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Bioinformatics Advance Access published online on November 3, 2005
Bioinformatics, 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@oxfordjournals.org
Received August 6, 2005
Revised October 9, 2005
Accepted November 2, 2005

Article

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

Zhaohui Qin 1*, Shyam Gopalakrishnan 2, and Gonçalo Abecasis 1

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

* To whom correspondence should be addressed.
Zhaohui Qin, E-mail: qin{at}umich.edu


  Abstract

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 all other markers.

Results: We devised an improved algorithm for tagSNP selection using the pairwise r2 criteria. 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, we evaluated multiple solutions that are equivalent according to the LD 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/.

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


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