GCORE

GCORE performs genome-wide gene–gene interaction testing in family-based trios by comparing interlocus correlations between transmitted and non-transmitted alleles to detect interactions contributing to complex traits.

Key Features:

• Efficiency in High-Volume Analysis: Performs testing of tens of billions of single-nucleotide polymorphism (SNP) interaction pairs suitable for genome-wide association studies (GWAS).
• Family-Based Approach: Specifically targets family trios (two parents and one affected sibling) for interaction analysis within familial contexts.
• Interlocus Correlation Comparison: Compares interlocus correlations at pairs of SNPs between transmitted and non-transmitted alleles to identify gene–gene interactions.
• Statistical Robustness: Evaluated by simulation studies showing controlled type I error rates and high statistical power under various scenarios.
• Practical Throughput Example: Applied to a family-based GWAS for autism with approximately 2,000 trios, testing over 22 billion SNP interaction pairs in 36 hours.

Scientific Applications:

• Family-based GWAS of complex traits: Genome-wide detection of gene–gene interactions in family cohorts to elucidate genetic architecture of complex traits and diseases.
• Genetic epidemiology: Investigation of hereditary patterns and genetic risk factors arising from gene–gene interactions within families.
• Autism genetics: Genome-wide interaction scanning in family-based autism studies to identify interaction effects contributing to disease risk.

Methodology:

Compares interlocus correlations at two SNPs between transmitted and non-transmitted alleles, with evaluation via simulation studies.