Title: Unidimensional nonnegative scaling for genome-wide Linkage Disequilibrium maps

Authors: Haiyong Liao, Michael Ng, Eric Fung, Pak C. Sham

Addresses: Centre for Mathematical Imaging and Vision, and Department of Mathematics, Hong Kong Baptist University, Kowloon Tong, Hong Kong. ' Centre for Mathematical Imaging and Vision, and Department of Mathematics, Hong Kong Baptist University, Kowloon Tong, Hong Kong. ' Centre for Mathematical Imaging and Vision, and Department of Mathematics, Hong Kong Baptist University, Kowloon Tong, Hong Kong. ' Genome Research Center, The University of Hong Kong, Pokfulam Road, Hong Kong

Abstract: The main aim of this paper is to propose and develop a unidimensional nonnegative scaling model to construct Linkage Disequilibrium (LD) maps. The proposed constrained scaling model can be efficiently solved by transforming it to an unconstrained model. The method is implemented in PC Clusters at Hong Kong Baptist University. The LD maps are constructed for four populations from Hapmap data sets with chromosomes of several ten thousand Single Nucleotide Polymorphisms (SNPs). The similarities and dissimilarities of the LD maps are studied and analysed. Computational results are also reported to show the effectiveness of the method using parallel computation.

Keywords: linkage equilibrium; unidimensional scaling; nonnegativity; hapmap; parallel computation; matrix-vector multiplication; linkage disequilibrium maps; SNPs; single nucleotide polymorphisms; bioinformatics.

DOI: 10.1504/IJBRA.2008.021177

International Journal of Bioinformatics Research and Applications, 2008 Vol.4 No.4, pp.417 - 434

Published online: 08 Nov 2008 *

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