Joint visualization of association study results and linkage disequilibrium

This webpage implements a visualization algorithm created by Eric Jorgenson as described in Eric's abstract that simultaneously plots the results of genetic association tests and linkage disequilibrium between variants. This provides investigators a tool to help localize the most likely source of an association signal and to visualize which signals are driven by their correlation with other associated SNPs.

Each row of the color density plot represents individual SNPs ordered by their location on the chromosome. Each column represents the same set of SNPs in the same order. The color of each cell (SNP_x, SNP_y) indicates the expected association signal for SNP_x due to its correlation with SNP_y. Along the diagonal, where SNP_x and SNP_y refer to the same SNP, the observed association signal for that SNP is plotted. Unlike the typical LD plot, this plot will generally not be symmetric about the SNP_x = SNP_y axis; this asymmetry provides a way to determine which SNPs are driving an observed association signal.

An example plot is shown below. This plot displays results from a prostate cancer association study by Haiman et al. and linkage disequilibrium information from the HapMap Yoruban (YRI) population. The strength of the association signal for each SNP is represented by the color scale displayed to the right of the matrix. The physical location of the SNPs is presented at the bottom of the matrix, which in this example indicates that the SNPs reside on chromosome 8 between 125,021,107 and 126,025,497 base pairs. The top SNP association signals are labeled on the vertical axis, with the most significant SNP labeled in red. SNPs are chosen for labeling if they pass two criteria: 1) SNPs must reach a specific significance threshold and 2) SNPs must demonstrate association above the level expected due to their correlation with neighboring SNPs. In other words, the color of the association signal for a given SNP (on the diagonal) must be warmer than the color of the signal for that SNP due to its correlation with another associated SNP (any off the diagonal cell in the same row). Consequently, labeled SNPs indicate the most likely source of the strongest association signals in the displayed region.

Please proceed to the application page