SLINK

SLINK simulates genotypes within pedigrees to assess empirical significance and the statistical power of linkage and association studies.

Key Features:

• Pedigree-based genotype simulation: Simulates genotypes for individuals in pedigrees to support linkage and association study evaluation.
• Conditional locus simulation: Simulates genotypes at one locus conditional on phenotypic data at a linked locus to assess empirical significance.
• Peeling-algorithm likelihood evaluation: Uses pedigree peeling algorithms for evaluating pedigree likelihoods, which constrains the number of linked markers that can be directly simulated.
• SUP integration and descent markers: Integrates with SUP by using descent markers generated by SLINK to simulate additional linked markers and markers potentially associated with a trait locus.
• Algorithmic heritage: Implements algorithms derived from the LINKAGE programs and incorporates faster algorithmic advances from FASTLINK.
• Version updates: Recent coordinated releases (SLINK 3.0 and SUP v090804) removed prior limitations such as the number of founders in a pedigree.

Scientific Applications:

• Power analysis for linkage studies: Assess statistical power of linkage studies using simulated pedigree genotypes.
• Power and significance assessment for association studies: Evaluate empirical significance and power in association analyses using simulated linked-marker data.
• Simulation of multiple linked markers: Generate scenarios with numerous linked markers (via SUP) to explore marker-trait associations.
• Complex pedigree simulations: Model large and complex pedigrees to study inheritance patterns and marker linkage under varied scenarios.

Methodology:

Simulates genotypes conditional on phenotype at a linked locus, evaluates pedigree likelihoods using peeling algorithms, generates descent markers, and uses SUP to expand simulations to additional linked markers; algorithms are derived from LINKAGE with FASTLINK improvements.