I'm new to FinnGen, where is the best place for me to start?

How to get started

For a start, see what kind of data is available in FinnGen for you to plan your FinnGen Analysis. FinnGen has health registry data combined with imputed genotype data. The registry and genotype data are available in a secure Sandbox and are also used to make FinnGen endpoints for FinnGen core analyses for several conditions.

Browse using Risteys

You can browse FinnGen Endpoints using Risteys and we recommend reading the section using Risteys as an Endpoint browser. This can be done without applying for any special permissions. (Note that you can write ICD10 codes directly into the Risteys search bar to see which Endpoints they are contained in)

Browse using PheWeb

From Risteys you can click directly to the ready-made association analyses at the FinnGen PheWeb to see if the condition you are interested in is already included in FinnGen core analyses. If you have not looked at Manhattan plots and association data we recommend the section on how to use PheWeb. We also recommend reading the GWAS Analysis section. (In the "Background Concepts" you will find suggestions for background reading on other genetic concepts as well.)

How to access FinnGen results and data

• You can see FinnGen aggregate level results older than one year publicly online.

• The most recent aggregate data (GWAS results and other results computed from at least 5 individuals) can be viewed by applying for "green level" data. This can also be downloaded from our green library once you have access.

• Individual-level data is only accessible within the secure Sandbox environment. To work with this data you must apply for red-level data access, a process that can take 1-4 months on average. The cost of the Sandbox is defined per Sandbox and by use.

What to do if the condition is not available

If the condition you are interested in is not in the FinnGen endpoints and red-level access, you can build your case-control cohorts in Sandbox by following the custom endpoint creation instructions. Atlas conducts searches on detailed longitudinal data including these registers. Note that before beginning such an analysis, you should submit a FinnGen Analysis Proposal and check that there are no overlapping analyses that already exist.

Your FinnGen Analysis proposal has been approved

Once your FinnGen Analysis Proposal has been approved, see instructions on how to define a cohort in Atlas and subsections about filtering criteria and code types options. Selecting cases and controls is an important step. See guidelines on how to select controls for your cases. You can also modify existing endpoints (not available for all endpoints). After case-control cohorts are made custom GWAS can be run using the custom GWAS tool or from the command line using finngen-cli tool.