In order to examine the possible effect of LD on linkage analysis, we decided to study the markers from a dense marker dataset, because the inter-marker distances are smaller and the simulated LD was higher. Single-nucleotide polymorphism (SNP) packets from the non-disease related regions that were generated with LD were bought and used for the analyses. The inter-marker distance was 0.29 cM on average among these markers (20 SNPs per packet). Pedigree samples from the Aipotu population of simulated GAW14 data were used for the analyses. There were 100 nuclear families in the replicate sample and at least two sibs were affected with Kofendrerd Personality Disorder (KPD) in each family. We treated parents from each family as unrelated individuals and used them to estimate haplotype frequencies and LD. Haplotype frequencies were estimated by using the expectation maximization algorithm [7] and pair-wise LD was calculated by using standard formula [8] that are implemented in the EMLD program. We randomly selected a single sib pair from each family to ensure independence of the sib pairs. We then studied each family either including
