Study of Stem Cell Transplant for Leukemia and Myelodysplastic Syndromes Using Clofarabine and Busulfan Regimen

Inclusion Criteria: Disease Criteria: * Acute myelogenous leukemia (AML) * Acute lymphocytic leukemia (ALL) * Myelodysplastic syndromes (MDS) Refractory anemia (RA) with adverse cytogenetics (SWOG criteria) or beyond (RAEB, RAEB-T, AML) * Other Myeloproliferative Disorders Myelofibrosis, Agnogenic Myeloid Metaplasia, Chronic Myelomonocytic Leukemia (CMML) * Chronic lymphocytic leukemia (CLL) High risk or advanced disease Other Inclusion Criteria: * 18 years of age or older * Related or unrelated donor with HLA criteria as follows: * Related donors: a serologic equivalent HLA Class I (A, B, and C) and Class II DRB1 or DQB1 matched donor OR a donor who is a single 1 antigen mismatched for A, B, C, DRB1, or DQB1 loci * Unrelated donors: sequence-based typing fully matched A, B, C, DRB1, and DQB1 allele-matched donor OR a donor who is no greater than 1 antigen mismatched for A, B, C, DRB1, or DQB1 loci * Able to provide valid informed consent. * Female patients must have a negative serum pregnancy test within 2 weeks prior to enrollment. * Male and female patients must use an effective contraceptive method during the study and for up to 12 months after study treatment. Exclusion Criteria: Organ Function Criteria: * Cardiac: symptomatic coronary artery disease or ejection fraction \<45% or uncontrolled cardiac failure * Pulmonary: FEV1 or DLCO (corrected) \<50% of predicted values and/or receiving continuous supplementary oxygen * Hepatic: Bilirubin ≥ 1.2 mg/dL or AST/ALT ≥ 3x upper limit of normal (ULN) unless the liver is involved with malignant disease * Renal: creatinine clearance \< 60 mL/min (24-hour urine collection) or \<50 mL/min (Glofil test) * Karnofsky score \<60% * Active CNS disease * Prior hematopoietic transplantation (autologous or allogeneic) \<6 months prior to study entry * Use of investigational agents less than or equal to 30 days before study entry. * Life threatening, or clinically significant infection * Any significant concurrent disease, illness, or psychiatric disorder that would compromise patient safety or compliance, interfere with consent, study participation, follow up, or interpretation of study results. * Female patients who are pregnant or breast feeding * HIV-positive