Rapid computer analysis of linkage data

A well tested and useful computer program for screening large amounts of pedigree data for linkage is described. All types of pedigree and genetic systems with up to six alleles present in the pedigree are allowed. An original procedure fills in uncertain genotypes and searches for internal inconsistencies in the data and is extremely thoroughgoing. Population gene frequencies are not used, although the program does take account of rare alleles. The scoring method is based on the division of the pedigree into sibships and the application of z-scores for the sexes considered separately wherever possible. About 2000 pedigrees have been analysed and scores for about the same number of pairs of loci are on tape. A mathematical exercise showed that the method of z-scores with score corrections, which is very much quicker than calculating complete likelihood, is acceptably efficient and its efficiency approaches 100% when scoring rare recessive systems. It is shown that the maximum value of the score is a good criterion for linkage, values of 3.1 and 4.0 indicating roughly 95% and 99% probabilities of linkage. The calculation of 2-unit support limits for the estimate of the recombination fraction between linked loci is advocated, and tables of these are given for syntenic loci. No new linkages were confirmed.