Dataset Information

General Relative Rate Models for the Analysis of Studies Using Case-Cohort Designs.

ABSTRACT: A standard approach to analysis of case-cohort data involves fitting log-linear models. In this paper, we describe how standard statistical software can be used to fit a broad class of general relative rate models to case-cohort data and derive confidence intervals. We focus on a case-cohort design in which a roster has been assembled and events ascertained but additional information needs to be collected on explanatory variables. The additional information is ascertained just for persons who experience the event of interest and for a sample of the cohort members enumerated at study entry. One appeal of such a case-cohort design is that this sample of the cohort may be used to support analyses of several outcomes. The ability to fit general relative rate models to case-cohort data may allow an investigator to reduce model misspecification in exposure-response analyses, fit models in which some factors have effects that are additive and others multiplicative, and facilitate estimation of relative excess risk due to interaction. We address model fitting for simple random sampling study designs as well as stratified designs. Data on lung cancer among radon-exposed men (Colorado Plateau uranium miners, 1950-1990) are used to illustrate these methods.

SUBMITTER: Richardson DB

PROVIDER: S-EPMC8045475 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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General Relative Rate Models for the Analysis of Studies Using Case-Cohort Designs.

Richardson David B DB Langholz Bryan B Kelly-Reif Kaitlin K

American journal of epidemiology 20190201 2

A standard approach to analysis of case-cohort data involves fitting log-linear models. In this paper, we describe how standard statistical software can be used to fit a broad class of general relative rate models to case-cohort data and derive confidence intervals. We focus on a case-cohort design in which a roster has been assembled and events ascertained but additional information needs to be collected on explanatory variables. The additional information is ascertained just for persons who ex ...[more]

PMID: 30339180

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Project description:BackgroundLarge prospective cohort studies have been fruitful for identifying exposure-disease associations. In a cohort where biospecimens (e.g., blood, urine) were collected at enrollment, analysts can exploit a case-cohort approach: Biospecimens from a random sample of cohort participants, called the "subcohort," plus a sample of incident cases that were not part of the subcohort are assayed. Reusing subcohort data for multiple disease outcomes can reduce costs and conserve specimen archives. Pooling biospecimen samples before assay could both save money and reduce depletion of the archive but has not been studied for cohort studies.ObjectivesWe develop and evaluate a biospecimen pooling strategy for case-cohort analyses that relate an exposure to risk of a rare disease.MethodsOur approach involves constructing pooling sets for cases not in the subcohort after grouping them according to time of diagnosis (e.g., age). In contrast, members of the subcohort are grouped by age at entry before constructing pooling sets. The analyst then fits a logistic regression model that jointly stratifies by age at risk and pooling set size and adjusts for confounders. We used simulations (288 sampling scenarios with 1,000 simulated datasets each) to evaluate the performance of this approach for several sizes of pooling sets and illustrated its application to environmental epidemiologic studies by reanalyzing Sister Study data.ResultsParameter estimates were nearly unbiased, and 95% confidence intervals constructed using a bootstrap estimate of the standard error performed well. In statistical tests also based on the bootstrap standard error, pooling up to 8 specimens per pool caused only modest loss of power. Assigning more cohort members to the subcohort and commensurately increasing the number of specimens per pool improved power and precision substantially while reducing the number of assays.DiscussionWhen using case-cohort analysis to study disease outcomes in relation to exposures assessed using biospecimens in a cohort study, epidemiologists should consider biospecimen pooling as a way to improve statistical power, conserve irreplaceable archives, and save money. https://doi.org/10.1289/EHP14476.

Project description:ImportanceLow academic achievement (AA) in childhood and adolescence is associated with increased substance use. Empirical evidence, using longitudinal epidemiologic data, may provide support for interventions to improve AA as a means to reduce risk of drug abuse (DA).ObjectiveTo clarify the nature of the association between adolescent AA and risk of DA by using instrumental variable and co-relative analysis designs.Design, setting, and participantsThis study, assessing nationwide data from individuals born in Sweden between 1971 and 1982, used instrumental variable and co-relative analyses of the association between AA and DA. The instrument was month of birth. Co-relative analyses were conducted in pairs of cousins (263 222 pairs), full siblings (154 295), and monozygotic twins (1623) discordant for AA, with raw results fitted to a genetic model. The AA-DA association was modeled using Cox regression. Data analysis was conducted from October 2017 to January 2018.ExposuresAcademic achievement assessed at 16 years of age (for instrumental variable analyses), and estimated discordance in AA in pairs of monozygotic twins (for co-relative analyses).Main outcomes and measuresDrug abuse registration in national medical, criminal, or pharmacy registries.ResultsThis instrumental variable analysis included 934 462 participants (478 341 males and 456 121 females) with a mean (SD) age of 34.7 (4.3) years at a mean follow-up of 19 years. Earlier month of birth was associated with a linear effect on AA, with the regression coefficient per month equaling -0.0225 SDs (95% CI, -0.0231 to -0.0219). Controlling for AA, month of birth had no association with risk of DA (hazard ratio [HR], 1.000; 95% CI, 0.997-1.004). Lower AA had a significant association with risk of subsequent DA registration (HR per SD, 2.33; 95% CI, 2.30-2.35). Instrumental variable analysis produced a substantial but modestly attenuated association (HR, 2.04; 95% CI, 1.75-2.33). Controlling for modest associations between month of birth and parental educational status and DA risk reduced the association to a HR of 1.92 (95% CI, 1.67-2.22). The genetic model applied to the results of co-relative analyses fitted the observed data well and estimated the AA-DA association in monozygotic twins discordant for AA to equal a HR of 1.79 (95% CI, 1.64-1.92).Conclusions and relevanceTwo different methodological approaches with divergent assumptions both produced results consistent with the hypothesis that the significant association observed between AA at 16 years of age and risk of DA into middle adulthood may be causal. These results provide empirical support for efforts to improve AA as a means to reduce risk of DA.

Project description:BackgroundThe rapid growth of high-throughput sequencing-based microbiome profiling has yielded tremendous insights into human health and physiology. Data generated from high-throughput sequencing of 16S rRNA gene amplicons are often preprocessed into composition or relative abundance. However, reproducibility has been lacking due to the myriad of different experimental and computational approaches taken in these studies. Microbiome studies may report varying results on the same topic, therefore, meta-analyses examining different microbiome studies to provide consistent and robust results are important. So far, there is still a lack of implemented methods to properly examine differential relative abundances of microbial taxonomies and to perform meta-analysis examining the heterogeneity and overall effects across microbiome studies.ResultsWe developed an R package 'metamicrobiomeR' that applies Generalized Additive Models for Location, Scale and Shape (GAMLSS) with a zero-inflated beta (BEZI) family (GAMLSS-BEZI) for analysis of microbiome relative abundance datasets. Both simulation studies and application to real microbiome data demonstrate that GAMLSS-BEZI well performs in testing differential relative abundances of microbial taxonomies. Importantly, the estimates from GAMLSS-BEZI are log (odds ratio) of relative abundances between comparison groups and thus are analogous between microbiome studies. As such, we also apply random effects meta-analysis models to pool estimates and their standard errors across microbiome studies. We demonstrate the meta-analysis examples and highlight the utility of our package on four studies comparing gut microbiomes between male and female infants in the first six months of life.ConclusionsGAMLSS-BEZI allows proper examination of microbiome relative abundance data. Random effects meta-analysis models can be directly applied to pool comparable estimates and their standard errors to evaluate the overall effects and heterogeneity across microbiome studies. The examples and workflow using our 'metamicrobiomeR' package are reproducible and applicable for the analyses and meta-analyses of other microbiome studies.

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General Relative Rate Models for the Analysis of Studies Using Case-Cohort Designs.

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General Relative Rate Models for the Analysis of Studies Using Case-Cohort Designs.

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