The Trait page

Now you are familiar with the data structure in the GWAS Catalog, we are going to look at one of the most popular GWAS Catalog queries: “Which variants have been associated with my trait?”

To view all the GWAS Catalog data for a particular trait, simply search for the trait in the main search bar. A drop down menu will auto-suggest terms (and synonyms) from the Catalog. The terms used in the Catalog are from the Experimental Factor Ontology (EFO), to make it easier to search and compare between studies – so for example, when you search for “diabetes” you also return “type 1 diabetes”,”type 2 diabetes” and other related traits.

In the frame below (Figure 12), try searching for “high blood pressure”. As you start to type, you will see the autosuggestion “blood pressure, high – synonym for hypertension”. Click on the autosuggestion to search, and then click through from the search result to view the dedicated page for that trait.

Figure 12 This frame is an interactive subset of https://www.ebi.ac.uk/gwas/search page.

Navigating the Trait page

At the top of the Trait page, the Information Table contains the definition of the trait, links out to find more information on the topic, and lists of synonyms and mapped terms in other ontologies. Click on the “Highlighted Study” box to see the study with the largest sample size to date.

Trait representation in the GWAS Catalog

Some important items in the information table are Reported traits, Child traits, and Background traits.

As well as mapping each GWAS to one or more terms from EFO, the GWAS Catalog also includes a more detailed trait description: the Reported trait. This is designed to capture the full detail of the trait studied (e.g. if all samples have a particular clinical background, such as smoking) and experimental design of the particular GWAS (e.g. interaction studies). You can view all the Reported traits associated with the EFO term by clicking the “+” button next to the number of reported traits.

The Child traits list includes any traits that are more specific child terms of the parent trait in the EFO hierarchy. For example, asthma has 6 child terms, glucose measurement has 11 (Figure 13a), and in the example above, hypertension has more than 60.

Background traits are shared by all participants in a study but are not directly tested in the GWAS (Figure 13b). By default, studies like this are not included in the search results. For example, consider a case-control study of allergic rhinitis in a population of individuals with asthma: searching for “asthma” would not include this type of study. However, if you are interested in these types of studies as well as direct associations with asthma, you can check the box “Include background traits data”.