Information-theoretic identification of predictive SNPs and supervised visualization of genome-wide association studies.
The size, dimensionality and the limited range of the data values makes 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 SNP datasets capable of identifying informative SNPs in genome-wide association studies. VizStruct is an interactive visualization technique that reduces multi-dimensional data to three dimensions using a combination of the discrete Fourier transform and the Kullback-Leibler divergence. The performance of 3D VizStruct was challenged with several diverse, biologically relevant published datasets including the human lipoprotein lipase (LPL) gene locus, the human Y-chromosome in several populations and a multi-locus genotype dataset of coral samples from four populations. In every case, the SNPs and or polymorphic markers identified by the 3D VizStruct mapping were predictive of the underlying biology.
Bhasi
Kavitha
K
Department of Pharmaceutical Sciences, Eastern Michigan University, Ypsilanti, MI 48197, USA.
Zhang
Li
L
Brazeau
Daniel
D
Zhang
Aidong
A
Ramanathan
Murali
M
D000818:Animals; D037421:Anthozoa / Q000235:genetics; D041322:Chromosomes, Human, Y; D003196:Computer Graphics; D005787:Gene Frequency; D023281:Genomics / Q000379:methods*; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D007257:Information Theory; D015810:Linkage Disequilibrium; D008071:Lipoprotein Lipase / Q000235:genetics; D008297:Male; D020641:Polymorphism, Single Nucleotide
D008071:Lipoprotein Lipase