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So per ICH GCP, patient data collected via an EDC system is part of the TMF. However, there is no requirement to manage all TMF components in a single system, especially when the primary system might not be suitable for managing data sets.
You should therefore manage the data sets in a system where they can be retrieved easily for business purposes (trial conduct) but also for potential inspection. This is still part of your TMF but may not be your primary eTMF. Most sponsors do not manage these data sets in their primary eTMF, which are usually best suited to documents.
There are no regulations that would prevent you storing EDC data sets in an eTMF (since they are part of the TMF) but you need to be sure there is appropriate roles / permissions and security model to restrict access appropriately. Actually, this would apply to any TMF content…. the security model should restrict access only to those with appropriate authorization.