When linkage was first applied to complex disorders it was performed using the established methods of the time, which required determining, a priori, an inheritance model. Many early efforts failed to find linkage and often declared exclusion of parts of the genome based on such analyses. It was slowly becoming clear however that the common disorders were much more likely to involve more than a single gene and that the “mutations” involved were likely to cause disease in some but not all carriers, consistent with prior segregation analyses results for schizophrenia (13). Traditional linkage methods were not meant for the investigation of such diseases. Numerous efforts for the development of new approaches to linkage analysis were undertaken in the 1990’s, most of which involved what eventually became the standard for linkage analysis of complex disorders, the analysis of shared alleles in each genomic location between affected relatives compared to the expected allele sharing for each type of pair of relatives. This makes a sacrifice in power, but avoids assumptions about inheritance, bypassing a significant problem of parametric linkage. At the
