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Data from: An evaluation of a novel estimator of linkage disequilibrium


Gianola, Daniel; Qanbari, Saber; Simianer, Henner (2013), Data from: An evaluation of a novel estimator of linkage disequilibrium, Dryad, Dataset,


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 employed metric for assessing LD. This was done via an empirical evaluation of LD in 806 Holstein-Friesian cattle using 771 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 r2 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 since the distribution of its estimator is less frequency-dependent than that of the standard estimator of r^2.

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