ArticleAmerican journal of human genetics2016
Retrospective Binary-Trait Association Test Elucidates Genetic Architecture of Crohn Disease.
Article in American journal of human genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
18 citing papers in PubMed.
- JASPER: Fast, powerful, multitrait association testing in structured samples gives insight on pleiotropy in gene expression.American journal of human genetics · 2024Article
- RETROSPECTIVE VARYING COEFFICIENT ASSOCIATION ANALYSIS OF LONGITUDINAL BINARY TRAITS: APPLICATION TO THE IDENTIFICATION OF GENETIC LOCI ASSOCIATED WITH HYPERTENSION.The annals of applied statistics · 2024Article
- JASPER: fast, powerful, multitrait association testing in structured samples gives insight on pleiotropy in gene expression.bioRxiv : the preprint server for biology · 2023Article
- BRASS: Permutation methods for binary traits in genetic association studies with structured samples.PLoS genetics · 2023Article
- Genome-Wide Association Study Identified Novel SNPs Associated with Chlorophyll Content in Maize.Genes · 2023Article
- Common genetic variants associated with melanoma risk or naevus count in patients with wildtype MC1R melanoma.The British journal of dermatology · 2022Article
- Comparison of mixed model based approaches for correcting for population substructure with application to extreme phenotype sampling.BMC genomics · 2022Article
- Retrospective Association Analysis of Longitudinal Binary Traits Identifies Important Loci and Pathways in Cocaine Use.Genetics · 2019Article
- Exploration of a diversity of computational and statistical measures of association for genome-wide genetic studies.BioData mining · 2019Article
- Two-way mixed-effects methods for joint association analysis using both host and pathogen genomes.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- L-GATOR: Genetic Association Testing for a Longitudinally Measured Quantitative Trait in Samples with Related Individuals.American journal of human genetics · 2018Article
- Transformation of Summary Statistics from Linear Mixed Model Association on All-or-None Traits to Odds Ratio.Genetics · 2018Article
- A Genome-Wide Association Study of Apple Quality and Scab Resistance.The plant genome · 2018Article
- Association testing of bisulfite-sequencing methylation data via a Laplace approximation.Bioinformatics (Oxford, England) · 2017Article
- Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease.PLoS genetics · 2017Article
- Mixed Model Association with Family-Biased Case-Control Ascertainment.American journal of human genetics · 2017Article
- CERAMIC: Case-Control Association Testing in Samples with Related Individuals, Based on Retrospective Mixed Model Analysis with Adjustment for Covariates.PLoS genetics · 2016Article
- Retrospective Association Analysis of Binary Traits: Overcoming Some Limitations of the Additive Polygenic Model.Human heredity · 2015Review
Corrections and comments
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Authors and funding
3 authors.
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Abstract
In genetic association testing, failure to properly control for population structure can lead to severely inflated type 1 error and power loss. Meanwhile, adjustment for relevant covariates is often desirable and sometimes necessary to protect against spurious association and to improve power. Many recent methods to account for population structure and covariates are based on linear mixed models (LMMs), which are primarily designed for quantitative traits. For binary traits, however, LMM is a misspecified model and can lead to deteriorated performance. We propose CARAT, a binary-trait association testing approach based on a mixed-effects quasi-likelihood framework, which exploits the dichotomous nature of the trait and achieves computational efficiency through estimating equations. We show in simulation studies that CARAT consistently outperforms existing methods and maintains high power in a wide range of population structure settings and trait models. Furthermore, CARAT is based on a retrospective approach, which is robust to misspecification of the phenotype model. We apply our approach to a genome-wide analysis of Crohn disease, in which we replicate association with 17 previously identified regions. Moreover, our analysis on 5p13.1, an extensively reported region of association, shows evidence for the presence of multiple independent association signals in the region. This example shows how CARAT can leverage known disease risk factors to shed light on the genetic architecture of complex traits.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.