Tutorial: LD and Haplotype Analysis

4. Comparing Multiple LD Plots

This step is covered as it may be useful in your own study to compare multiple LD plots to understand how the correlation structure in one dataset compares to that of a similar dataset, e.g. comparing a random set of Caucasians in your study with CEU samples of HapMap. Another useful example is comparing a less dense array (e.g. Affymetrix 500K) with a denser array (e.g. Affymetrix 6.0).

Though not a standard practice, for demonstration purposes this tutorial compares the overall LD structure of all HapMap populations with that of only Yorubans.

• From the Project Navigator, open the HapMap Phenotype + 500K Genotypes spreadsheet, right-click on the Ethnicity column and select Activate by Category.
• Select YRI and click OK.


Figure 4a. Comparing LD between all
HapMap and Yorubans.

A new spreadsheet node, named HapMap Phenotype + 500k Genotype - Mapped Sheet 2, will be created with only the YRI samples activated.

• From the Project Navigator, rename this node, YRI.
• Now, from within the –log10 P + LD plot, select User Graphs in the Graph Control Interface, click the drop down menu under Add Graph and click Select Spreadsheet... Select the YRI spreadsheet and click OK.
• Select Linkage Disequilibrium and click Add.

You should now have a P-value plot stacked on top of two LD plots (Figure 4a).

In this instance there is a slight difference in LD structure displayed in the two plots. If you observed this in your own data, you would want to investigate why such a difference exits.

• Go ahead and delete the YRI LD plot by right-clicking its associated node in the Graph Control Interface and selecting Delete.