ABSTRACT
This chapter provides an introduction to the data management and analysis needed to conduct these linkage studies. The goal of linkage studies is to assign the genetic factors responsible for a trait phenotype to specific chromosome regions by examining their cosegregation with marker loci. Most modern linkage studies have relied on the method of maximum likelihood as the principle technique for statistical estimation of recombination rates and evaluation of linkage. Trait phenotypes are usually indirect measures of the genotype of interest that are often presented as categorical data or quantitative measurements. Many computer programs for linkage analysis consider categorical variables as binary responses, e.g., affected or nonaffected for a genetic disease phenotype. Most marker systems are codominant, with corresponding marker phenotypes that can be represented as a unique genotype composed of two alleles.
