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SCAN: SNP and copy number annotation.
Gamazon, Eric R; Zhang, Wei; Konkashbaev, Anuar; Duan, Shiwei; Kistner, Emily O; Nicolae, Dan L; Dolan, M Eileen; Cox, Nancy J.
Afiliación
  • Gamazon ER; Department of Medicine, The University of Chicago, Chicago, IL, USA.
Bioinformatics ; 26(2): 259-62, 2010 Jan 15.
Article en En | MEDLINE | ID: mdl-19933162
MOTIVATION: Genome-wide association studies (GWAS) generate relationships between hundreds of thousands of single nucleotide polymorphisms (SNPs) and complex phenotypes. The contribution of the traditionally overlooked copy number variations (CNVs) to complex traits is also being actively studied. To facilitate the interpretation of the data and the designing of follow-up experimental validations, we have developed a database that enables the sensible prioritization of these variants by combining several approaches, involving not only publicly available physical and functional annotations but also multilocus linkage disequilibrium (LD) annotations as well as annotations of expression quantitative trait loci (eQTLs). RESULTS: For each SNP, the SCAN database provides: (i) summary information from eQTL mapping of HapMap SNPs to gene expression (evaluated by the Affymetrix exon array) in the full set of HapMap CEU (Caucasians from UT, USA) and YRI (Yoruba people from Ibadan, Nigeria) samples; (ii) LD information, in the case of a HapMap SNP, including what genes have variation in strong LD (pairwise or multilocus LD) with the variant and how well the SNP is covered by different high-throughput platforms; (iii) summary information available from public databases (e.g. physical and functional annotations); and (iv) summary information from other GWAS. For each gene, SCAN provides annotations on: (i) eQTLs for the gene (both local and distant SNPs) and (ii) the coverage of all variants in the HapMap at that gene on each high-throughput platform. For each genomic region, SCAN provides annotations on: (i) physical and functional annotations of all SNPs, genes and known CNVs within the region and (ii) all genes regulated by the eQTLs within the region. AVAILABILITY: http://www.scandb.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Asunto(s)

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Programas Informáticos / Dosificación de Gen / Polimorfismo de Nucleótido Simple Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2010 Tipo del documento: Article País de afiliación: Estados Unidos

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Programas Informáticos / Dosificación de Gen / Polimorfismo de Nucleótido Simple Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2010 Tipo del documento: Article País de afiliación: Estados Unidos