veqtl-mapper

veqtl-mapper maps genetic loci associated with variance in molecular phenotypes, particularly gene expression, to identify variants that influence trait variability rather than mean levels.

Key Features:

• Variance-focused mapping: Identifies loci associated with variance in molecular phenotypes, with a specific focus on cis-regulatory elements.
• Additive model: Employs an additive statistical model to test associations between genetic variants and phenotype variance.
• Parent-of-origin effects detection: Detects differences in variance between homozygous and heterozygous alleles indicative of parent-of-origin or imprinting-related effects.

Scientific Applications:

• Genetic interaction analysis: Reveals loci involved in genetic interactions that affect trait variability not captured by mean-level analyses.
• Gene-by-environment studies: Enables investigation of how environmental factors interact with genetic variants to modulate phenotype variance.
• Epigenetic research: Supports study of parent-of-origin and imprinting effects on gene expression variance.

Methodology:

Applied to the Geuvadis gene expression dataset using an additive model, identifying 816 loci associated with gene expression variance and 32 loci showing variance differences between homozygous and heterozygous alleles.