SNPsnap

SNPsnap generates matched sets of single-nucleotide polymorphisms (SNPs) to provide calibrated background controls for enrichment analyses of GWAS-associated variants.

Key Features:

• Matched background SNP sets: Provides randomly drawn SNP sets matched to query SNPs to serve as calibrated backgrounds for enrichment testing.
• Matching criteria: Matches SNPs based on allele frequency, number of SNPs in linkage disequilibrium (LD), distance to the nearest gene, and gene density.
• Bias mitigation: Controls for biases from co-localization in gene-dense regions, regions of high LD, and correlations related to gene size, location, and function.
• Enrichment evaluation: Facilitates assessment of whether disease- or trait-associated SNPs show significant enrichment for specific biological annotations.

Scientific Applications:

• Post-GWAS enrichment analysis: Provides calibrated background sets to support enrichment analyses following genome-wide association studies (GWAS).
• Annotation enrichment testing: Enables testing of enrichment of GWAS-associated SNPs for specific biological annotations while accounting for genomic confounders.
• Discrimination of biological signal from genomic structure: Helps discern genuine trait- or disease-relevant signals from artifacts introduced by linkage disequilibrium or gene-density patterns.

Methodology:

Identifies sets of randomly drawn SNPs matched to query SNPs by allele frequency, number of SNPs in linkage disequilibrium (LD), distance to the nearest gene, and gene density to create calibrated backgrounds for enrichment analysis.