Association Browser

Learn more about the feature that enables you to view results from genome- or phenome-wide association studies.

NOTE: Not all features are included in all packages. Please contact sales@dnanexus.com for more information.

Overview

Using the Association Browser, you can view results from genome- or phenome-wide association studies as well as associations at the gene level. More specifically, you can do all of the following:

  • Interactively browse through results by Phenotype, Variant location (or RSID), or gene.

  • Explore a visual representation (Manhattan Plot and PheWAS Plot) of GWAS or PheWAS results along with the corresponding table-view of results.

  • Interact with the plots by selecting a region and zooming in.

  • Select a genomic locus of interest on a GWAS plot to toggle to the corresponding PheWAS plot for that locus and vice versa.

  • Navigate to a gene of interest in the GWAS Manhattan plot Identify significant and/or interesting results by sorting or filtering tables by p-value.

Accessing the Association Browser

You can access the Association Browser either throw a direct URL provided by your administrator or via the Data Manager.

To access the Association Browser via the Data Manager

  1. Navigate to the Data Manager, locate the dataset of interest, and select Explore Data.

2. The Welcome screen appears. Either enter a variant or gene in the search box or click select a phenotype... to choose a phenotype.

The Welcome screen

Viewing GWAS Results in the Association Browser

GWAS results are presented in a Manhattan plot showing the top 30,000 loci most associated with the selected phenotype across the entire genome.

To view GWAS results in the Association Browser

  1. Click select a phenotype.. to open the Phenotype Selector.

  2. Locate a phenotype by either browsing the tree of study results or using one in the search box. Note: you can also enter a term in the search box to search across all studies (folders) for a match.

Phenotype Selector: Browse or search for a phenotype of interest.

3. Click Select in the right hand side of the window to view the GWAS results.

Manhattan Plot displaying top associations for selected phenotype

View Associations by P-value

Below the chart is a table view of the associations, sorted by most significant p-value. Use the column headers to sort by value or to search for a specific value range.

Zooming In

After you access a Manhattan Plot, you can zoom in on selected areas.

To zoom in

  1. Use the search box on the right side of the Manhattan plot to zoom in on a specific gene or genomic range of up to 5 million bases.

Zoomed in view: Use the search box to narrow in on a specific gene or genomic range

Viewing PheWAS Results in the Association Browser

PheWAS results are presented in an Association Chart and Table that you can use to view each phenotype associated with the variant across all studies.

To view PheWAS results

  1. Use the center search box to view PheWAS results for a specific variant. Enter either an RSID or a variant ID in the format: 1_55064980_A_G.

PheWAS Search: Search by gene, RSID, or variant ID

2. Press Enter. The Associations Chart and Table shows a point for each phenotype associated with the variant across all studies.

Sample PheWAS chart
  • The y-axis is the the -log10(p-value) for the p-value of the association as provided by the input study data.

  • The x-axis spacing is set such that phenotypes from the same category are grouped together, but otherwise has no scientific meaning.

  • The color of the points corresponds to the category listed along the x-axis.

3. Hover over a point on the chart to see association details.

View Associations by P-value

Below the chart is a table view of the associations, sorted by most significant p-value. Use the column headers to sort by value or to search for a specific value range.

In the table, you can select any phenotype link to navigate to its GWAS view.

Viewing Top Associations by Gene

You can view associations for variants in a given gene, sorted by highest p-value.

To view top associations by gene

  1. Use the center search box to search on a gene name.

Gene search: enter a gene name

2. Use the column headers to sort by value or to search for a specific value range.

Gene Associations: table sorted by highest p-value.