<P> A genetic map is not a physical map (such as a radiation reduced hybrid map) or gene map . </P> <P> Linkage analysis may be either parametric (if we know the relationship between phenotypic and genetic similarity) or non-parametric . Parametric linkage analysis is the traditional approach, whereby the probability that a gene important for a disease is linked to a genetic marker is studied through the LOD score, which assesses the probability that a given pedigree, where the disease and the marker are cosegregating, is due to the existence of linkage (with a given linkage value) or to chance . Non-parametric linkage analysis, in turn, studies the probability of an allele being identical by descent with itself . </P> <P> The LOD score (logarithm (base 10) of odds), developed by Newton Morton, is a statistical test often used for linkage analysis in human, animal, and plant populations . The LOD score compares the likelihood of obtaining the test data if the two loci are indeed linked, to the likelihood of observing the same data purely by chance . Positive LOD scores favour the presence of linkage, whereas negative LOD scores indicate that linkage is less likely . Computerised LOD score analysis is a simple way to analyse complex family pedigrees in order to determine the linkage between Mendelian traits (or between a trait and a marker, or two markers). </P> <P> The method is described in greater detail by Strachan and Read. (1) Briefly, it works as follows: </P>

What happens in the case of two genes which are far apart on the same chromosome