Association Testing in Unrelated Individuals
In association testing we are interested in the effect of a specific allele in the population. We ask the question: "Is allele X1 more common in affected individuals than unaffected individuals?" We do not need family data to answer this, but we can use it if we have it.
Recall that Linkage Disequilibrium is the tendency for alleles at two loci closely linked on a chromosome to be associated in a population. Linkage is done within a family (referring to alleles inherited together), and LD is done within a population (alleles found at two loci together on a haplotype more often than expected).