Overall LD

Overall LD assesses linkage disequilibrium across multiple genetic markers to quantify overall deviation from random association for gene mapping and population history inference.

Key Features:

• Overall LD Assessment: Evaluates linkage disequilibrium across several markers by summarizing deviations from random association.
• Permutation-Based Estimation: Estimates the LD measure using a permutation-based procedure with validation via simulation studies to assess robustness and significance.
• Application to Complex Genetic Systems: Handles multiple highly polymorphic markers to provide more detailed information than simpler two-marker analyses.

Scientific Applications:

• Positional Cloning Studies: Assists gene mapping by characterizing LD patterns to identify candidate regions associated with traits or diseases.
• Population History Reconstruction: Informs historical genetic relationships and migrations by analyzing LD across populations.

Methodology:

The method introduces a measure summarizing overall deviation from random association among markers, estimates this measure via a permutation-based procedure validated by simulations, and has been applied to population data at the dopamine D2 receptor locus (DRD2) and the homeobox B (HOXB) gene cluster.