- Article -
| In Silico Biology 4, 0035 (2004); ©2004, Bioinformation Systems e.V. |
Selecting SNPs for association studies based on population frequencies: A novel interactive tool and its application to polygenic diseases
Steffen Möller1, *, Dirk Koczan1, Pablo Serrano-Fernandez1, Uwe K. Zettl2, Hans-Jürgen Thiesen1 and Saleh M. Ibrahim1
1 University of Rostock, Institute of Immunology, Schillingallee 70, 18055 Rostock, Germany
Email: moeller@pzr.uni-rostock.de
2 University of Rostock, Department of Neurology, Gehlsheimer Str. 20, 18147 Rostock, Germany
* corresponding author
Edited by E. Wingender; received April 02, 2004; revised June 25, 2004; accepted June 25, 2004; published July 26, 2004
Abstract
Common complex polygenic diseases as autoimmune diseases have not been completely understood on a molecular level. While many genes are known to be involved in the pathways responsible for the phenotype, explicit causes for the susceptibility of the disease remain to be elucidated. The susceptibility to disease is thought to be the result of genetic epistatic interactions between common polymorphic genes. This polymorphism is mostly caused by single nucleotide polymorphisms (SNPs). Human subpopulations are known to differ in the susceptibility to the diseases and generally in the distribution of single nucleotide polymorphisms.
The here presented approach retrieves SNPs with the most divergent frequencies for selected human subpopulations to help defining properties for the experimental verification of SNPs within defined regions. A web-accessible program implementing this approach was evaluated for multiple sclerosis (MS), a common human polygenic disease. A link to a summary of data from "The SNP Consortium" (TSC) with sex-dependencies of SNPs is available. Associations of SNPs to genes, genetic markers and chromosomal loci are retrieved from the Ensembl project. This tool is recommended to be used in conjunction with microarray analyses or marker association studies that link genes or chromosomal loci to particular diseases.
Availability: http://qtl.pzr.uni-rostock.de/snpselect.php
Key words: SNP selection by population frequencies, association studies, Multiple Sclerosis, Ensembl