships, demonstrating the potential benefit of including them in future metagenomic studies.ConclusionsMutual information (MI) can uncover complex pairwise relationships in biological data that may be missed by traditional measures of association. The inclusion of such relationships when constructing co-occurrence networks can result in a more comprehensive analysis than the use of correlation alone.
| S-EPMC11323399 | biostudies-literature
Project description:OBJECTIVE:The aim was to compare multimorbidity patterns identified with the two most commonly used methods: hierarchical cluster analysis (HCA) and exploratory factor analysis (EFA) in a large primary care database. Specific objectives were: (1) to determine whether choice of method affects the composition of these patterns and (2) to consider the potential application of each method in the clinical setting. DESIGN:Cross-sectional study. Diagnoses were based on the 263 corresponding blocks of the International Classification of Diseases version 10. Multimorbidity patterns were identified using HCA and EFA. Analysis was stratified by sex, and results compared for each method. SETTING AND PARTICIPANTS:Electronic health records for 408 994 patients with multimorbidity aged 45-64 years in 274 primary health care teams from 2010 in Catalonia, Spain. RESULTS:HCA identified 53 clusters for women, with just 12 clusters including at least 2 diagnoses, and 15 clusters for men, all of them including at least two diagnoses. EFA showed 9 factors for women and 10 factors for men. We observed differences by sex and method of analysis, although some patterns were consistent. Three combinations of diseases were observed consistently across sex groups and across both methods: hypertension and obesity, spondylopathies and deforming dorsopathies, and dermatitis eczema and mycosis. CONCLUSIONS:This study showed that multimorbidity patterns vary depending on the method of analysis used (HCA vs EFA) and provided new evidence about the known limitations of attempts to compare multimorbidity patterns in real-world data studies. We found that EFA was useful in describing comorbidity relationships and HCA could be useful for in-depth study of multimorbidity. Our results suggest possible applications for each of these methods in clinical and research settings, and add information about some aspects that must be considered in standardisation of future studies: spectrum of diseases, data usage and methods of analysis.
| S-EPMC5875653 | biostudies-literature
Project description:BACKGROUND:Pathway enrichment extensively used in the analysis of Omics data for gaining biological insights into the functional roles of pre-defined subsets of genes, proteins and metabolites. A large number of methods have been proposed in the literature for this task. The vast majority of these methods use as input expression levels of the biomolecules under study together with their membership in pathways of interest. The latest generation of pathway enrichment methods also leverages information on the topology of the underlying pathways, which as evidence from their evaluation reveals, lead to improved sensitivity and specificity. Nevertheless, a systematic empirical comparison of such methods is still lacking, making selection of the most suitable method for a specific experimental setting challenging. This comparative study of nine network-based methods for pathway enrichment analysis aims to provide a systematic evaluation of their performance based on three real data sets with different number of features (genes/metabolites) and number of samples. RESULTS:The findings highlight both methodological and empirical differences across the nine methods. In particular, certain methods assess pathway enrichment due to differences both across expression levels and in the strength of the interconnectedness of the members of the pathway, while others only leverage differential expression levels. In the more challenging setting involving a metabolomics data set, the results show that methods that utilize both pieces of information (with NetGSA being a prototypical one) exhibit superior statistical power in detecting pathway enrichment. CONCLUSION:The analysis reveals that a number of methods perform equally well when testing large size pathways, which is the case with genomic data. On the other hand, NetGSA that takes into consideration both differential expression of the biomolecules in the pathway, as well as changes in the topology exhibits a superior performance when testing small size pathways, which is usually the case for metabolomics data.
| S-EPMC6829999 | biostudies-literature
Project description:PURPOSE:To describe patterns of utilization, survival and infectious events in patients treated with rituximab at the University Hospital of Siena (UHS) to explore the feasibility of combining routinely collected administrative and hospital-pharmacy data for examining the real-world use of intravenous antineoplastic drugs. METHODS:A retrospective, longitudinal cohort study was conducted using data from the Hospital Pharmacy of Siena (HPS) and the Regional Administrative Database of Tuscany (RAD). Patients aged ≥18 years with ≥1 rituximab administration recorded between January 2012 and June 2016 were identified in the HPS database. Anonymized patient-level data were linked to RAD. Rituximab utilization during the first year of treatment was described using HPS. Hospital diagnoses of adverse infectious events that occurred during the first year of follow-up and four-year survival were observed using RAD. RESULTS:A total of 311 new users of rituximab were identified: 264 patients received rituximab for non-Hodgkin's lymphoma (NHL) and 47 were treated for chronic lymphocytic leukemia (CLL). Among new users with one complete year of follow-up (n = 203) over 95% received rituximab as the first-line treatment, and approximately 70% of them received 5-8 doses. No patient in the CLL group received >8 administrations. Four-year survival was approximately 70% in both CLL and NHL patients. Sepsis was the most frequent infectious event observed (5.1%). CONCLUSION:HPS and RAD provided complementary information on rituximab utilization, demonstrating their potential for future pharmacoepidemiological studies on antineoplastic medications administered in the Italian hospital setting. Overall, this general description of the real-world utilization of rituximab in patients treated for NHL and CLL at UHS was in line with treatment guidelines and current knowledge on the rituximab safety profile.
| S-EPMC7067445 | biostudies-literature
Project description:BackgroundThe presence of diverse types of nanomaterials (NMs) in commerce is growing at an exponential pace. As a result, human exposure to these materials in the environment is inevitable, necessitating the need for rapid and reliable toxicity testing methods to accurately assess the potential hazards associated with NMs. In this study, we applied biclustering and gene set enrichment analysis methods to derive essential features of altered lung transcriptome following exposure to NMs that are associated with lung-specific diseases. Several datasets from public microarray repositories describing pulmonary diseases in mouse models following exposure to a variety of substances were examined and functionally related biclusters of genes showing similar expression profiles were identified. The identified biclusters were then used to conduct a gene set enrichment analysis on pulmonary gene expression profiles derived from mice exposed to nano-titanium dioxide (nano-TiO2), carbon black (CB) or carbon nanotubes (CNTs) to determine the disease significance of these data-driven gene sets.ResultsBiclusters representing inflammation (chemokine activity), DNA binding, cell cycle, apoptosis, reactive oxygen species (ROS) and fibrosis processes were identified. All of the NM studies were significant with respect to the bicluster related to chemokine activity (DAVID; FDR p-value = 0.032). The bicluster related to pulmonary fibrosis was enriched in studies where toxicity induced by CNT and CB studies was investigated, suggesting the potential for these materials to induce lung fibrosis. The pro-fibrogenic potential of CNTs is well established. Although CB has not been shown to induce fibrosis, it induces stronger inflammatory, oxidative stress and DNA damage responses than nano-TiO2 particles.ConclusionThe results of the analysis correctly identified all NMs to be inflammogenic and only CB and CNTs as potentially fibrogenic. In addition to identifying several previously defined, functionally relevant gene sets, the present study also identified two novel genes sets: a gene set associated with pulmonary fibrosis and a gene set associated with ROS, underlining the advantage of using a data-driven approach to identify novel, functionally related gene sets. The results can be used in future gene set enrichment analysis studies involving NMs or as features for clustering and classifying NMs of diverse properties.
| S-EPMC4734442 | biostudies-literature