Linkage and Association: The Transmission/Disequilibrium Test for QTLs

Usually, the probability of observing a particular allele at one locus is independent of the alleles observed at another locus. However, this is not the case when two alleles are ‘associated.’ For instance, let the frequency of allele 1 at locus 1 by p ₁ and the frequency of allele 2 at locus 2 be p ₂ . If the two alleles are not associated, then the frequency with which they appear together is p ₁ p ₂ . If their joint frequency is greater than p ₁ p ₂ the two alleles are said to be positively associated. If their joint frequency is less than p ₁ p ₂ , the two alleles are said to be negatively associated. Association is the nonindependence of allele frequencies at different loci.