SNPsnap：一个用于识别和注释匹配单核苷酸多态性的基于网络的工具。
SNPsnap: a Web-based tool for identification and annotation of matched SNPs.
作者信息
Pers Tune H, Timshel Pascal, Hirschhorn Joel N
机构信息
Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 2142, USA, Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 2142, USA, Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 2142, USA, Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
出版信息
Bioinformatics. 2015 Feb 1;31(3):418-20. doi: 10.1093/bioinformatics/btu655. Epub 2014 Oct 13.
SUMMARY
An important computational step following genome-wide association studies (GWAS) is to assess whether disease or trait-associated single-nucleotide polymorphisms (SNPs) enrich for particular biological annotations. SNP-based enrichment analysis needs to account for biases such as co-localization of GWAS signals to gene-dense and high linkage disequilibrium (LD) regions, and correlations of gene size, location and function. The SNPsnap Web server enables SNP-based enrichment analysis by providing matched sets of SNPs that can be used to calibrate background expectations. Specifically, SNPsnap efficiently identifies sets of randomly drawn SNPs that are matched to a set of query SNPs based on allele frequency, number of SNPs in LD, distance to nearest gene and gene density.
AVAILABILITY AND IMPLEMENTATION
SNPsnap server is available at http://www.broadinstitute.org/mpg/snpsnap/.
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
全基因组关联研究（GWAS）之后的一个重要计算步骤是评估疾病或性状相关的单核苷酸多态性（SNP）是否富集特定的生物学注释。基于SNP的富集分析需要考虑诸如GWAS信号与基因密集和高连锁不平衡（LD）区域的共定位，以及基因大小、位置和功能的相关性等偏差。SNPsnap网络服务器通过提供可用于校准背景预期的匹配SNP集来实现基于SNP的富集分析。具体而言，SNPsnap能够根据等位基因频率、处于LD中的SNP数量、与最近基因的距离和基因密度，高效识别与一组查询SNP匹配的随机抽取的SNP集。
可用性与实现方式
SNPsnap服务器可在http://www.broadinstitute.org/mpg/snpsnap/获取。
联系方式
补充信息
补充数据可在《生物信息学》在线获取。
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