Genetic association is when one or more genotypes within a population co-occur with a phenotypic trait more often than would be expected by chance occurrence.
[citation needed] Linkage disequilibrium (LD) is a term used in the study of population genetics for the non-random association of alleles at two or more loci, not necessarily on the same chromosome.
In genetic case-control studies, the frequency of alleles or genotypes is compared between the cases and controls.
The cases will have been diagnosed with the disease under study, or have the trait under test; the controls, who are either known to be unaffected, or who have been randomly selected from the population.
One problem with the case-control design is that genotype and haplotype frequencies vary between ethnic or geographic populations.
Family based association designs aim to avoid the potential confounding effects of population stratification by using the parents or unaffected siblings as controls for the case (the affected offspring/sibling).