Improved programs for the affected-pedigree-member method of linkage analysis

The affected-pedigree-member (APM) method is a non-parametric method of linkage analysis, which requires no assumptions about how the trait of interest is inherited [Weeks and Lange, 1988, 1991, 1992; Lange and Weeks, 1990; Weeks et al., 1992]. The APM method uses only the affected members of each pedigree who are typed for the marker(s). Based on the affected members' marker genotypes and the relationships of the affecteds to each other, the APM method computes a statistic which provides a measure of marker similarity. If the affected members are significantly more similar at the marker locus than expected by chance, then one may conclude that the marker is not segregating independently of the disease. Since the APM method tests a hypothesis about marker similarity, and not about recombination between the marker and disease, it makes and requires no assumptions about the mode of inheritance of the disease. For this reason, the APM method has been used for complex diseases such as Alzheimer's, breast cancer, and melanoma [Pericak-Vance et al., 1989, 1990; Haile et al., 1990; Hall et al., 1990; St George-Hyslop et al., 1990; Cannon-Albright et al., 1992]. We would like to announce the availability of a much improved version of the APM program package. This version has been improved in several ways, as outlined below.