GOLD - Background Information

As ancestral haplotypes propagate through a population, their physical length is reduced by recombination events. Recombination events between markers separated by very short distances are very rare. Thus, genotypes at nearby markers are not independent and their association may reflect ancestral founding haplotypes.

Traditional linkage analysis, based on allele sharing between relatives, identifies broad chromosomal regions that are likely to contain disease genes. However, the resolution of these methods is limited by recombination events in typical pedigrees. Methods based on linkage disequilibrium take into account ancestral recombination and may be better suited to the identification of positional candidates.

Linkage disequilibrium is commonly described by pair-wise measures. However, the number of pair-wise statistics rises exponentially with the number of markers so that their interpretation is cumbersome for dense maps. As a consequence, it is exceedingly difficult to draw meaningful conclusions from tabular summaries of disequilibrium coefficients.