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In the paralance of medical research, a guinea pig is a research subject, particularly a human one. Strangely enough, real guinea pigs are rarely used in medical research.
Cuddy is often afraid that House is treating his patients as experimental subjects. There is some truth in this, and there have been several episodes where House has used an untested and revolutionary technique on a patient.
Even Foreman is not above being treated as an experimental subject. In Euphoria (Part 2), House exposed the very ill Foreman to Legionnaires' Disease in the hope, which turned out to be correct, that it would slow down the progress of his condition.