The question frames the concept of "autonomy" as an issue of "rights". From this perspective (which seems to be quite prevalent in the secular world), a patient's "autonomy" is associated with his/her freedom to choose a course of action based on their own personal wishes, independent of external influence or authority. This viewpoint may be expressed in a patient's assertion that, "It's my body, and I am free to do as I wish with it".

From a Jewish perspective however, an individual is not viewed as an owner, but rather as a steward of his/her body, which has been entrusted to him/her by G-d, the creator and owner of all lives. Thus, a Jewish conception of patient autonomy means that rather than asserting, "I am free to choose as I please with my own body," he/she will always ask the question, "What are my Divine responsibilities in order to be a proper steward over this body that is entrusted to me by G-d?" 

Of course, the answer to this question is found in the Divine values and instructions given by G-d in the Torah, and further elaborated upon by the Rabbis. Clear examples of these responsibilities include the prohibition of committing suicide and of wantonly defacing or harming one's body, along with the affirmative injunction that it is incumbent upon us to preserve and nurture one's good health.  

Nevertheless, a complicated medical issue may make it difficult for a patient to determine the proper choice that is required by their Divine responsibility of stewardship over the body.