During a pharma acquisition, what would be the reasons for keeping the acquired company its own entity? (I.e BMS-Juno, Gilead-Kite, Roche-Genentech, AZ-Alexion)

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In rare disease (like Alexion) you’d want to keep the brand name also because patients/families are reallly really a focus in rare disease (patients help in all stages of development and research processes and join company meetings to talk about their experience on drugs). And they would never thing a big org like AZ truly cared about them or their family members, just bc how large that team is vs Alexion

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Brand recognition? Maybe it also has legal issues with patents and licensing

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Also big pharma is notorious for processes and bureaucracy that slow things down. You'll often hear about companies staying separate to keep that biotech nimbleness with big pharma $$

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Can vouch

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Brand recognition and trying to maintain the existing culture/team identity/employees

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Maybe if you want to preserve the entire pipeline and think the existing team is the right one to progress it.

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