We review this methodology here for sake of completeness, as it dominated the field of genetics for many years. It is now recognized that linkage analyses were underpowered to detect common alleles with small individual effects on the outcome of interest. Although rare alleles with larger effects do seem likely to contribute to some common diseases, common alleles of small effect are generally believed to constitute the genetic influences on most complex behavioral outcomes. However, the use of linkage evidence in conjunction with other kinds of genetic evidence has proven to be a useful strategy in gene identification in some projects (Dick and Bierut, 2006). There are situations where linkage analyses may be more powerful than association analyses (discussed below), such as when many different alleles (e.g., individual disease-predisposing or causal mutations) are present in a single gene. In addition, linkage analyses may have some utility for finding the rare variants mentioned above. It remains to be seen whether multiply affected families have substantially different kinds of genetic risks than unselected cases from the population.
