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I advise my customers (I am an eTMF/eISF vendor) to file such records only once, and to attribute them to as many studies as are relevant to the record. The studies are not de-identified and may be visible as record metadata in addition to being within the readable record content. In this way, the same exact record is never duplicated within the customers’ eTMF.
I have heard from a few customers some concern that if the TMF for Study A includes a reference to Study B, then there is a risk that an inspector may then expand scope of their inspection to Study B. While I can understand that perspective, I also assume that if the inspector does decide to expand the scope, there must be a good reason for it…and it is better for all parties (including patients) that such problems be identified early rather than late.