No, you do not have to be partnered with an academic institution to apply, however, individuals may not apply.
Any private-sector research organization, including nonprofit and for-profit organizations; any public-sector research organizations, universities, colleges, hospitals, laboratories, and healthcare systems; and units of state, local, and federal governments, may submit an application to PCORI. All U.S. applicant organizations must be recognized by the Internal Revenue Service. Foreign organizations and nondomestic components of organizations based in the U.S. may also apply; their application should clearly demonstrate the benefits of their research to the U.S. healthcare system and U.S. patient-centered research.
For more information, please see our What and Who We Fund page.