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Four of the Institute's Core Facilities were established in 2008 with funding from a Wellcome Trust Strategic Award. The purpose of the facilities is to improve and accelerate access to:

- key vaccine components, eg. adjuvants and vectors 
- core technical expertise and equipment 
- new vaccine candidates to be tested in small scale clinical trials

The Core Facilities consist of the following units:

Bioprocess and Analytical Development (BiPAD)

Flowcytometry Facility

QiaSymphony Automated Nucleic Acid Extraction Facility (QANE)

Viral Vector Core Facility

The Facilities are extensively used by Jenner Investigators, Group Leaders, staff and students throughout the vaccine research and development process. Some commissions are also undertaken for external academic and industry collaborators.

Clinical Biomanufacturing Facility (CBF)

Uniquely for an academic setting, the Jenner Institute is able to manufacture own vaccines for Phase I and II clinical trials according to EU GMP via the MHRA authorised Clinical BioManufacturing Facility (CBF). The CBF is located adjacent to the Centre Clinical Vaccinology and Tropical Medicine on the Churchill Hospital site in Oxford, where the Institute's Phase I trials take place. In addition to manufacturing, the CBF also undertakes QP Certification and labelling of Investigational Medicinal Products (IMPs, manufactured either by the CBF or third parties) for clinical trials.

The CBF also supports the Jenner Investigators by facilitating the importation of IMPs from outside the EU.