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Chunk #31 — Background — Details of data simulation — 3. Phenotypes

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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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There are three underlying latent traits designated P1, P2, and P3 (see Figure 1), the genetic dependencies of which are described in Table 1. In addition, there are 12 subclinical phenotypes or traits that occur in both affected and unaffected family members. Ten of these traits are entirely genetic with reduced penetrance, and two are entirely randomly assigned. The genotype-phenotype relationships of the genetic traits are shown in Table 3.