SCAN: SNP and copy number annotation
SCAN: SNP and copy number annotation
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DOI：
10.1093/bioinformatics/btp644
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发表时间：
2010-01-15
期刊：
影响因子：
5.8
通讯作者：
Cox, Nancy J.
中科院分区：
文献类型：
--
作者：
Gamazon, Eric R.;Zhang, Wei;Cox, Nancy J.
动机：全基因组关联研究（GWAS）产生数十万个单核苷酸多态性（SNP）和复杂表型之间的关系。传统上被忽视的拷贝数变化（CNV）对复杂性状的贡献也得到了积极研究。为了促进对数据的解释和后续实验验证的设计，我们开发了一个数据库，通过结合几种方法，可实现这些变体的明智优先级，不仅涉及公开可用的物理和功能注释，而且还涉及多端口链接不平衡（ ld）注释以及表达定量性状基因座（eqtls）的注释。注重：对于每个SNP，扫描数据库提供：（i）在HAPMAP CEU（UT，UT，US，US）和YRI（来自尼日利亚伊巴丹市的Yoruba People）中，来自HAPMAP SNP到基因表达的EQTL映射到基因表达（由Affymetrix Exon阵列评估）的摘要信息样品； （ii）在HAPMAP SNP的情况下，LD信息，包括具有变体的强LD（成对或多焦点LD）的基因变化，以及SNP被不同的高通量平台所覆盖的程度； （iii）从公共数据库获得的摘要信息（例如，物理和功能注释）； （iv）来自其他GWAS的摘要信息。对于每个基因，扫描提供：（i）基因（局部和远处SNP）的EQTL和（ii）在每个高通量平台上该基因的所有变体中所有变体的覆盖率。对于每个基因组区域，扫描提供了以下注释：（i）该区域内所有SNP，基因和已知CNV的物理和功能注释以及（ii）由该区域内EQTL调节的所有基因。
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.