SPOT

SPOT prioritizes single nucleotide polymorphisms (SNPs) after genome-wide association studies (GWAS) by integrating genomic annotation data and biological databases to identify SNPs for follow-up investigation.

Key Features:

• Integration with biological databases: Integrates genomic annotation data and biological databases to provide biological context for SNP evaluation.
• Genomic Information Network (GIN) method: Implements the Genomic Information Network (GIN) method to evaluate SNP biological relevance by considering proximity to phenotype-related genes and potential impacts on gene expression, including splice sites.
• GWAS P-value and SNP input handling: Processes lists of SNPs with corresponding GWAS P-values to generate prioritized SNP rankings.
• Customizable prioritization criteria: Supports specification of prioritization criteria such as candidate genes or genomic regions and adjustable prioritization levels.

Scientific Applications:

• Post-GWAS SNP selection: Prioritizes SNPs for selection for genotyping and follow-up in independent replication samples.
• Identification of functionally relevant variants: Highlights SNPs with higher likelihood to affect gene expression or reside near phenotype-related genes, facilitating candidate variant selection for downstream studies.

Methodology:

Applies the Genomic Information Network (GIN) method using genomic annotation data and biological databases to score SNPs from input lists with GWAS P-values based on proximity to phenotype-related genes and predicted impacts on gene expression, including splice sites.