FBAT

FBAT performs family-based association testing to identify associations between genetic variants and phenotypic traits within family-based study designs.

Key Features:

• Admixture Adjustment: Uses the conditional distribution of offspring genotypes to adjust for population admixture and obtain accurate test statistics in admixed populations.
• Phenotype Flexibility: Supports both dichotomous traits (e.g., disease presence/absence) and measured continuous traits (e.g., height, blood pressure).
• Inclusion of Phenotype-Unknown Subjects: Handles subjects with unknown phenotypes without excluding them from analysis.
• Family Structures: Accommodates nuclear families, sibships, and combinations of these family configurations.
• Pedigree Analysis: Permits inclusion of multiple nuclear families from a single pedigree.
• Marker Data Integration: Accepts di-allelic and multi-allelic marker data.
• Genetic Models: Supports additive, dominant, and recessive inheritance models.
• Covariate Adjustment: Allows adjustment for covariates within the association analysis.
• Gene-by-Environment Interactions: Enables adjustment for gene-by-environment interactions to assess environmental modification of genetic effects.

Scientific Applications:

• Genetic Epidemiology: Testing hereditary components of diseases and quantitative traits within family structures.
• Analysis of Admixed Populations: Producing robust association statistics in the presence of population admixture.
• Gene–Environment Interaction Studies: Assessing how environmental factors modify genetic associations with traits.

Methodology:

Computes a test statistic based on the covariance between a user-specified function of genotype and a user-specified function of the trait, using the conditional distribution of offspring genotypes for admixture adjustment.