According to FDA, you can start with sequence number 0000 or you can use any other sequence number. Your software should allow you to change the sequence number from the default to any number, so I recommend that you continue with the sequence numbering you’ve been using in your paper submissions. From experience, I can tell you that this will avoid the logistical complications that crop up when you restart the sequence numbering at 0000 for your first eCTD submission.
UPDATE: Thanks to Missy Fussell of Allegro Solutions for updated information regarding sequence numbering. The post has been updated to incorporate the information she provided.
Please find more information by clicking the following weblink:
THE eCTD SUMMIT: Transitioning from Paper to eCTD - Updated Information
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