1. Generating LD Plots

The general workflow outlined in this tutorial is intended to emulate a study, whereby one does a whole genome scan on individual markers and then hones in on significant regions for a more in-depth investigation of LD and haplotypes.

A. Open the Project

• Launch Golden Helix SVS and choose File >Open Project.
• Navigate to the LD and Haplotypes Tutorial.ghp file downloaded previously and click Open.

You’ll notice a couple datasets already created in the project including a joined spreadsheet of phenotype and genotype data for the HapMap samples (HapMap Phenotype + 500K Genotypes) as well as an association test results spreadsheet (Association Tests (Genotypic Tests)).

B. Generate a –log10 P-value plot

• Open the Association Tests (Genotypic Tests) spreadsheet.
• Right-click on the Chi-Squared –log10 P column (2) and select Plot Variable in Genome Browser.

A p-value plot is created. Notice, there are two regions of significance, one on chr14 and the other on chr22. In this tutorial we will focus on the chr22 region.

Figure 2a. P-value plot initial zoom

• Before you move on, go back to the Project Navigator and rename the plot node just created to -log10 P + LD (right-click on the node and select Rename Node).
• Now, from the –log10 P + LD plot make sure Graph 1 is selected in the Graph Control Interface and then copy and paste chr22:35613887-35677604 into the Region: text box under the Graph tab. Press Enter to complete the “zoom”.

You should now be zoomed into a region on 22q12.3 covering approximately 35kb (Figure 2a).

C. Add LD Plot

You can add an LD plot to an existing graph from any spreadsheet that contains column marker mapped genotype data. In this case you want to generate an LD plot from the same genotype spreadsheet used to produce the association test results.

• From the -log10 P + LD plot, select the User Graphs node in the Graph Control Interface.

Under the Add Graph tab, you’ll notice that the same spreadsheet used to create the initial p-value plot is selected by default with corresponding options of graphs you can add based on the spreadsheet selected. You want to change this spreadsheet to HapMap Phenotype + 500K Genotypes.

• Click the drop down arrow and choose Select Spreadsheet... Select the HapMap Phenotype + 500K Genotypes spreadsheet and click OK.
• Select Linkage Disequilibrium and click Add.

Figure 2b. P-value and LD plot.

An LD plot will now appear under the p-value plot and an LD node (HapMap Phenotype + 500K Genotypes) will appear in the Graph Control Interface along with its associated Haplotype Block Set graph item (Figure 2b).

Notice the apparent block of LD (red) in the middle of the plot interrupted by a single SNP that is uncorrelated (blue) with the other markers.