Data from: 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 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.