PEDIBD

PEDIBD reconstructs haplotypes from pedigree genomic data by inferring identical-by-descent (IBD) segments to enable haplotype recovery in large or incompletely genotyped families.

Key Features:

• Pairwise IBD inference: Infers pairwise identical-by-descent (IBD) segments between family members, identifying genomic regions inherited from a common ancestor without recombination.
• Global IBD reconstruction: Reconstructs the global IBD structure across the entire pedigree using pairwise IBD information.
• Haplotype restoring: Restores haplotypes based on the inferred global IBD data to determine linkage patterns between genetic variants.
• Support for large and incomplete pedigrees: Accommodates large pedigrees and families with many ungenotyped (missing) members.
• IBD-based haplotyping: Leverages the concept of identical-by-descent (IBD) segments within genomic data to drive haplotype inference.
• Enhanced power and scalability: Provides increased power and scalability for recovering haplotype information compared to traditional haplotyping approaches.

Scientific Applications:

• Family-based disease studies: Facilitates haplotype recovery in family-based disease studies where pedigrees are large or genotyping is incomplete.
• Linkage and inheritance analysis: Enables analysis of linkage patterns and inheritance of dispersed genetic variations via reconstructed haplotypes.
• Genetic basis of traits and diseases: Supports investigation of the genetic basis of human traits and diseases by providing haplotype information.

Methodology:

Computational steps comprise pairwise IBD inference, global IBD reconstruction across the pedigree, and haplotype restoring based on the inferred global IBD, with pairwise IBD identifying regions inherited from a common ancestor without recombination.