Chunk #24 — Background — Details of data simulation — 2. Areas with LD/unique characteristics

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Construction of the model for the Genetic Analysis Workshop 14 simulated data: genotype-phenotype relationships, gene interaction, linkage, association, disequilibrium, and ascertainment effects for a complex phenotype.

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Region 1 was created without LD, that is, the probabilities of all haplotypes were randomly generated, but we chose a restricted number of haplotypes to act as controls on the procedures we described above. Thirty haplotypes were chosen arbitrarily to carry the disease allele and their frequencies adjusted so that their sum equaled the disease gene frequency.