Requesting a User-defined Endpoint to be included in Core Analysis

If your user-defined endpoint provides interesting new results not seen in the core GWAS analyses, you may wish to have it become part of the core GWAS analysis with each data freeze (to note: all core analysis results can be viewed on PheWeb and include useful cross-linking to other FinnGen and external results).

Conditions that must be met before an endpoint can become a core endpoint

• it must be available in userresults.finngen.fi. This is done by running the Custom GWAS tool either from the GUI or using Custom GWAS command line CLI.

• it should have < 90% case overlap with existing core endpoints. Tip! For a fast and easy check of the overlap percentage use the Cohort Operations tool.

• it should provide novel genetic results

• it should be definable within the grammar used to specify FinnGen Endpoints

Guidelines for endpoint creation:

• Endpoint should be created/modified by the user using Atlas tool in Sandbox or by another appropriate method

• The newly created/modified endpoint should be run by user using Custom GWAS tool in Sandbox or another appropriate method

• The newly created/modified endpoint request and link to Custom GWAS results need to be submitted via online form to Endpoint team. In cases where the online form is not sufficient you can also contact the Endpoint team by sending email to: [e-mail].