• Incidence of grade ≥3 regimen related toxicity . [ Time Frame: at day 100 ] [ Designated as safety issue: Yes ]
• Incidence of secondary graft failure at 100 days. [ Time Frame: 100 days ] [ Designated as safety issue: No ]
• Incidence of acute graft-versus-host disease (GVHD) [ Time Frame: at 100 days. ] [ Designated as safety issue: No ]
• Incidence of chronic GVHD . [ Time Frame: at one year ] [ Designated as safety issue: No ]
• Probability of survival . [ Time Frame: at one year ] [ Designated as safety issue: No ]
• Incidence of infections . [ Time Frame: at 100 days, 6 months and one year ] [ Designated as safety issue: No ]
• Immune reconstitution . [ Time Frame: at 100 days, 6 month and one year ] [ Designated as safety issue: No ]

• Incidence of grade ≥3 regimen related toxicity at day 100.
• Incidence of secondary graft failure at 100 days.
• Incidence of acute graft-versus-host disease (GVHD) at 100 days.
• Incidence of chronic GVHD at one year.
• Probability of survival at one year.
• Incidence of infections at 100 days, 6 months and one year.
• Immune reconstitution at 100 days, 6 month and one year.

This is a single arm, total body irradiation (TBI) trial. All patients will be prescribed TBI 300 cGy with the goal of evaluating secondary endpoints.

Study Treatment: 1. If the subject is to receive total body irradiation with thymic shielding, it will be given six days before the stem cells are given (day -6). 2. Day -5 through Day -2, subjects will receive a chemotherapy regimen of Fludarabine, Cyclophosphamide, anti-thymocyte globulin (ATG), and Methylprednisone (a steroid used to help make sure the transplant "takes") via central line (i.e. Hickman or Broviac). On days -5 to -1, subjects will receive ATG and Methylprednisone. The methylprednisone will continue until about three weeks after transplant.3. Starting Day -3, subjects will be given cyclosporin A (CSA) therapy to help prevent graft-versus-host-disease. We will continue to give CSA until about six months after the transplant. 4. If the subject is receiving bone marrow or "peripheral" stem cells (cells collected from the donor's arm via a cell separator), on the day of transplantation, the stem cells taken from the donor will be put into a machine which will separate the lymphocytes (the cells that cause graft-versus-host disease [GVHD]) from the stem cells. If the subject is receiving an umbilical cord blood, the lymphocytes will not be removed because the risk of GVHD is not as high. Otherwise all patients will receive the same treatment. The stem cells are given as an infusion into the subject's existing catheter over 1-2 hours on day 0.5. On the day after transplant (day +1) subjects will be given G-CSF to stimulate the growth of the transplanted cells. 6. While receiving treatment and until the subject's blood counts recover he/she will have daily blood tests, and several bone marrow biopsies and aspirates. After recovery, subjects will be seen once a month for a health assessment and blood tests until at least 3 months after the cells have been infused. Additional blood tests or assessments may be done as medically indicated.

• Drug: Cyclophosphamide
• Drug: Fludarabine
• Drug: anti-thymocyte globulin (ATG)
• Procedure: Total Body Irradiation
• Procedure: Bone Marrow Transplantation

Inclusion Criteria:

• Standard risk patients must be <18 years of age with a diagnosis of Fanconi anemia (FA)with aplastic anemia (AA), myelodysplastic syndrome without excess blasts, or high risk genotype as defined below:

  • Aplastic anemia is defined as having at least one of the following when not receiving growth factors or transfusions:
• platelet count <20 x 10^9/L
• absolute neutrophil count (ANC) <5 x 10^8/L

• hemoglobin (Hgb) <8 g/dL

  • Myelodysplastic syndrome with multilineage dysplasia with or without chromosomal anomalies
  • High risk genotype (e.g. IVS-4 or exon 14 FANCC mutations, or BRCA1 or 2 mutations)

• High risk FA patients must have at least one of the following:

  • History at any time of systemic fungal or gram negative infection
  • Severe renal disease with a creatinine clearance <40 mL/min
  • Recipient age > or = 18 years
  • Advanced myelodysplastic syndrome (MDS) (i.e., RAEB or RAEBt) or acute leukemia
• Patients must have a ≤1 antigen mismatched HLA-A, B, DRB1 unrelated donor or ≤1 antigen mismatched related (non-HLA-matched sibling) or ≤2 antigen mismatched unrelated UCB donor.
• Adequate major organ function including: cardiac - ejection fraction >45%, hepatic - bilirubin, AST/ALT, ALP <5x normal, Karnofsky performance status >70% or Lansky >50%
• Women of child-bearing age must be using adequate birth control and have a negative pregnancy test.

Exclusion Criteria:

• Available HLA-genotypically identical related donor.
• Refractory anemia with excess blasts, or leukemia.
• Active CNS leukemia at time of hematopoietic stem cell transplant(HSCT).
• History of squamous cell carcinoma of the head/neck/cervix within 2 years of HSCT.
• Pregnant or lactating female.
• Prior radiation therapy that prevents further total body irradiation (TBI).