Effect of transmission model specification on lod score analysis (3)

Suppose that this pedigree is analysed as if the disease has a Mendelian dominant mode of transmission:

The first 9 sibs are nonrecombinant while the last is recombinant. The pedigree produces a maximum lod of 1.6 at a recombination fraction of 0.1.

Now suppose that the pedigree were analysed as though the mode of transmission were recessive:

With the implied genotypes at the affection locus, the disease appears completely unlinked to the marker. There are 5 nonrecombinants and 5 recombinants.

Now suppose that the pedigree is analysed as Mendelian dominant but that one of the subjects previously affected is a non-penetrant carrier:

There now appear to be 8 nonrecombinants and 2 recombinants, producing a maximum lod of 0.84 at a recombination fraction of 0.2.

If the pedigree is analysed with the penetrance parameter set to 0.8 then a maximum lod of 1.14 is obtained at a recombination fraction of 0.02.