Project Goals
The goal of this project is to aid genetic association studies of addiction by creating a resource of biologically relevant genes, pathways and single nucleotide polymorphisms (SNPs). The primary users of the NeuroSNP resource are investigators conducting genome-wide association studies (GWASs) of addiction-related phenotypes. NeuroSNP will allow investigators to identify biologically relevant genes for addiction based on curated expert knowledge, and assess the coverage of these genes provided by commercial SNP microarrays. If investigators wish to ensure the coverage of certain addiction-related genes is optimal, NeuroSNP provides a mechanism for supplementation.
While commercial SNP microarrays offer affordable and comprehensive coverage of the human genome, some diseases have biologically relevant genomic regions that may require additional coverage. Addiction, for example, is believed to be influenced by complex interactions involving several genes and pathways. NIDA has assembled a number of investigators specializing in fields such as genetics, pharmacogenetics, bioinformatics and neurobiology through a Request for Information. These investigators have pooled their expert knowledge to produce a database of addiction-related genes and SNPs. Commercial SNP microarrays, such as those offered by Affymetrix and Illumina, are then analyzed to determine how well certain addiction-related genes are covered. When the coverage is less than optimal, a SNP prioritization scheme is used to supplement the commercial array with the most biologically informative markers. For example, SNPs in coding regions, promoters, and evolutionary conserved regions are selected first.
Related Papers
Supplementing high-density SNP microarrays for additional coverage of disease-related genes: addiction as a paradigm. Saccone SF, Bierut LJ, Chesler EJ, Kalivas PW, Lerman C, Saccone NL, Uhl GR, Li CY, Philip VM, Edenberg HJ, Sherry ST, Feolo M, Moyzis RK, Rutter JL. PLoS ONE 2009; 4(4):e5225. Epub 2009 Apr 21. PMCID: PMC2668711
Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. Saccone SF, Saccone NL, Swan GE, Madden PA, Goate AM, Rice JP, Bierut LJ. Bioinformatics 2008 Aug 15; 24(16):1805-1811. Epub 2008 Jun 19. PMCID: PMC2610477
Questions
Please contact Scott Saccone – ssaccone@wustl.edu.