INTACT

INTACT integrates colocalization probabilities from colocalization analysis with transcriptome-wide association study (TWAS) scan summary statistics to implicate genes that may be biologically relevant to a complex trait.

Key Features:

• Probabilistic TWAS-Colocalization Integration: The package constrains the TWAS scan z-score-based likelihood using a gene-level colocalization probability.
• Gene Set Enrichment Analysis: Given gene set annotations, the package estimates gene set enrichment using posterior probabilities from the TWAS-colocalization integration step.

Scientific Applications:

• Gene Implication for Complex Traits: Identifies genes that may be biologically relevant to a complex trait by combining colocalization probabilities with TWAS summary statistics.
• Gene Set Enrichment Estimation: Quantifies enrichment of functional gene sets using integrated posterior probabilities from TWAS and colocalization analyses.

Methodology:

The package implements a probabilistic framework that constrains TWAS scan z-score-based likelihood with gene-level colocalization probability, then derives posterior probabilities for gene set enrichment estimation.