PedCut

PedCut partitions complex pedigrees into smaller sub-pedigrees to enable linkage analysis using the Lander-Green-Kruglyak algorithm while enforcing user-defined bit-size constraints.

Key Features:

• User-Specified Bit-Size Limit: Enforces a maximum bit-size per subpedigree based on a user-defined limit to keep subunits computationally tractable.
• Maximal Subject Assignment: Maximizes inclusion of subjects of interest (e.g., patients) by identifying common ancestors and assigning individuals to subpedigrees that retain genetic relevance.
• Comparison with Existing Methods: Demonstrates superior performance relative to maximum clique partitioning methods in assigning more patients to subpedigrees, especially in deep pedigrees with dispersed subjects connected through multiple genealogical links.

Scientific Applications:

• Genome-wide linkage scans: Facilitates genome-wide linkage scans for identifying rare mutations in large pedigrees from genetically isolated populations.
• Genetic-disorder studies (e.g., Alzheimer's disease): Supports linkage analyses of complex family structures, exemplified by application to a pedigree of 50 patients from an isolated Dutch population.

Methodology:

Splits large pedigrees into subpedigrees that maximize the number of subjects sharing a common ancestor while adhering to user-specified bit-size constraints and is compared to maximum clique partitioning methods.