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

AbstractFor a fully penetrant trait, apparent recombinants between the trait and marker loci result in an estimate of the recombination fraction θ > 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 θ 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 θ = 0. Despite maximization at θ = 0, presence of apparent recombinants reduces the maximum lod score in comparison to its value if no apparent recombinants are present. ©1995 Wiley‐Liss, Inc.