The idea that data on a modest set of genetic variants measured in a number of related individuals can provide useful information about other genetic variants in those individuals forms the theoretical underpinning of genetic linkage studies and of haplotype mapping approaches in founder populations (23, 24, 50). These studies typically use <10,000 genetic markers to survey the entire human genome. These markers are used to identify stretches of chromosome inherited from a common ancestor. The shared stretches will usually span several megabases and include thousands of genetic variants. Both approaches have been incredibly successful in the identification of genes responsible for single gene Mendelian disorders (9). In contrast, both these approaches have had only limited success in the context of gene mapping studies for complex traits, although success stories do exist (40, 42, 75, 83).
