LIden

LIden identifies linked regions from high-density single nucleotide polymorphism (SNP) genotype data by determining allele sharing status among family members.

Key Features:

• Handling Incomplete Parental Chromosome Genotypes: Manages cases where genotype data for an entire chromosome of one parent in a nuclear family are missing while determining allele sharing.
• Minimum Recombinant Model: Applies the minimum recombinant model for haplotype inference within pedigrees to minimize inferred recombination events.
• Local Optimization Algorithms: Utilizes several local optimization algorithms to infer individual haplotypes and refine linked region detection.
• Combining Nuclear Families: Incorporates a method to combine nuclear families to reduce linked region length and improve localization.
• Computational Complexity and Scalability: Operates with computational complexity O(mn), where m is the number of family members and n is the number of SNP sites on the chromosome.

Scientific Applications:

• Genetic Linkage Mapping: Identifies linked regions for genetic linkage studies using high-density SNP datasets.
• Pedigree-based Haplotype Inference: Infers haplotypes and allele sharing within pedigrees, including complex family structures.
• Hereditary Disease Locus Localization: Localizes candidate regions for hereditary disease gene mapping in large pedigrees.
• Analysis with Missing Parental Genotypes: Enables linkage analysis when parental chromosome genotypes are partially or entirely missing.

Methodology:

Determines allele sharing from SNP genotypes; handles missing entire parental chromosome genotype in a nuclear family; employs the minimum recombinant model for haplotype inference; applies local optimization algorithms to infer haplotypes and detect linked regions; combines nuclear families to shorten linked regions; runs with computational complexity O(mn) (m = number of family members, n = number of SNP sites).