Pilots

Gene-by-environment (GxE) interaction studies

We are investigating how to improve the ontology representation of gene-by-environment interaction studies in the GWAS Catalog.

We want to make it clearer when an EFO term refers to a human phenotype and when it refers to an environmental exposure.

Examples of exposures include drugs, allergens, toxins, social factors and physiological measurements. These exposures may interact with genetic variants to influence a phenotype.

We propose adding a field for exposure terms while leaving the phenotype in the existing EFO traits field.

We have prepared a GxE interaction studies reannotation proposal using Catalog data up to November 2024.

The spreadsheet shows existing annotations for 882 studies and proposed reannotations, with separate EFO terms for the phenotype (efo-phenotype-term) and exposure (efo-exposure-term).

It also includes available degrees-of-freedom annotations and comments where applicable.