For multipoint linkage analysis of affected sib-pair data, for which parental phase information is inferred from the sib pairs, usual methods of linkage analysis assume linkage equilibrium between multiple linked markers and assigns equal probabilities to all possible phases. This assumption can cause overestimation of multipoint identity by decent (IBD) sharing and induces false positives for both model-free and parametric linkage analysis, as showed by Huang et al. [6]. This study further confirmed this observation by studying independently generated data that were simulated to reflect conditions that might be found in a genome scan. Among the markers that we studied, false-positive evidence for linkage was only obtained for a small subset of markers that showed high LD. We also showed here that including markers that are not in LD can reduce the false-positive evidence of linkage induced by markers in high LD. This indicated that including markers that are not in strong LD ensures that the haplotype frequencies are closer to those expected under the linkage equilibrium assumption and thus may help to reduce false-positive linkage findings. We also found
