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Bioinformatics Advance Access originally published online on November 3, 2005
Bioinformatics 2006 22(2):220-225; doi:10.1093/bioinformatics/bti762
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria

Zhaohui S. Qin 1,*, Shyam Gopalakrishnan 1,2 and Gonçalo R. Abecasis 1

1Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan 1420 Washington Heights, Ann Arbor, MI 48109-2029, USA
2Department of Electrical Engineering and Computer Science, University of Michigan Ann Arbor, MI 48109-2122, USA

*To whom correspondence should be addressed.

Motivation: Selecting SNP markers for genome-wide association studies is an important and challenging task. The goal is to minimize the number of markers selected for genotyping in a particular platform and therefore reduce genotyping cost while simultaneously maximizing the information content provided by selected markers.

Results: We devised an improved algorithm for tagSNP selection using the pairwise r2 criterion. We first break down large marker sets into disjoint pieces, where more exhaustive searches can replace the greedy algorithm for tagSNP selection. These exhaustive searches lead to smaller tagSNP sets being generated. In addition, our method evaluates multiple solutions that are equivalent according to the linkage disequilibrium criteria to accommodate additional constraints. Its performance was assessed using HapMap data.

Availability: A computer program named FESTA has been developed based on this algorithm. The program is freely available and can be downloaded at http://www.sph.umich.edu/csg/qin/FESTA/

Contact: qin{at}umich.edu

Supplementary information: http://www.sph.umich.edu/csg/qin/FESTA/

Received on August 6, 2005; revised on October 9, 2005; accepted on November 2, 2005

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