Obelisc

Obelisc performs nonparametric linkage analysis by applying SNP streak-based identity-by-descent (IBD) mapping and runs of homozygosity (ROH) mapping to localize genetic loci without requiring structured pedigrees or specified inheritance models.

Key Features:

• Nonparametric linkage analysis: Enables SNP streak-based IBD mapping and runs of homozygosity (ROH) mapping without requiring structured pedigree information or specified model parameters.
• Applicability to dominant and recessive traits: The SNP streak approach extends applicability to both dominant and recessive inheritance models, while ROH mapping is limited to recessive traits.
• Compatibility with haplotype phasing: Supports corroboration of shared IBD haplotypes using population-based haplotype phasing.
• Visualization capabilities: Produces visual outputs for interpretation of IBD and ROH mapping results.

Scientific Applications:

• Pseudo-pedigree analysis of BioBank Japan data: Demonstrated using a pseudo-pedigree generated from the BioBank Japan Project genome-wide genotype dataset to identify regions with inherited IBD haplotypes.
• Genetic mapping: Applied to mapping of Mendelian diseases and complex traits.

Methodology:

Uses the SNP streak approach for IBD mapping and runs of homozygosity (ROH) mapping without predefined inheritance models or fixed parameters, and corroborates shared haplotypes via population-based haplotype phasing using a pseudo-pedigree generated from the BioBank Japan genome-wide genotype dataset.