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Genetics, Vol. 167, 959-965, June 2004, Copyright © 2004
doi:10.1534/genetics.103.025437
A Quantitative Trait Locus Mixture Model That Avoids Spurious LOD Score Peaks
Bjarke Feenstra1 and Ib M. Skovgaard
Department of Natural Sciences, Royal Veterinary and Agricultural University, DK-1871 Frederiksberg C, Denmark
1 Corresponding author: Department of Natural Sciences, Royal Veterinary and Agricultural University, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.
E-mail: bjarke{at}dina.kvl.dk
In standard interval mapping of quantitative trait loci (QTL), the QTL effect is described by a normal mixture model. At any given location in the genome, the evidence of a putative QTL is measured by the likelihood ratio of the mixture model compared to a single normal distribution (the LOD score). This approach can occasionally produce spurious LOD score peaks in regions of low genotype information (e.g., widely spaced markers), especially if the phenotype distribution deviates markedly from a normal distribution. Such peaks are not indicative of a QTL effect; rather, they are caused by the fact that a mixture of normals always produces a better fit than a single normal distribution. In this study, a mixture model for QTL mapping that avoids the problems of such spurious LOD score peaks is presented.
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  B. Feenstra, I. M. Skovgaard, and K. W. Broman Mapping Quantitative Trait Loci by an Extension of the Haley-Knott Regression Method Using Estimating Equations Genetics, August 1, 2006; 173(4): 2269 - 2282. [Abstract] [Full Text] [PDF]
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