VizStruct for visualization of genome-wide SNP analyses

Department of Pharmaceutical Sciences, State University of New York Buffalo, NY 14260, USA.
Bioinformatics (Impact Factor: 4.98). 08/2006; 22(13):1569-76. DOI: 10.1093/bioinformatics/btl144
Source: PubMed


MOTIVATION: The size, dimensionality and the limited range of the data values make visualization of single nucleotide polymorphism (SNP) datasets challenging. The purpose of this study is to evaluate the usefulness of 3D VizStruct, a novel multi-dimensional data visualization technique for analyzing patterns in SNP datasets. RESULTS: VizStruct is an interactive visualization technique that reduces multi-dimensional data to two dimensions using the complex-valued harmonics of the discrete Fourier transform (DFT). In the 3D VizStruct extension, the multi-dimensional SNP data vectors are reduced to three dimensions using a combination of the DFT and the Kullback-Leibler divergence. The performance of 3D VizStruct was challenged with several biologically relevant published datasets that included human Chromosome 21, the human lipoprotein lipase (LPL) gene locus and the multi-locus genotypes of coral populations. In every case, the 3D VizStruct mapping provided an intuitive visual description of the key characteristics of the underlying multi-dimensional genotype.

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    • "Information theoretic methods have considerable promise for enhancing single nucleotide (SNP), gene-gene interaction (GGI) and GEI analysis [3-6]. The Kullback-Leibler divergence (KLD), an information theoretic measure of the 'distance' between two distributions, has been proposed for 2-group comparisons such as those used to evaluate ancestry informative markers [7-9], as a multi-locus linkage disequilibrium (LD) measure to enable identification of TagSNPs [6] and for analytical visualization [4,5]. Entropy-based statistics to test for allelic association with a phenotype [10-12] and for two-locus interactions have also been proposed [13]. "
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