Can I use FinnGen endpoints like medical codes in Atlas?
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In the DataFreeze 7 Atlas CDM database we loaded a selected/partial set of FinnGen priority endpoints as observations and we plan to continue this in future releases. This process enables you to use them in the definition of Concept Sets. For example, you might wish to include everyone in a FinnGen endpoint plus additional ones from primary care (AvoHilmo) or that had a particular procedure.
To note, If you follow the procedure below and the endpoint you are interested in is not in the current release then you can recreate a FinnGen endpoint in Atlas using this method: replicate FinnGen endpoint
The first event that puts an individual in an endpoint exists in the Atlas CDM as an observation event (these are therefore visible in Atlas at FinnGen Sandbox). The observation event has the date at which the defining event occurred and the name of the endpoint.
To create a cohort using FinnGen endpoints:
select Atlas configuration to at least DF7 (at the time of writing this it is the most recent, but we plan to include this functionality in later data freezes as well).
Next, we need to create a new Concept set to hold the endpoint(s) of interest (Figure below). Go to the search page in Atlas (1. in fig below) and type in your search word (for example asthma, 2. in fig below). From the Vocabulary menu on the left, select ENDPOINT(3. in fig below). In our example, there are 33 endpoints found for the search word asthma. from which the top four have records. Select the endpoints you want to include by clicking a shopping cart icon (4. in fig below). The number of record counts and descendant record counts for each code are shown in RC and DRC columns.
3. Now continue to cohort building. Note that endpoints will act as non-standard codes in cohort building and must be searched as an observation event.
For Data Freeze 6 data the endpoints in Atlas are only for partial data. Some of the patients belonging to the endpoint may not be included to the analysis. Therefore, we do not recommend to use endpoints within Atlas for DF6. However, you can replicate FinnGen endpoint in Atlas.
