Generalized genetic association study with samples of related individuals
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Publication:652373
Nonparametric hypothesis testing (62G10) Applications of statistics to biology and medical sciences; meta analysis (62P10) Hypothesis testing in multivariate analysis (62H15) Generalized linear models (logistic models) (62J12) Genetics and epigenetics (92D10) Testing in survival analysis and censored data (62N03)
Abstract: Genetic association study is an essential step to discover genetic factors that are associated with a complex trait of interest. In this paper we present a novel generalized quasi-likelihood score (GQLS) test that is suitable for a study with either a quantitative trait or a binary trait. We use a logistic regression model to link the phenotypic value of the trait to the distribution of allelic frequencies. In our model, the allele frequencies are treated as a response and the trait is treated as a covariate that allows us to leave the distribution of the trait values unspecified. Simulation studies indicate that our method is generally more powerful in comparison with the family-based association test (FBAT) and controls the type I error at the desired levels. We apply our method to analyze data on Holstein cattle for an estimated breeding value phenotype, and to analyze data from the Collaborative Study of the Genetics of Alcoholism for alcohol dependence. The results show a good portion of significant SNPs and regions consistent with previous reports in the literature, and also reveal new significant SNPs and regions that are associated with the complex trait of interest.
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Cites work
- scientific article; zbMATH DE number 3522963 (Why is no real title available?)
- Generalized genetic association study with samples of related individuals
- Multiple outputation: inference for complex clustered data by averaging analyses from independent data
- Quasi-likelihood and its application. A general approach to optimal parameter estimation
Cited in
(13)- A robust distribution-free test for genetic association studies of quantitative traits
- Unifying genetic association tests via regression: Prospective and retrospective, parametric and nonparametric, and genotype‐ and allele‐based tests
- Data-adaptive multi-locus association testing in subjects with arbitrary genealogical relationships
- Association study for the relationship between a haplotype or haplotype set and multiple quantitative responses
- Leveraging local identity-by-descent increases the power of case/control GWAS with related individuals
- SNP selection for predicting a quantitative trait
- The generalized odds ratio as a measure of genetic risk effect in the analysis and meta-analysis of association studies
- A generalized robust allele‐based genetic association test
- A genome-wide association study of multiple longitudinal traits with related subjects
- An incomplete-data quasi-likelihood approach to haplotype-based genetic association studies on related individuals
- Gene-based association testing of dichotomous traits with generalized functional linear mixed models using extended pedigrees: applications to age-related macular degeneration
- The power of generalized odds ratio in assessing association in genetic studies with known mode of inheritance
- Generalized genetic association study with samples of related individuals
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