PRIMUS

PRIMUS reconstructs pedigrees using genome-wide identity by descent (IBD) estimates to infer family relationships consistent with observed genetic data.

Key Features:

• Genome-wide IBD estimates: Uses genome-wide identity by descent estimates to generate pedigrees that align with observed genetic data.
• mtDNA and NRY haplotype integration: Incorporates mitochondrial DNA (mtDNA) and non-recombining Y chromosome (NRY) haplotypes to exclude pedigree structures inconsistent with haplotype discordances.
• Handling missing individuals: Supports reconstruction when some individuals' genetic data are missing and evaluates multiple potential pedigree structures.
• Ambiguity resolution: Narrows the set of compatible pedigrees by eliminating structures inconsistent with combined autosomal IBD and uniparental haplotype data.
• Implementation: Implemented in PERL.

Scientific Applications:

• Pedigree reconstruction in genetic studies: Infers familial relationships for studies that require accurate family trees from genotype data.
• Population genetics: Supports analyses that rely on reconstructed pedigrees to study population structure and relatedness.
• Medical research: Enables identification of familial relationships relevant to studies of hereditary disease and genetic epidemiology.

Methodology:

Pedigrees are inferred from genome-wide IBD estimates and filtered using mitochondrial DNA (mtDNA) and non-recombining Y chromosome (NRY) haplotype discordances; the implementation is in PERL.