Pilot Trial of Clofarabine Added to Standard Busulfan and Fludarabine for Conditioning Prior to Allogeneic Hematopoietic Cell Transplantation

Inclusion Criteria: * Patients must be ≥ 3 months and ≤30 years of age. * Stratum A: Non-Malignant Diseases, including: * Bone Marrow Failure Syndromes * Hemoglobinopathies or transfusion-dependent red blood cell (RBC) defects * Congenital Immunodeficiencies * Metabolic Diseases known to be treatable with Hematopoietic cell transplantation (HCT) (e.g. Hurler's) * Other Bone Marrow Stem Cell Defects (e.g. Osteopetrosis) * Severe Immune Dysregulation / Autoimmune Syndromes with at least transient prior response to immunosuppressive therapy * Stratum B: Myeloid Malignancies, including: * acute myeloid leukemia (AML), in greater than first clinical remission, or in CR1 but with detectable disease (≥0.1% Blasts by minimal residual disease (MRD) or Flow, or Positive Cytogenetics), or in CR1 but with a matched sibling Umbilical cord blood (UCB) donor. * Myelodysplastic syndromes (MDS) * Juvenile myelomonocytic leukemia (JMML) * Chronic myeloid leukemia (CML), with detectable disease by polymerase chain reaction (PCR) * Patients must have a suitable donor based on the University of California, San Francisco (UCSF) Pediatric Bone Marrow Transplant (BMT) standard operating procedures (SOP). 10/10 (HLA-A, -B, -C, -DR, -DQ) matching will be done for related and adult unrelated donors; 8/8 (HLA-A, -B, -C, -DR) for umbilical cord blood donors. Patients with non-malignant diseases will generally be eligible only if they have a mismatched donor, or an accepted clinical reason to be considered high-risk for rejection. * Liver transaminases (aspartate aminotransferase (AST)/alanine aminotransferase (ALT)) and Direct Bilirubin less than twice the upper limit of normal within 2 weeks of admission. * Cardiac Shortening Fraction ≥27% within 4 weeks of admission. * Creatinine clearance by Schwartz formula, glomerular filtration rate (GFR) or 24 hr urine collection ≥50 cc/min/1.73 m2, within 4 weeks of admission. * Pulmonary diffusion capacity ≥50% of predicted corrected for anemia/lung volume within 4 weeks of admission. If unable to do Pulmonary function testing(PFTs), then no active lung disease by chest x-ray (CXR) and/or oxygen (O2) Saturation ≥90% on room air. Exclusion Criteria: * Fanconi Anemia * Dyskeratosis Congenita * A known syndrome with increased sensitivity to radiation or alkylating agents * Severe Combined Immunodeficiency Disease eligible for a non-myeloablative HCT Trial * A mismatched donor for whom ex vivo T-cell depletion of the donor stem cells is planned