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Bioinformatics Advance Access originally published online on August 7, 2006
Bioinformatics 2006 22(20):2558-2561; doi:10.1093/bioinformatics/btl420
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MLR-tagging: informative SNP selection for unphased genotypes based on multiple linear regression

Jingwu He and Alexander Zelikovsky *

Department of Computer Science, Georgia State University Atlanta, GA 30303, USA

*To whom correspondence should be addressed.

Summary: The search for the association between complex diseases and single nucleotide polymorphisms (SNPs) or haplotypes has recently received great attention. For these studies, it is essential to use a small subset of informative SNPs accurately representing the rest of the SNPs. Informative SNP selection can achieve (1) considerable budget savings by genotyping only a limited number of SNPs and computationally inferring all other SNPs or (2) necessary reduction of the huge SNP sets (obtained, e.g. from Affymetrix) for further fine haplotype analysis.

A novel informative SNP selection method for unphased genotype data based on multiple linear regression (MLR) is implemented in the software package MLR-tagging. This software can be used for informative SNP (tag) selection and genotype prediction. The stepwise tag selection algorithm (STSA) selects positions of the given number of informative SNPs based on a genotype sample population. The MLR SNP prediction algorithm predicts a complete genotype based on the values of its informative SNPs, their positions among all SNPs, and a sample of complete genotypes.

An extensive experimental study on various datasets including 10 regions from HapMap shows that the MLR prediction combined with stepwise tag selection uses fewer tags than the state-of-the-art method of Halperin et al. (2005).

Availability: MLR-Tagging software package is publicly available at http://alla.cs.gsu.edu/~software/tagging/tagging.html

Contact: alexz{at}cs.gsu.edu

Received on December 7, 2005; revised on July 12, 2006; accepted on July 28, 2006

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