GePhEx

GePhEx analyzes variant-disease associations from SNP arrays and Next Generation Sequencing data to explore phenotypic relationships supported by genetic evidence.

Key Features:

• Phenotype-wide Genetic Variant Retrieval: Retrieves comprehensive lists of genetic variants associated with specified diseases from publicly available variant-disease association datasets derived from SNP arrays and Next Generation Sequencing studies.
• Visual Exploration of Joint Genetic Architecture: Provides visualization of joint genetic architecture across diseases by leveraging publicly available variant-disease associations to detect known and novel disease relationships.
• Linkage Disequilibrium Analysis: Performs linkage disequilibrium analysis between disease-associated variants to assess genetic correlations across phenotypes.
• Integration with Genes, Pathways, and Drug-Targets: Links variants to genes, biological pathways, and drug-targets to enable multi-layered analysis of potential disease connections.

Scientific Applications:

• Cross-disease genetic association discovery: Identifies shared genetic variants and correlations across multiple diseases to reveal potential pleiotropy.
• Investigation of genotype–phenotype interplay: Supports studies into pathophysiological mechanisms underlying multifactorial conditions by connecting variants to genes and pathways.
• Case example: Has been applied to detect potential relationships between schizophrenia and lung cancer by analyzing variant-disease associations and linkage disequilibrium.

Methodology:

Integration of genetic data with phenotypic information, analysis of publicly available variant-disease associations, and linkage disequilibrium analysis to construct networks of potential disease relationships.