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Nucleic Acids Research Advance Access published online on November 4, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn756
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system

Alexander R. Pico1,*, Ivan V. Smirnov2, Jeffrey S. Chang3, Ru-Fang Yeh3, Joseph L. Wiemels3, John K. Wiencke2, Tarik Tihan4, Bruce R. Conklin1,5,6 and Margaret Wrensch2

1Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, CA 94158, 2Department of Neurological Surgery, Neuroepidemiology Division, 3Department of Epidemiology and Biostatistics, 4Department of Pathology, 5Department of Medicine and 6Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94122, USA

*To whom correspondence should be addressed. Tel: +1 415 734 2741; Fax:+1 415 355 0960; Email: apico{at}gladstone.ucsf.edu

Received August 16, 2008. Revised October 3, 2008. Accepted October 6, 2008.

SNPLogic (http://www.snplogic.org) brings together single nucleotide polymorphism (SNP) information from numerous sources to provide a comprehensive SNP selection, annotation and prioritization system for design and analysis of genotyping projects. SNPLogic integrates information about the genetic context of SNPs (gene, chromosomal region, functional location, haplotypes tags and overlap with transcription factor binding sites, splicing sites, miRNAs and evolutionarily conserved regions), genotypic data (allele frequencies per population and validation method), coverage of commercial arrays (ParAllele, Affymetrix and Illumina), functional predictions (modeled on structure and sequence) and connections or established associations (biological pathways, gene ontology terms and OMIM disease terms). The SNPLogic web interface facilitates construction and annotation of user-defined SNP lists that can be saved, shared and exported. Thus, SNPLogic can be used to identify and prioritize candidate SNPs, assess custom and commercial arrays panels and annotate new SNP data with publicly available information. We have found integration of SNP annotation in the context of pathway information and functional prediction scores to be a powerful approach to the analysis and interpretation of SNP-disease association data.


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