GENESIS

GENESIS performs population- and pedigree-aware genetic analyses by integrating PC-AiR and PC-Relate to infer and adjust for population structure and relatedness in genome-wide single nucleotide polymorphism (SNP) data.

Key Features:

• PC-AiR: Performs principal component analysis on genome-wide single nucleotide polymorphism (SNP) data to detect population structure while accommodating known and cryptic relatedness (Principal Component Analysis—Ancestry Informative Reference; Conomos et al.).
• PC-Relate: Estimates pairwise relatedness using ancestry-representative principal components to adjust for population structure and ancestry (Conomos et al.).
• Bioconductor integration: Distributed as an R/Bioconductor package for interoperability with other Bioconductor packages.

Scientific Applications:

• Genome-Wide Association Studies (GWAS): Adjusts for population stratification and relatedness to reduce confounding in association analyses.
• Population Genetics: Identifies genetic substructure and supports analyses of genetic diversity and population relationships.
• Pedigree Analysis: Accounts for familial relatedness and cryptic relatedness in family-based study designs.

Methodology:

Implements PC-AiR to compute principal components from genome-wide SNP data and PC-Relate to estimate relatedness while adjusting for ancestry via ancestry-representative principal components.