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Nucleic Acids Research Advance Access originally published online on August 28, 2007
Nucleic Acids Research 2007 35(17):e113; doi:10.1093/nar/gkm621
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Nucleic Acids Research, 2007, Vol. 35, No. 17 e113
© 2007 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.

Methods Online

Efficacy assessment of SNP sets for genome-wide disease association studies

Andreas Wollstein1,2, Alexander Herrmann2,3, Michael Wittig2, Michael Nothnagel4, Andre Franke2, Peter Nürnberg1, Stefan Schreiber2, Michael Krawczak4 and Jochen Hampe2,3,*

1Cologne Center for Genomics, Cologne, 2Institute of Clinical Molecular Biology, Christian-Albrechts University, 3Ist Department of Medicine and 4Institute of Medical Informatics and Statistics, Christian-Albrechts University, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany

*To whom correspondence should be addressed. Tel: +49 431 597 1246; Fax: +49 431 597 1842; Email: J.Hampe{at}1med.uni-kiel.de

Received May 31, 2007. Revised July 30, 2007. Accepted July 30, 2007.

The power of a genome-wide disease association study depends critically upon the properties of the marker set used, particularly the number and physical spacing of markers, and the level of inter-marker association due to linkage disequilibrium. Extending our previously devised theoretical framework for the entropy-based selection of genetic markers, we have developed a local measure of the efficacy of a marker set, relative to including a maximally polymorphic single nucleotide polymorphism (SNP) at the map position of interest. Using this quantitative criterion, we evaluated five currently available SNP sets, namely Affymetrix 100K and 500K, and Illumina 100K, 300K and 550K in the CEU, YRI and JPT + CHB HapMap populations. At 50% relative efficacy, the commercial marker sets cover between 19 and 68% of the human genome, depending upon the population under study. An optimal technology-independent 500K marker set constructed from HapMap for Caucasians, in contrast, would achieve 73% coverage at the same relative efficacy.


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