Abstract

SPOT (http://spot.cgsmd.isi.edu), the SNP prioritization online tool, is a web site for integrating biological databases into the prioritization of single nucleotide polymorphisms (SNPs) for further study after a genome-wide association study (GWAS). Typically, the next step after a GWAS is to genotype the top signals in an independent replication sample. Investigators will often incorporate information from biological databases so that biologically relevant SNPs, such as those in genes related to the phenotype or with potentially non-neutral effects on gene expression such as a splice sites, are given higher priority. We recently introduced the genomic information network (GIN) method for systematically implementing this kind of strategy. The SPOT web site allows users to upload a list of SNPs and GWAS P-values and returns a prioritized list of SNPs using the GIN method. Users can specify candidate genes or …

Date

July 1, 2010

Authors

Scott F Saccone, Raphael Bolze, Prasanth Thomas, Jiaxi Quan, Gaurang Mehta, Ewa Deelman, Jay A Tischfield, John P Rice

Journal

Nucleic acids research

Volume

38

Issue

suppl_2

Pages

W201-W209

Publisher

Oxford University Press