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Once a suitable donor has been identified, stem cells are harvested (collected) from either the bone marrow or from the bloodstream and the cells are frozen for later use. The patient (transplant recipient) then begins and completes a cycle of high-dose chemotherapy to destroy the remaining leukemic cells. Patients are also given antirejection drugs such as tacrolimus or cyclosporine (sometimes in combination with prednisone or methotrexate) in order to reduce the likelihood that the patient will reject the donor's transplanted stem cells. The donor's frozen stem cells are then thawed and infused into the recipient via an intravenous line.

Although success rates of allogeneic SCT after initial chemotherapy for chronic myelogenous leukemia vary among different transplant centers, data from the International Bone Marrow Transplant Registry www.ibmtr.org indicates that about 60% of patients in the early chronic phase of chronic myelogenous leukemia who received transplants from a related (sibling) donor were alive and disease-free at 5-years post-transplantation. Unfortunately, the success rate of allogeneic SCT is not as favorable for accelerated phase chronic myelogenous leukemia and blastic phase chronic myelogenous leukemia as compared to the chronic phase of the disease.

In the United States, many transplant centers recommend that allogeneic SCT should be performed in the early chronic phase of chronic myelogenous leukemia within 12-months of diagnosis. The most successful results are achieved in patients 40 years or younger who are transplanted in the early chronic phase within one-year of diagnosis.

Unfortunately, allogeneic SCT is still a procedure that is associated with significant potential complications the most serious of which is graft-versus-host-disease (GVHD). As mentioned previously, in an allogeneic transplant, the source of the stem cells used for transplantation is another individual who serves as the donor. Graft-versus-host disease (GVHD) occurs when the donor's transplanted cells (the graft) begins to attack the recipient's (the host's) own tissues and organs. It should be noted that GVHD can occur with an allogeneic transplant even in cases where the donor and recipient's HLA markers are a "perfect match". This is because currently the degree of compatibility (match) between the donor and recipient is determined on the basis of evaluating similarities of tissue types for six major HLA markers. However, there are other markers (antigens) present on the donor's transplanted cells which may differ slightly from those of the recipient's own cells that can lead to the development of GVHD.

Graft-versus-host disease that develops within the first 3 months following allogeneic SCT is called acute GVHD; if it develops 3 or more months after allogeneic SCT it is called chronic GVHD.

Symptoms of acute GVHD include:

• An itchy, red rash on the hands and feet
• Nausea, diarrhea, and severe stomach cramps
• Jaundice (due to liver damage)

The chronic form of GVHD can be very severe and disabling and, in some cases, may even be fatal. Patients who develop GVHD are treated with various combinations of immunosuppressive drugs such as cyclosporine, methotrexate, and corticosteroids.