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The chemotherapy or irradiation given immediately prior to a transplant is called the conditioning or preparative regimen, the purpose of which is to help eradicate the patient's disease prior to the infusion of HSC and to suppress immune reactions.
The bone marrow can be ablated with dose-levels that cause minimal injury to other tissues.
In allogeneic transplants a combination of cyclophosphamide with busulfan or total body irradiation is commonly employed.
This treatment also has an immunosuppressive effect that prevents rejection of the HSC by the recipient's immune system.
The post-transplant prognosis often includes acute and chronic graft-versus-host disease that may be life-threatening.
However in certain leukemias this can coincide with protection against cancer relapse owing to the graft versus tumor effect.
Autologous transplants may also use similar conditioning regimens, but many other chemotherapy combinations can be used depending on the type of disease.

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