The Textile Plot: A New Linkage Disequilibrium Display of Multiple-Single Nucleotide Polymorphism Genotype Data
Natsuhiko Kumasaka1*, Yusuke Nakamura1,2, Naoyuki Kamatani1
1 Center for Genomic Medicine, RIKEN, Tokyo, Japan, 2 The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
Advances in high-throughput genotyping technology have enabled us to identify remarkably dense SNP (Single Nucleotide Polymorphism) genotype markers on human chromosomes [1]. Linkage disequilibrium (LD) is a topic of interest because it impacts the search for disease-susceptibility loci in genome-wide association studies [2], [3] and can reveal underlying historical and biological processes, such as selection [4], [5], mutation [6], recombination [7], [8] and population history [9].
Graphical representations of LD for multiple-SNP genotypes have been developed to assess the presence of LD in practical data sets. Various pairwise LD statistics, such as 
or 
(reviewed in, e.g., [10]), can be shown by triangular heat map displays [11] in which the color shading indicates the strength and distribution of the pairwise LD. A segment with consistently high LD, a so-called LD block, is visually apparent in such displays. From these displays, it is clear that LD is discontinuous and heterogeneous over entire human chromosomes [7]. To incorporate such heterogeneity into further genetic and statistical analyses, the visualization of pairwise LD is now being recognized as a way to maximize insight into the LD present in multiple-SNP genotype data.
http://bioinformatics.oxfordjournals.org/content/21/2/263.long
Haploview: analysis and visualization of LD and haplotype maps or (reviewed in, e.g., [10]), can be shown by triangular heat map displays [11] in which the color shading indicates the strength and distribution of the pairwise LD. A segment with consistently high LD, a so-called LD block, is visually apparent in such displays. From these displays, it is clear that LD is discontinuous and heterogeneous over entire human chromosomes [7]. To incorporate such heterogeneity into further genetic and statistical analyses, the visualization of pairwise LD is now being recognized as a way to maximize insight into the LD present in multiple-SNP genotype data.http://bioinformatics.oxfordjournals.org/content/21/2/263.long
1. J. C. Barrett1,*,
2. B. Fry2,
3. J. Maller1 and
4. M. J. Daly1,3
http://www.broad.mit.edu/mpg/haploview/
No comments:
Post a Comment