Ascertainment correction for Markov chain Monte Carlo segregation and linkage analysis of a quantitative trait

2007 ◽  
Vol 31 (6) ◽  
pp. 594-604 ◽  
Author(s):  
Jianzhong Ma ◽  
Christopher I. Amos ◽  
E. Warwick Daw
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Linkage Analysis ◽  
Quantitative Trait ◽  
Ascertainment Correction

scholarly journals Mapping-Linked Quantitative Trait Loci Using Bayesian Analysis and Markov Chain Monte Carlo Algorithms

Genetics ◽  
1997 ◽  
Vol 146 (2) ◽  
pp. 735-743 ◽  
Author(s):  
Pekka Uimari ◽  
Ina Hoeschele
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Allele Frequencies ◽  
Mcmc Methods ◽  
Substitution Effects ◽  
Indicator Variable ◽  
Trait Loci

A Bayesian method for mapping linked quantitative trait loci (QTL) using multiple linked genetic markers is presented. Parameter estimation and hypothesis testing was implemented via Markov chain Monte Carlo (MCMC) algorithms. Parameters included were allele frequencies and substitution effects for two biallelic QTL, map positions of the QTL and markers, allele frequencies of the markers, and polygenic and residual variances. Missing data were polygenic effects and multi-locus marker-QTL genotypes. Three different MCMC schemes for testing the presence of a single or two linked QTL on the chromosome were compared. The first approach includes a model indicator variable representing two unlinked QTL affecting the trait, one linked and one unlinked QTL, or both QTL linked with the markers. The second approach incorporates an indicator variable for each QTL into the model for phenotype, allowing or not allowing for a substitution effect of a QTL on phenotype, and the third approach is based on model determination by reversible jump MCMC. Methods were evaluated empirically by analyzing simulated granddaughter designs. All methods identified correctly a second, linked QTL and did not reject the one-QTL model when there was only a single QTL and no additional or an unlinked QTL.

scholarly journals Markov chain monte carlo linkage analysis of a complex qualitative phenotype

1999 ◽  
Vol 17 (S1) ◽  
pp. S615-S620 ◽  
Author(s):  
Anthony Hinrichs ◽  
Jennifer H. Lin ◽  
Theodore Reich ◽  
Laura Bierut ◽  
Brian K. Suarez
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Linkage Analysis
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