We recently introduced the genomic information network (GIN) model for systematically incorporating biological databases into the prioritization of SNPs after a GWAS (4). SPOT implements the GIN prioritization method using a secure, interactive web-based approach. The user uploads a list of SNPs and may optionally include P-values from statistical tests of genotype–phenotype correlation. The user may also upload a list of genes, genomic regions or specific SNPs with custom prioritization scores that determine how SPOT uses the GIN method to prioritize the SNPs. The results may be viewed directly in the web browser or downloaded in various formats. The GIN prioritization method is not designed to predict causal variants, and the prioritization results are not intended to be used to interpret the statistical significance of the GWAS results. Rather, it is intended to assist users in incorporating a broad range of biological hypotheses into the prioritization process using a transparent method of specifying their specific biological priorities and to provide results that are easily interpreted in terms of what went into the model and exactly how that information was used to prioritize the SNPs.
