ArticleBMC medical research methodology2015
Permutation-based variance component test in generalized linear mixed model with application to multilocus genetic association study.
Article in BMC medical research methodology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM).PLoS computational biology · 2025Article
- Long-term adverse influence of smoking during pregnancy on height and body size of offspring at ten years old in the UK Biobank cohort.SSM - population health · 2023Article
- How can childhood maltreatment affect post-traumatic stress disorder in adult: Results from a composite null hypothesis perspective of mediation analysis.Frontiers in psychiatry · 2023Article
- A comprehensive comparison of multilocus association methods with summary statistics in genome-wide association studies.BMC bioinformatics · 2022Article
- IUSMMT: Survival mediation analysis of gene expression with multiple DNA methylation exposures and its application to cancers of TCGA.PLoS computational biology · 2021Article
- Detection of Genetic Overlap Between Rheumatoid Arthritis and Systemic Lupus Erythematosus Using GWAS Summary Statistics.Frontiers in genetics · 2021Article
- Extending Tests of Random Effects to Assess for Measurement Invariance in Factor Models.Statistics in biosciences · 2018Article
- Detecting heritable phenotypes without a model using fast permutation testing for heritability and set-tests.Nature communications · 2018Article
- Boosting Gene Mapping Power and Efficiency with Efficient Exact Variance Component Tests of Single Nucleotide Polymorphism Sets.Genetics · 2016Article
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5 authors.
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Abstract
backgroundIn many medical studies the likelihood ratio test (LRT) has been widely applied to examine whether the random effects variance component is zero within the mixed effects models framework; whereas little work about likelihood-ratio based variance component test has been done in the generalized linear mixed models (GLMM), where the response is discrete and the log-likelihood cannot be computed exactly. Before applying the LRT for variance component in GLMM, several difficulties need to be overcome, including the computation of the log-likelihood, the parameter estimation and the derivation of the null distribution for the LRT statistic.
methodsTo overcome these problems, in this paper we make use of the penalized quasi-likelihood algorithm and calculate the LRT statistic based on the resulting working response and the quasi-likelihood. The permutation procedure is used to obtain the null distribution of the LRT statistic. We evaluate the permutation-based LRT via simulations and compare it with the score-based variance component test and the tests based on the mixture of chi-square distributions. Finally we apply the permutation-based LRT to multilocus association analysis in the case-control study, where the problem can be investigated under the framework of logistic mixed effects model.
resultsThe simulations show that the permutation-based LRT can effectively control the type I error rate, while the score test is sometimes slightly conservative and the tests based on mixtures cannot maintain the type I error rate. Our studies also show that the permutation-based LRT has higher power than these existing tests and still maintains a reasonably high power even when the random effects do not follow a normal distribution. The application to GAW17 data also demonstrates that the proposed LRT has a higher probability to identify the association signals than the score test and the tests based on mixtures.
conclusionsIn the present paper the permutation-based LRT was developed for variance component in GLMM. The LRT outperforms existing tests and has a reasonably higher power under various scenarios; additionally, it is conceptually simple and easy to implement.
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