The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.
Bayesian LASSO for Quantitative Trait Loci Mapping
Open accessAbstract
The mapping of quantitative trait loci (QTL) is to identify molecular markers or genomic loci that influence the variation of complex traits. The problem is complicated by the facts that QTL data usually contain a large number of markers across the entire genome and most of them have little or no effect on the phenotype. In this article, we propose several Bayesian hierarchical models for mapping multiple QTL that simultaneously fit and estimate all possible genetic effects associated with all markers. The proposed models use prior distributions for the genetic effects that are scale mixtures of normal distributions with mean zero and variances distributed to give each effect a high probability of being near zero. We consider two types of priors for the variances, exponential and scaled inverse-χ2 distributions, which result in a Bayesian version of the popular least absolute shrinkage and selection operator (LASSO) model and the well-known Student's t model, respectively. Unlike most applications where fixed values are preset for hyperparameters in the priors, we treat all hyperparameters as unknowns and estimate them along with other parameters. Markov chain Monte Carlo (MCMC) algorithms are developed to simulate the parameters from the posteriors. The methods are illustrated using well-known barley data.
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Cites
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“The former prior results in a Bayesian LASSO model (Tibshirani 1996; Yuan and Lin 2005; Park and Casella 2007), and the latter includes Jeffrey’s noninformative prior as a special case (Gelman 2006).”
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Cited by
Polygenic prediction via Bayesian regression and continuous shrinkage priors
Ge, T., Chen, C.-Y., Ni, Y., Feng, Y.-C. A., & Smoller, J. W. (2019) · Nature Communications · doi:10.1038/s41467-019-09718-5 · Cited by 1,922
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Beyond Missing Heritability: Prediction of Complex Traits
Makowsky, R., Pajewski, N. M., Klimentidis, Y. C., Vazquez, A. I., Duarte, C. W., Allison, D. B., & de los Campos, G. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002051 · Cited by 254
Combined linkage disequilibrium and linkage mapping: Bayesian multilocus approach
Pikkuhookana, P., & Sillanpää, M. J. (2014) · Heredity · doi:10.1038/hdy.2013.111 · Cited by 13
Metadata
- Authors
- Yi, N., & Xu, S.
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-06-01
- Volume
- 179
- Issue
- 2
- Pages
- 1045-1055
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- OpenAlex
- W2050029156
- Cited by
- 344
- References
- 39
- FWCI
- 12.66
- Type
- journal article
- Language
- en
- Open access
- bronze
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