Department for Crop and Animal Sciences, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany.
Bioinformatics. 2010 Apr 1;26(7):969-70. doi: 10.1093/bioinformatics/btq068. Epub 2010 Feb 19.
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.
The CandiSNPer server is freely available at http://www2.hu-berlin.de/wikizbnutztier/software/CandiSNPer. The source code is available to academic users 'as is' upon request. The web site is implemented in Perl and R and runs on an Apache server. The Ensembl database is queried for SNP data via Perl APIs.
人类单核苷酸多态性（SNP）芯片可用于全基因组关联研究（GWAS），能够同时对多达 400 万个 SNP 进行基因分型。迄今为止，已经有大约 1000 个人类 SNP 被确定与疾病或其他感兴趣的特征具有统计学显著相关性。已识别的 SNP 不一定是因果变异，而是与它处于连锁不平衡（LD）状态。CandiSNPer 是一种软件工具，用于从 GWAS 中确定显著 SNP 周围的 LD 区域。它提供了一个包含 LD 区域中发现的 SNP 的功能注释和 LD 值的列表。该列表不仅包含可进行基因分型数据的 SNP，还包含所有带有 rs-ID 的 SNP，从而增加了包含因果变异的可能性。此外，还生成显示 LD 值的图。CandiSNPer 方便了对因果变异候选 SNP 的预选。
CandiSNPer 服务器可在 http://www2.hu-berlin.de/wikizbnutztier/software/CandiSNPer 上免费获得。源代码可应学术用户的要求“原样”提供。该网站使用 Perl 和 R 实现，在 Apache 服务器上运行。通过 Perl API 从 Ensembl 数据库查询 SNP 数据。
