Using dominance relationship coefficients based on linkage disequilibrium and linkage with a general complex pedigree to increase mapping resolution

Lee, S. H. and Van der Werf, J. H. J. (2006) Using dominance relationship coefficients based on linkage disequilibrium and linkage with a general complex pedigree to increase mapping resolution. Genetics, 174 2: 1009-1016. doi:10.1534/genetics.106.060806


Author Lee, S. H.
Van der Werf, J. H. J.
Title Using dominance relationship coefficients based on linkage disequilibrium and linkage with a general complex pedigree to increase mapping resolution
Journal name Genetics   Check publisher's open access policy
ISSN 0016-6731
Publication date 2006-10
Sub-type Article (original research)
DOI 10.1534/genetics.106.060806
Volume 174
Issue 2
Start page 1009
End page 1016
Total pages 8
Place of publication Bethesda, MD United States
Publisher Genetics Society of America
Language eng
Formatted abstract
Dominance (intralocus allelic interactions) plays often an important role in quantitative trait variation.  However, few studies about dominance in QTL mapping have been reported in outbred animal or human populations. This is because common dominance effects can be predicted mainly for many full sibs, which do not often occur in outbred or natural populations with a general pedigree. Moreover, incomplete
genotypes for such a pedigree make it infeasible to estimate dominance relationship coefficients between individuals. In this study, identity-by-descent (IBD) coefficients are estimated on the basis of populationwide linkage disequilibrium (LD), which makes it possible to track dominance relationships between unrelated founders. Therefore, it is possible to use dominance effects in QTL mapping without full sibs. 
Incomplete genotypes with a complex pedigree and many markers can be efficiently dealt with by a Markov chain Monte Carlo method for estimating IBD and dominance relationship matrices (DRM). It is shown by simulation that the use of DRM increases the likelihood ratio at the true QTL position and the mapping accuracy and power with complete dominance, overdominance, and recessive inheritance modes when using 200 genotyped and phenotyped individuals.
Keyword Quantitative Trait Loci
Variance Component Approach
Average Information Reml
Maximum-Likelihood
Theoretical Basis
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Brain Institute Publications
 
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