Recombination fraction estimate of zero in the presence of apparent recombinants: Effects of incomplete penetrance and sporadic cases

For a fully penetrant trait, apparent recombinants between the trait and marker loci result in an estimate of the recombination fraction theta > 0. Given allowance for reduced penetrance and/or sporadic cases, this no longer need be true. In this short communication, we describe conditions under which theta is estimated to be zero despite the presence of apparent recombinants. We demonstrate that even if a large proportion of unaffected individuals are apparent recombinants and the penetrance is moderately high, the lod score may be maximized at theta = 0. Despite maximization at theta = 0, presence of apparent recombinants reduces the maximum lod score in comparison to its value if no apparent recombinants are present.