SNPsnap: a Web-based tool for identification and annotation of matched SNPs

Tune H Pers; Pascal Timshel; Joel N Hirschhorn

doi:10.1093/bioinformatics/btu655

SNPsnap: a Web-based tool for identification and annotation of matched SNPs

Bioinformatics. 2015 Feb 1;31(3):418-20. doi: 10.1093/bioinformatics/btu655. Epub 2014 Oct 13.

Authors

Tune H Pers¹, Pascal Timshel¹, Joel N Hirschhorn¹

Affiliation

¹ 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.

Abstract

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: joelh@broadinstitute.org

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Genome-Wide Association Study*
Humans
Internet
Linkage Disequilibrium
Molecular Sequence Annotation*
Polymorphism, Single Nucleotide / genetics*
Software*

Abstract

Publication types

MeSH terms

Grants and funding