SUP

SUP simulates marker loci and haplotypes in pedigrees conditioned on trait locus genotypes to enable analysis of linkage and linkage disequilibrium for qualitative and quantitative traits.

Key Features:

• Two-Step Algorithm Implementation: Implements a two-step algorithm that first invokes SLINK to simulate genotypes at a trait locus from observed trait values and to produce an indicator of the descent path, and second generates marker alleles or haplotypes in founders conditioned on those trait locus genotypes.
• Recombination Simulation: Simulates recombination between marker loci conditional on the descent path and trait locus genotypes.
• Linkage Disequilibrium Capability: Enables simulation of large numbers of marker loci that may be in linkage disequilibrium with a trait locus.
• Flexibility in Trait Simulation: Supports simulation of qualitative and quantitative traits with specified liability classes, enabling gene-environment interaction scenarios and multi-locus effects between unlinked susceptibility regions.
• Computational Efficiency: The two-step implementation often improves computational efficiency for large-scale marker simulations.

Scientific Applications:

• Association Mapping: Generates extensive marker datasets for association mapping studies involving pedigrees.
• Evaluation of Statistical Tests: Provides realistic simulated data for assessment and validation of statistical methods for linkage and association analyses.
• Gene-Environment Interaction Studies: Enables simulation of scenarios with specified liability classes to investigate gene-environment interactions in complex traits.
• Complex Trait and Genetic Epidemiology: Facilitates simulation-based studies of complex trait architectures in pedigrees, including multi-locus and linkage disequilibrium contexts.

Methodology:

First, SLINK is used to simulate genotypes at the trait locus from observed trait values and to generate an indicator of the descent path; second, marker alleles or haplotypes are generated in founders conditioned on the trait locus genotypes, with recombination between marker loci simulated conditional on the descent path and trait locus genotypes.