LAMPLINK

LAMPLINK detects high-order epistatic interactions among single nucleotide polymorphisms (SNPs) in genome-wide association study (GWAS) data to identify combinatorial genetic effects contributing to missing heritability.

Key Features:

• Epistasis Detection: Identifies high-order epistatic interactions, i.e., combinations of two or more SNPs that jointly influence a trait.
• Integration with PLINK: Extends and integrates with PLINK to enable combinatorial epistasis analysis within GWAS workflows.
• Multiple Testing Correction (LAMP): Employs the LAMP (Likelihood-based Association Mapping Procedure) multiple-testing procedure to evaluate statistical significance of SNP combinations.
• Genome-wide Case-Control Application: Applied to genome-wide case-control datasets, including the 1000 Genomes Project, and reported detection of a five-SNP combination enriched in the Japanese population.
• Addressing Missing Heritability: Targets the missing heritability problem by detecting multi-locus effects not captured by single-SNP association tests.

Scientific Applications:

• Complex Trait Architecture: Investigating the multi-locus genetic architecture of complex traits and diseases by revealing epistatic contributions to phenotypic variation.
• GWAS Case-Control Analysis: Analysis of genome-wide case-control studies, including datasets such as the 1000 Genomes Project.
• Population-specific Epistasis Detection: Identifying combinatorial SNP accumulations specific to populations, exemplified by the five-SNP finding in the Japanese population.

Methodology:

LAMPLINK integrates with PLINK, detects high-order epistatic interactions among SNPs, and applies the LAMP (Likelihood-based Association Mapping Procedure) multiple-testing correction; it has been applied to genome-wide case-control datasets such as the 1000 Genomes Project.