CLIN_SKAT

CLIN_SKAT performs extraction, weighting, and SKAT-based gene-level association analyses to prioritize clinically relevant rare and common genetic variants from next-generation sequencing (NGS) data.

Key Features:

• Extraction of Clinically Relevant Variants: Extracts rare and common variants identified as clinically relevant from next-generation sequencing datasets.
• Gene-Based Association Analysis: Groups selected variants by gene and performs gene-level association analysis using SKAT (Sequence Kernel Association Test).
• Customizable Pre-Analysis Steps: Provides customizable pre-analysis steps, including incorporation of ethnicity-based priors to refine variant selection and weighting.
• Weighted Case-Control Analysis: Calculates weights from global healthy population data and performs weighted case-control association analyses.
• Visualization Tools: Includes plotting functions for visualization of analysis results.

Scientific Applications:

• Complex Disease Genetics: Enables identification of genetic contributors to complex diseases, particularly where heritability is not fully explained by common variants, by prioritizing rare variants with potentially larger effect sizes.
• Dimensionality Reduction and Causal Variant Discovery: Reduces data dimensionality by focusing on biologically meaningful variant subsets to facilitate discovery of causal associations.

Methodology:

Performs variant extraction from NGS datasets; groups variants by gene and applies SKAT (Sequence Kernel Association Test); implements customizable pre-analysis including ethnicity-based priors; calculates weights from global healthy population data and conducts weighted case-control analyses; and provides plotting functions for result visualization.