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Polyunphased: an extension to polytomous outcomes of the Unphased package for family-based genetic association analysis
- Source :
- Statistical Applications in Genetics and Molecular Biology. 16:75-81
- Publication Year :
- 2017
- Publisher :
- Walter de Gruyter GmbH, 2017.
-
Abstract
- Polytomous phenotypes arise when a disease has multiple subtypes or when two dichotomous phenotypes are analyzed simultaneously. Few software programs offer the option to analyze such phenotypes in family studies, and none implements conditional polytomous logistic regression for within-family analysis robust to population stratification. We introduce Polyunphased, an extension to polytomous phenotypes of the Unphased package, a flexible software tool for genetic association analysis in nuclear families. Like Unphased, Polyunphased is written in C++ and runs from the command line or from a Java graphical user interface. Most Unphased options remain available in Polyunphased, including those handling missing parental genotypes while preserving robustness to population stratification, and the modelling options. Simulation studies confirmed the expected statistical behaviour of the maximum likelihood estimates of the association parameters of the conditional logistic regression model when the corresponding association parameters in the parental term of the likelihood function are set to 0, but revealed convergence problems when estimating these parental association parameters separately. The former approach is thus recommended with polytomous phenotypes.
- Subjects :
- 0301 basic medicine
Statistics and Probability
Genotype
Computer science
Population stratification
Logistic regression
Article
03 medical and health sciences
Statistics
Genetics
Econometrics
Humans
Computer Simulation
Molecular Biology
Nuclear family
Genetic Association Studies
Family Health
Likelihood Functions
Models, Genetic
Robustness (evolution)
Polytomous Rasch model
Genetic association analysis
Computational Mathematics
Logistic Models
Phenotype
030104 developmental biology
Likelihood function
Family based
Subjects
Details
- ISSN :
- 15446115 and 21946302
- Volume :
- 16
- Database :
- OpenAIRE
- Journal :
- Statistical Applications in Genetics and Molecular Biology
- Accession number :
- edsair.doi.dedup.....a7b8f64894f4c44009b0d2109a2de8a6