A hybrid parametric and empirical likelihood model for evaluating interactions in case-control Studies.
Ontology highlight
ABSTRACT:
SUBMITTER: Qin J
PROVIDER: S-EPMC8247649 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:This paper develops a hybrid likelihood (HL) method based on a compromise between parametric and nonparametric likelihoods. Consider the setting of a parametric model for the distribution of an observation Y with parameter θ. Suppose there is also an estimating function m(·, μ) identifying another parameter μ via Em(Y, μ) = 0, at the outset defined independently of the parametric model. To borrow strength from the parametric model while obtaining a degree of robustness from the empirical likelihood method, we formulate inference about θ in terms of the hybrid likelihood function Hn (θ) = Ln (θ)1-a Rn (μ(θ)) a . Here a ∈ [0,1) represents the extent of the compromise, Ln is the ordinary parametric likelihood for θ, Rn is the empirical likelihood function, and μ is considered through the lens of the parametric model. We establish asymptotic normality of the corresponding HL estimator and a version of the Wilks theorem. We also examine extensions of these results under misspecification of the parametric model, and propose methods for selecting the balance parameter a.
| S-EPMC6602551 | biostudies-literature
Project description:In the past few years, case-control studies of common diseases have shifted their focus from single genes to whole exomes. New sequencing technologies now routinely detect hundreds of thousands of sequence variants in a single study, many of which are rare or even novel. The limitation of classical single-marker association analysis for rare variants has been a challenge in such studies. A new generation of statistical methods for case-control association studies has been developed to meet this challenge. A common approach to association analysis of rare variants is the burden-style collapsing methods to combine rare variant data within individuals across or within genes. Here, we propose a new hybrid likelihood model that combines a burden test with a test of the position distribution of variants. In extensive simulations and on empirical data from the Dallas Heart Study, the new model demonstrates consistently good power, in particular when applied to a gene set (e.g., multiple candidate genes with shared biological function or pathway), when rare variants cluster in key functional regions of a gene, and when protective variants are present. When applied to data from an ongoing sequencing study of bipolar disorder (191 cases, 107 controls), the model identifies seven gene sets with nominal p-values < 0.05, of which one MAPK signaling pathway (KEGG) reaches trend-level significance after correcting for multiple testing.
| S-EPMC3554549 | biostudies-literature
Project description:BACKGROUND: Epistasis, i.e., the interaction of alleles at different loci, is thought to play a central role in the formation and progression of complex diseases. The complexity of disease expression should arise from a complex network of epistatic interactions involving multiple genes. METHODOLOGY: We develop a general model for testing high-order epistatic interactions for a complex disease in a case-control study. We incorporate the quantitative genetic theory of high-order epistasis into the setting of cases and controls sampled from a natural population. The new model allows the identification and testing of epistasis and its various genetic components. CONCLUSIONS: Simulation studies were used to examine the power and false positive rates of the model under different sampling strategies. The model was used to detect epistasis in a case-control study of inflammatory bowel disease, in which five SNPs at a candidate gene were typed, leading to the identification of a significant three-locus epistasis.
| S-EPMC2909900 | biostudies-literature
Project description:Bayes factor analysis has the attractive property of accommodating the risks of both false negatives and false positives when identifying susceptibility gene variants in genome-wide association studies (GWASs). For a particular SNP, the critical aspect of this analysis is that it incorporates the probability of obtaining the observed value of a statistic on disease association under the alternative hypotheses of non-null association. An approximate Bayes factor (ABF) was proposed by Wakefield (Genetic Epidemiology 2009;33:79-86) based on a normal prior for the underlying effect-size distribution. However, misspecification of the prior can lead to failure in incorporating the probability under the alternative hypothesis. In this paper, we propose a semi-parametric, empirical Bayes factor (SP-EBF) based on a nonparametric effect-size distribution estimated from the data. Analysis of several GWAS datasets revealed the presence of substantial numbers of SNPs with small effect sizes, and the SP-EBF attributed much greater significance to such SNPs than the ABF. Overall, the SP-EBF incorporates an effect-size distribution that is estimated from the data, and it has the potential to improve the accuracy of Bayes factor analysis in GWASs.
| S-EPMC8110551 | biostudies-literature
Project description:The sizes of the data matrices assembled to resolve branches of the tree of life have increased dramatically, motivating the development of programs for fast, yet accurate, inference. For example, several different fast programs have been developed in the very popular maximum likelihood framework, including RAxML/ExaML, PhyML, IQ-TREE, and FastTree. Although these programs are widely used, a systematic evaluation and comparison of their performance using empirical genome-scale data matrices has so far been lacking. To address this question, we evaluated these four programs on 19 empirical phylogenomic data sets with hundreds to thousands of genes and up to 200 taxa with respect to likelihood maximization, tree topology, and computational speed. For single-gene tree inference, we found that the more exhaustive and slower strategies (ten searches per alignment) outperformed faster strategies (one tree search per alignment) using RAxML, PhyML, or IQ-TREE. Interestingly, single-gene trees inferred by the three programs yielded comparable coalescent-based species tree estimations. For concatenation-based species tree inference, IQ-TREE consistently achieved the best-observed likelihoods for all data sets, and RAxML/ExaML was a close second. In contrast, PhyML often failed to complete concatenation-based analyses, whereas FastTree was the fastest but generated lower likelihood values and more dissimilar tree topologies in both types of analyses. Finally, data matrix properties, such as the number of taxa and the strength of phylogenetic signal, sometimes substantially influenced the programs' relative performance. Our results provide real-world gene and species tree phylogenetic inference benchmarks to inform the design and execution of large-scale phylogenomic data analyses.
| S-EPMC5850867 | biostudies-literature
Project description:BACKGROUND:Standard random-effects meta-analysis methods perform poorly when applied to few studies only. Such settings however are commonly encountered in practice. It is unclear, whether or to what extent small-sample-size behaviour can be improved by more sophisticated modeling. METHODS:We consider likelihood-based methods, the DerSimonian-Laird approach, Empirical Bayes, several adjustment methods and a fully Bayesian approach. Confidence intervals are based on a normal approximation, or on adjustments based on the Student-t-distribution. In addition, a linear mixed model and two generalized linear mixed models (GLMMs) assuming binomial or Poisson distributed numbers of events per study arm are considered for pairwise binary meta-analyses. We extract an empirical data set of 40 meta-analyses from recent reviews published by the German Institute for Quality and Efficiency in Health Care (IQWiG). Methods are then compared empirically as well as in a simulation study, based on few studies, imbalanced study sizes, and considering odds-ratio (OR) and risk ratio (RR) effect sizes. Coverage probabilities and interval widths for the combined effect estimate are evaluated to compare the different approaches. RESULTS:Empirically, a majority of the identified meta-analyses include only 2 studies. Variation of methods or effect measures affects the estimation results. In the simulation study, coverage probability is, in the presence of heterogeneity and few studies, mostly below the nominal level for all frequentist methods based on normal approximation, in particular when sizes in meta-analyses are not balanced, but improve when confidence intervals are adjusted. Bayesian methods result in better coverage than the frequentist methods with normal approximation in all scenarios, except for some cases of very large heterogeneity where the coverage is slightly lower. Credible intervals are empirically and in the simulation study wider than unadjusted confidence intervals, but considerably narrower than adjusted ones, with some exceptions when considering RRs and small numbers of patients per trial-arm. Confidence intervals based on the GLMMs are, in general, slightly narrower than those from other frequentist methods. Some methods turned out impractical due to frequent numerical problems. CONCLUSIONS:In the presence of between-study heterogeneity, especially with unbalanced study sizes, caution is needed in applying meta-analytical methods to few studies, as either coverage probabilities might be compromised, or intervals are inconclusively wide. Bayesian estimation with a sensibly chosen prior for between-trial heterogeneity may offer a promising compromise.
| S-EPMC6330405 | biostudies-literature
Project description:In genetic association studies it is becoming increasingly imperative to have large sample sizes to identify and replicate genetic effects. To achieve these sample sizes, many research initiatives are encouraging the collaboration and combination of several existing matched and unmatched case-control studies. Thus, it is becoming more common to compare multiple sets of controls with the same case group or multiple case groups to validate or confirm a positive or negative finding. Usually, a naive approach of fitting separate models for each case-control comparison is used to make inference about disease-exposure association. But, this approach does not make use of all the observed data and hence could lead to inconsistent results. The problem is compounded when a common case group is used in each case-control comparison. An alternative to fitting separate models is to use a polytomous logistic model but, this model does not combine matched and unmatched case-control data. Thus, we propose a polytomous logistic regression approach based on a latent group indicator and a conditional likelihood to do a combined analysis of matched and unmatched case-control data. We use simulation studies to evaluate the performance of the proposed method and a case-control study of multiple myeloma and Inter-Leukin-6 as an example. Our results indicate that the proposed method leads to a more efficient homogeneity test and a pooled estimate with smaller standard error.
| S-EPMC2889167 | biostudies-literature
Project description:Systematic reviews of diagnostic tests often involve a mixture of case-control and cohort studies. The standard methods for evaluating diagnostic accuracy only focus on sensitivity and specificity and ignore the information on disease prevalence contained in cohort studies. Consequently, such methods cannot provide estimates of measures related to disease prevalence, such as population averaged or overall positive and negative predictive values, which reflect the clinical utility of a diagnostic test. In this paper, we propose a hybrid approach that jointly models the disease prevalence along with the diagnostic test sensitivity and specificity in cohort studies, and the sensitivity and specificity in case-control studies. In order to overcome the potential computational difficulties in the standard full likelihood inference of the proposed hybrid model, we propose an alternative inference procedure based on the composite likelihood. Such composite likelihood based inference does not suffer computational problems and maintains high relative efficiency. In addition, it is more robust to model mis-specifications compared to the standard full likelihood inference. We apply our approach to a review of the performance of contemporary diagnostic imaging modalities for detecting metastases in patients with melanoma.
| S-EPMC4401477 | biostudies-literature
Project description:Nested case-control (NCC) design is used frequently in epidemiological studies as a cost-effective subcohort sampling strategy to conduct biomarker research. Sampling strategy, on the other hoand, creates challenges for data analysis because of outcome-dependent missingness in biomarker measurements. In this paper, we propose inverse probability weighted (IPW) methods for making inference about the prognostic accuracy of a novel biomarker for predicting future events with data from NCC studies. The consistency and asymptotic normality of these estimators are derived using the empirical process theory and convergence theorems for sequences of weakly dependent random variables. Simulation and analysis using Framingham Offspring Study data suggest that the proposed methods perform well in finite samples.
| S-EPMC3276269 | biostudies-other
Project description:BackgroundCase-control studies based on pharmaco-epidemiological databases typically use decision rules to determine exposure status from information on dates of prescription redemptions, although this induces misclassification. The reverse Waiting Time Distribution has been suggested as a likelihood based model to estimate the latent exposure status, and we therefore suggest to extend this into a joint likelihood based model, which incorporates both the latent exposure status and the exposure-outcome association. This will achieve consistency and efficiency of the estimates, i.e. they can be expected to be asymptotically unbiased and have optimal precision.MethodsWe established a joint likelihood for the observed case-control status and last prescription redemption before the index date. The likelihood combines the ordinary logistic regression likelihood and the reverse Waiting Time Distribution, and allows inclusion of covariates in both parts to adjust for observed confounders. We conducted a simulation study of the new model and standard models based on decision rules for exposure and the probability of being exposed, respectively, to assess the relative bias and variability of estimates. Lastly, we applied the models to a case-control study on use of nonsteroidal anti-inflammatory drugs and risk of upper-gastrointestinal bleeding.ResultsIn simulation studies the new model had low relative bias (< 1.4%) and largely retained nominal coverage probabilities (90.2% to 95.1% of nominal 95% confidence intervals), also when moderate misspecification was introduced. All standard methods generally had substantial bias (-21.1% to 17.0%) and low coverage probabilities (0.0% to 68.9%). When analyzing the empirical case-control study, the new method estimated the effect of nonsteroidal anti-inflammatory drugs on risk of with upper-gastrointestinal bleeding hospitalization to 2.52 (1.59 - 3.45), whereas the other methods had estimates ranging from 3.52 (2.19 - 5.65) to 5.17 (2.40 - 11.11).ConclusionsUnlike standard methods, the proposed model gave nearly unbiased estimates with adequate coverage probabilities in simulation studies. The developed model demonstrates the potential for the reverse Waiting Time Distribution to be integrated with existing likelihood based analyses in pharmacoepidemiological studies.
| S-EPMC8265059 | biostudies-literature