PBAT

PBAT performs family-based genome-wide association analysis using the Pairwise Bayesian Association Test to detect associations between genetic variants (single nucleotide polymorphisms, SNPs) and phenotypic traits in nuclear families and extended pedigrees.

Key Features:

• Family structure handling: Analyzes nuclear families with missing parental genotypes and extended pedigrees with incomplete genotypic information.
• Genetic variant analysis: Supports genome-wide analysis of single nucleotide polymorphisms (SNPs).
• Haplotype and quantitative trait analysis: Performs haplotype reconstruction using sliding windows and supports quantitative, multivariate, and longitudinal trait analysis.
• Time-to-onset phenotypes: Analyzes time-to-onset phenotypes to investigate genetic effects on disease progression or onset timing.
• Covariate adjustment and interaction modeling: Models covariate adjustment and gene/environment interactions.
• Multiple comparisons management: Implements screening tools to manage large-scale SNP analyses (e.g., >100,000 SNPs) and control false positives.
• Computational efficiency: Enables large-scale scans with reported performance (example: 300,000 SNPs across 2,000 trios in ~4 CPU-days).

Scientific Applications:

• Family-based genome-wide association studies (GWAS): Detects genetic associations within family and pedigree data for genome-wide scans.
• Haplotype and inheritance analyses: Reconstructs and analyzes haplotypes to study inheritance patterns and variant combinations.
• Longitudinal and time-to-event genetic studies: Investigates genetic influences on multivariate, longitudinal, and time-to-onset phenotypes, including multifactorial diseases.

Methodology:

Implements the Pairwise Bayesian Association Test, haplotype reconstruction using sliding windows, screening procedures for large SNP datasets, covariate adjustment and gene–environment interaction modeling, and supports quantitative, multivariate, longitudinal and time-to-onset phenotype analyses while handling missing parental genotypes and extended pedigree structures.