CandiSNPer: a web tool for the identification of candidate SNPs for causal variants
CandiSNPer: a web tool for the identification of candidate SNPs for causal variants
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DOI：
10.1093/bioinformatics/btq068
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发表时间：
2010-04-01
期刊：
影响因子：
5.8
通讯作者：
Brockmann, Gudrun A.
中科院分区：
文献类型：
--
作者：
Schmitt, Armin O.;Assmus, Jens;Brockmann, Gudrun A.
用于全基因组关联研究 (GWAS) 的人类单核苷酸多态性 (SNP) 芯片可同时对多达 400 万个 SNP 进行基因分型。迄今为止，大约 1000 个人类 SNP 已被确定与某种疾病或其他感兴趣的性状具有统计显着相关性。所识别的 SNP 不一定是因果变异，但它与其存在连锁不平衡 (LD)。 CandiSNPer 是一款软件工具，可通过 GWAS 确定重要 SNP 周围的 LD 区域。它提供了一个列表，其中包含 LD 区域中发现的 SNP 的功能注释和 LD 值。该列表不仅包含可获得基因分型数据的 SNP，还包含具有 rs-ID 的所有 SNP，从而增加了包含因果变异的可能性。此外，还生成了显示 LD 值的图。 CandiSNPer 有助于预选因果变异的候选 SNP。
Human single nucleotide polymorphism (SNP) chips which are used in genome-wide association studies (GWAS) permit the genotyping of up to 4 million SNPs simultaneously. To date, about 1000 human SNPs have been identified as statistically significantly associated with a disease or another trait of interest. The identified SNP is not necessarily the causal variant, but it is rather in linkage disequilibrium (LD) with it. CandiSNPer is a software tool that determines the LD region around a significant SNP from a GWAS. It provides a list with functional annotation and LD values for the SNPs found in the LD region. This list contains not only the SNPs for which genotyping data are available, but all SNPs with rs-IDs, thus increasing the likelihood to include the causal variant. Furthermore, plots showing the LD values are generated. CandiSNPer facilitates the preselection of candidate SNPs for causal variants.