An evaluation of a novel estimator of linkage disequilibrium.
The analysis of systems involving many loci is important in population and quantitative genetics. An important problem is the study of linkage disequilibrium (LD), a concept relevant in genome-enabled prediction of quantitative traits and in exploration of marker-phenotype associations. This article introduces a new estimator of a LD parameter (ρ(2)) that is much easier to compute than a maximum likelihood (or Bayesian) estimate of a tetra-choric correlation. We examined the conjecture that the sampling distribution of the estimator of ρ(2) could be less frequency dependent than that of the estimator of r(2), a widely used metric for assessing LD. This was done via an empirical evaluation of LD in 806 Holstein-Friesian cattle using 771 single-nucleotide polymorphism (SNP) markers and of HapMap III data on 21,991 SNPs (chromosome 3) observed in 88 unrelated individuals from Tuscany. Also, 1600 haplotypes over a region of 1 Mb simulated under the coalescent were used to estimate LD using the two measures. Subsequently, a simulation study compared the new estimator with that of r(2) using several scenarios of LD and allelic frequencies. From these studies, it is concluded that ρ(2) provides a useful metric for the study of LD as the distribution of its estimator is less frequency dependent than that of the standard estimator of r(2).
1] Departments of Animal Sciences, Dairy Science, and Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA [2] Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway.
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D000818:Animals; D001499:Bayes Theorem; D002417:Cattle; D003198:Computer Simulation; D060148:HapMap Project; D016013:Likelihood Functions; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide