Should I include primary care registry (PRIM_OUT) codes in my cohort definitions?

ICD-codes from PRIM_OUT registry may sometimes be usefull, but be cautious when using them

When creating your own endpoint (or cohort), using for example Atlas, you may consider whether to add codes, for example ICD-codes, from the primary care registry (PRIM_OUT) to your endpoint. PRIM_OUT ICD-codes may sometimes be helpful, and add cases to your endpoint. However, they may be less usefull than you think because they may be manifesting less severe disease than the ICD-codes given in the hospital (codes in the inpatient registry) or they may not be as accurate as those given by the specialist (codes in the specialist outpatient registry).

Codes assigned by physician or nurse

ICD-codes are safe in the sense that they are always assigned by a physician, but it is worth keeping in mind that ICPC2 (diagnosis codes) and SPAT (operation codes) from the PRIM_OUT registry can be assigned by a nurse. This is why we recommend you to consider whether to use ICPC2/SPAT codes in your endpoints. Physicians can decide whether they prefer to use ICD or ICPC2 codes, and this preference may also change regionally in Finland.

Some FinnGen endpoints include ICD-codes from PRIM_OUT registry

Most FinnGen endpoints do not include PRIM_OUT codes, but after consideration of the endpoint team, PRIM_OUT ICD-codes have been added to some FinnGen endpoint definitions (suffix _INCLAVO in the endpoint name). Upset Plots are usefull tool for reviewing what registry codes from which registries each FinnGen endpoint consist. You can find Upset Plot for each FinnGen endpoints from the Risteys browser (upper right corner of the Risteys page). By looking at the upset plot, you can see whether PRIM_OUT codes have been used for that specific endpoint and how many cases it has added to the endpoint; and if PRIM_OUT codes have not been used, you can also see how many cases using of these codes would add to the endpoint.

Take a look also related sections: Detailed longitudinal data, Atlas, and Health code sets.