An antigen was a substance or molecule that elicited an immune response. Antigens were frequently peptides or carbohydrates derived either from the host ("self-antigens" or "autoantigens") or from pathogens such as bacteria or viruses. Antigens were presented on the surface of cell by specialized protein complexes in a manner that elicited either an antibody response or a cytotoxic effector cell response.
Doctor Julian Bashir administered an antigen to several Teplan patients in late 2372, hoping it would help cure the Teplan blight. Although it was later determined injecting patients with antigens would not cure them of the Dominion-created disease, the antigen was able to allow the children of the Teplans to be immune, as the antigen was absorbed by the placenta, and could prevent them from developing the blight. (DS9: "The Quickening")
In 2373, The Doctor created a synthetic antigen to treat the macrovirus outbreak on USS Voyager. Although the original plan was to release the antigen via the ship's environmental systems, when the Tak Tak attacked Voyager to prevent the spread of the virus, causing damage to the ship's power systems, Captain Janeway had to improvise, creating a holodeck simulation to lure the virus into one place. With the virus contained in one area, Janeway threw an antigen bomb into the holodeck, destroying the virus. (VOY: "Macrocosm")
In 2377, The Doctor injected Administrator Chellick of the Dinaali Hospital Ship 4-2 with chromovirus, as well as antigens from Tebbis, a low-TC patient who had died from that disease. This caused the Allocator to read Chellick as Tebbis and deny him cytoglobin, forcing him to change his policies regarding medical allocation. (VOY: "Critical Care")