Title: Select Your SNPs (SYSNPs): a web tool for automatic and massive selection of SNPs

Authors: Belén Lorente-Galdos; Ignacio Medina; Carlos Morcillo-Suarez; Txema Heredia; Ángel Carreño-Torres; Ricardo Sangrós; Josep Alegre; Guillermo Pita; Gemma Vellalta; Nuria Malats; David G. Pisano; Joaquín Dopazo; Arcadi Navarro

Addresses: Institut de Biologia Evolutiva (UPF-CSIC), Barcelona Biomedical Research Park (PRBB), Spain; CIBER en Epidemiología y Salud Pública (CIBERESP), Spain ' Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain ' Institut de Biologia Evolutiva (UPF-CSIC), Barcelona Biomedical Research Park (PRBB), Spain; Spanish National Institute for Bioinformatics (INB), Spain ' Institut de Biologia Evolutiva (UPF-CSIC), Barcelona Biomedical Research Park (PRBB), Spain; Spanish National Institute for Bioinformatics (INB), Spain ' Institut de Biologia Evolutiva (UPF-CSIC), Barcelona Biomedical Research Park (PRBB), Spain; Spanish National Institute for Bioinformatics (INB), Spain ' Institut de Biologia Evolutiva (UPF-CSIC), Barcelona Biomedical Research Park (PRBB), Spain; Spanish National Institute for Bioinformatics (INB), Spain ' Institut de Biologia Evolutiva (UPF-CSIC), Barcelona Biomedical Research Park (PRBB), Spain; Spanish National Institute for Bioinformatics (INB), Spain ' Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain ' Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; Institut Municipal d'Investigació Mèdica (IMIM), Barcelona, Spain ' Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain ' Spanish National Institute for Bioinformatics (INB), Spain; Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain ' Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain; Spanish National Institute for Bioinformatics (INB), Spain; CIBER en Enfermedades Raras (CIBERER), Spain ' Institut de Biologia Evolutiva (UPF-CSIC), Barcelona Biomedical Research Park (PRBB), Spain; CIBER en Epidemiología y Salud Pública (CIBERESP), Spain; Spanish National Institute for Bioinformatics (INB), Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Universitat Pompeu Fabra, Barcelona, Spain

Abstract: Association studies are the choice approach in the discovery of the genomic basis of complex traits. To carry out such analysis, researchers frequently need to (1) select optimally informative sets of Single Nucleotide Polymorphisms (SNPs) in candidate regions and (2) annotate the results of associations found by means of genome-wide SNP arrays. These are complex tasks, since many criteria have to be considered, including the SNPs' functional properties, technological information and haplotype frequencies in given populations. SYSNPs implements algorithms that allow for efficient and simultaneous consideration of all the relevant criteria to obtain sets of SNPs that properly cover arbitrarily large lists of genes or genomic regions. Complementarily, SYSNPs allows for comprehensive functional annotation of SNPs linked to any given marker SNP. SYSNPs dramatically reduces the effort needed for SNP selection from days of searching various databases to a few minutes using a simple browser.

Keywords: SNPs; single nucleotide polymorphisms; tag-SNPs; tagger; linkage disequilibrium; association; complex diseases; PUPASuite; genome-wide association studies; SNP arrays; SNP selection; bioinformatics.

DOI: 10.1504/IJDMB.2012.049249

International Journal of Data Mining and Bioinformatics, 2012 Vol.6 No.3, pp.324 - 334

Accepted: 06 Nov 2010
Published online: 17 Dec 2014 *

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