To generate the LD, we generated 13- or 15-SNP haplotypes based on two-SNP haplotype probabilities derived from actual data from a small region of human chromosome 6. Using these probabilities, we generated between 200 and 2,000 haplotypes. We then inserted the disease gene into a proportion of these haplotypes. We tested whether disease association could be detected with SNPs surrounding the disease mutation and tried to adjust the gene frequencies so that association with the neighboring SNPs could be detected in at least 50% of the datasets. We used two different approaches to choosing those haplotypes destined to be carriers of the disease allele:
