The lead economics expert in the Federal Trade Commission’s antitrust suit against Facebook has parted ways with the agency, two individuals familiar with the case said — adding yet another impediment to the regulator’s largest court fight.

The FTC is now looking for a new expert, just three weeks before the agency must decide whether to file the new version of the Facebook lawsuit after a D.C.-based judge threw it out last month.

The expert, University of California-Berkeley economist...

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