Define a simple ICD control cohort in Atlas

This example shows how to build a simple "all who are not cases" control cohort using the Finnish-specific H81 ICD10fi codes.

Step 1: Clone the case cohort

• Click the Cohort Definitions on the left menu and open your case cohort (e.g. Test_Cohort_Cases_MN):

• Clone the cohort by clicking the copy button

• The name of the cloned cohort is "COPY OF ...". Rename the cohort as the controls cohort (e.g. Test_Cohort_Controls_MN)

• Save the cohort by clicking the save button

Step 2: Change the Inclusion Criteria

• Open the Inclusion Criteria by clicking its name (e.g. TestPhenotypeCases). This will open the inclusion criteria specified for the cases cohort.

• Rename the Inclusion Criteria (e.g. TestPhenotypeControls).

• Change the Inclusion Criteria from "at least 1” to "with exactly 0” and leave all other settings unchanged:

• Save the cohort by clicking the save button

Step 3: Generate the control cohort

• Open the Generation tab and generate the cohort by clicking the Generate button next to the same FinnGen data release you used to create the case cohort (FinnGen CDM R11 in the screenshot below). The cohort generation will take a few minutes and the speed is not dependent on the size of the sandbox IVM.

The control cohort is now ready. This cohort can (and should) be explored within Atlas and used in Cohort Operations and Trajectory Visualization tool. The cohort may also be exported from Atlas for further analyses like those described in the General Workflows for the most common analyses.