Parametric Linkage Analysis

“Linkage” describes the situation in which two syntenic loci are inherited together. More specifically, two loci are said to be linked if they are close enough to each other on a chromosome that recombination during meiosis is uncommon enough for their cosegregation to be detectable within families. Thus, linkage is a property of loci . All linkage techniques are essentially designed to test for a statistical association between a marker (genetic or biochemical) and a phenotypic trait. Classical model-based (parametric) linkage analysis was developed to investigate the cosegregation of a genetic marker and a binary trait (generally, disease affection status) within pedigrees. Model-based linkage analysis of quantitative traits is also possible and forms the basis of this chapter. Methods based on the exact likelihood calculation are described in this chapter; Markov chain Monte Carlo methods are described in Chapter 6 .