The Textile Plot: A New Linkage Disequilibrium Display of Multiple-Single Nucleotide Polymorphism Genotype Data

Abstract

Linkage disequilibrium (LD) is a major concern in many genetic studies because of the markedly increased density of SNP (Single Nucleotide Polymorphism) genotype markers. This dramatic increase in the number of SNPs may cause problems in statistical analyses, such as by introducing multiple comparisons in hypothesis testing and colinearity in logistic regression models, because of the presence of complex LD structures. Inferences must be made about the underlying genetic variation through the LD structure before applying statistical models to the data. Therefore, we introduced the textile plot to provide a visualization of LD to improve the analysis of the genetic variation present in multiple-SNP genotype data. The plot can accentuate LD by displaying specific geometrical shapes, and allowing for the underlying haplotype structure to be inferred without any haplotype-phasing algorithms. Application of this technique to simulated and real data sets illustrated the potential usefulness of the textile plot as an aid to the interpretation of LD in multiple-SNP genotype data. The initial results of LD mapping and haplotype analyses of disease genes are encouraging, indicating that the textile plot may be useful in disease association studies.