ArticleGenetics2010
Bayesian quantitative trait locus mapping using inferred haplotypes.
Article in Genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Article
- Article
- Article
- Identification of new loci involved in the host susceptibility to Salmonella Typhimurium in collaborative cross mice.BMC genomics · 2018Article
- New Rodent Population Models May Inform Human Health Risk Assessment and Identification of Genetic Susceptibility to Environmental Exposures.Environmental health perspectives · 2017Review
- Heterogeneous Stock Populations for Analysis of Complex Traits.Methods in molecular biology (Clifton, N.J.) · 2017Article
- MAGIC populations in crops: current status and future prospects.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2015Review
- Susceptibility to Klebsiella pneumonaie infection in collaborative cross mice is a complex trait controlled by at least three loci acting at different time points.BMC genomics · 2014Article
- Article
- QTL mapping in outbred populations: successes and challenges.Physiological genomics · 2014Review
- Identification of a major locus interacting with MC1R and modifying black coat color in an F₂ Nellore-Angus population.Genetics, selection, evolution : GSE · 2014Article
- Fine-mapping diabetes-related traits, including insulin resistance, in heterogeneous stock rats.Physiological genomics · 2012Article
- Article
- Genetic analysis of complex traits in the emerging Collaborative Cross.Genome research · 2011Article
- Measurement of serum PON-3 concentration: method evaluation, reference values, and influence of genotypes in a population-based study.Journal of lipid research · 2011Article
- A new mapping method for quantitative trait loci of silkworm.BMC genetics · 2011Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
We describe a fast hierarchical Bayesian method for mapping quantitative trait loci by haplotype-based association, applicable when haplotypes are not observed directly but are inferred from multiple marker genotypes. The method avoids the use of a Monte Carlo Markov chain by employing priors for which the likelihood factorizes completely. It is parameterized by a single hyperparameter, the fraction of variance explained by the quantitative trait locus, compared to the frequentist fixed-effects model, which requires a parameter for the phenotypic effect of each combination of haplotypes; nevertheless it still provides estimates of haplotype effects. We use simulation to show that the method matches the power of the frequentist regression model and, when the haplotypes are inferred, exceeds it for small QTL effect sizes. The Bayesian estimates of the haplotype effects are more accurate than the frequentist estimates, for both known and inferred haplotypes, which indicates that this advantage is independent of the effect of uncertainty in haplotype inference and will hold in comparison with frequentist methods in general. We apply the method to data from a panel of recombinant inbred lines of Arabidopsis thaliana, descended from 19 inbred founders.
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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 OpenQuestion graph.