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 allo

SUBMITTER: Kumasaka N 

PROVIDER: S-EPMC2860502 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature