KIR Favorable Mismatched Haplo Transplant and KIR Polymorphism in ALL/AML/MDS Allo-HCT Children

Inclusion Criteria: 2.3.1 Inclusion Criteria for the Biology (KIR2DL1 Polymorphisms/ALL MRD), Comparative Outcomes, and Cost Effectiveness Trial 1. Any patient with ALL, AML, or MDS who is deemed eligible for and undergoes HCT at participating centers who provides consent for the KIR2DL1 polymorphisms, comparative outcomes and cost-effectiveness portion of the trial. 2. Any ALL patient undergoing allogeneic HCT at participating centers is eligible for the ALL deep sequence MRD portion of the trial. 3. Patients ineligible for the KIR-favorable haploidentical phase II trial who require T-cell depletion may be treated using TCR αβ+CD3+/CD19+ cell depletion. These patients will be followed descriptively on this portion of the trial. Preparative regimen will be at the discretion of the transplant center, but the options associated with this protocol are recommended. 2.3.2 Inclusion Criteria for the KIR-favorable Haploidentical Phase II trial: 1. Age \< 22 years 2. Disease and disease status: * ALL high-risk in first remission (\<5% blasts by morphology pre-transplant) meeting criteria for transplant. Example CR1 indications: induction failure (\>5% blasts by morphology on post-induction BM), minimal residual disease greater than or equal to 1% marrow blasts by morphology after induction, minimal residual disease by flow cytometry \>0.01% after consolidation, hypodiploidy (\<44 chromosomes), persistent or recurrent cytogenetic or molecular evidence of disease during therapy requiring additional therapy after induction to achieve remission (e.g. persistent molecular BCR-ABL positivity). * ALL in second remission: B-cell; early (less than or equal to 36 months from initiation of therapy) BM relapse, late BM relapse with MRD \>0.1% by flow cytometry after first induction therapy; T-cell or Ph+ with BM relapse at any time; very early (less than 18 months from initiation of therapy) isolated extramedullary relapse (T or B-cell) * Myelodysplastic syndrome (MDS): Any 2001 WHO classification subtype (Appendix I). RAEB-2 patients may proceed directly to transplant, but may also receive induction chemotherapy before transplant. Patients with ≥20% morphologic marrow blasts will require induction therapy to reduce morphologic marrow blasts below 5% before transplant. * High-risk AML defined as monosomy 5, del 5q, monosomy 7, M6, M7, t(6;9), FLT3-ITD, or patients who have greater than or equal to 25% blasts by morphology after induction, or who do not achieve CR after 2 courses of therapy. Also, patients with ≥ 0.1% MRD or evidence of progressive extramedullary disease after induction chemotherapy. * AML in second or subsequent morphologic remission. 3. Has not received a prior allogeneic hematopoietic stem cell transplant. 4. Does not have a suitable HLA-matched sibling donor available for stem cell donation. 5. Does not have a suitable matched or single antigen mismatched related or unrelated donor available at any time (noted by search), or it is in the patient's best interest as judged by the attending to move forward with stem cell transplantation rather than wait for an unrelated donor to become available (refer to subsection 2.5.1 for further details). 6. Has a suitable HLA KIR favorable haploidentical matched family member available for stem cell donation. 7. Karnofsky Index or Lansky Play-Performance Scale ≥ 60 % on pre-transplant evaluation. Karnofsky scores must be used for patients \> 16 years of age and Lansky scores for patients \< 16 years of age. 8. Able to give informed consent if \> 18 years, or with a legal guardian capable of giving informed consent if \< 18 years. 9. Adequate organ function (within 4 weeks of initiation of preparative regimen), defined as: * Pulmonary: FEV1, FVC, and corrected DLCO must all be ≥ 50% of predicted by pulmonary function tests (PFTs). For children who are unable to perform for PFTs due to age, the criteria are: no evidence of dyspnea at rest and no need for supplemental oxygen. * Renal: Creatinine clearance or radioisotope GFR ³ 70 mL/min/1.73 m2 or a serum creatinine based on age/gender as follows: Age Maximum Serum Creatinine (mg/dL) Male Female 1 to \< 2 years 0.6 0.6 2 to \< 6 years 0.8 0.8 6 to \< 10 years 1 1 10 to \< 13 years 1.2 1.2 13 to \< 16 years 1.5 1.4 ≥ 16 years 1.7 1.4 The threshold creatinine values in this Table were derived from the Schwartz formula for estimating GFR utilizing child length and stature data published by the CDC.45 * Cardiac: Shortening fraction of ≥ 27% by echocardiogram or radionuclide scan (MUGA) or ejection fraction of ≥ 50% by echocardiogram or radionuclide scan (MUGA), choice of test according to local standard of care. * Hepatic: \\SGOT (AST) or SGPT (ALT) \< 5 x upper limit of normal (ULN) for age. Conjugated bilirubin \< 2.5 mg/dL, unless attributable to Gilbert's Syndrome. Exclusion Criteria: 1. Pregnant or lactating females are ineligible as many of the medications used in this protocol could be harmful to unborn children and infants. 2. Patients with HIV or uncontrolled fungal, bacterial or viral infections are excluded. Patients with history of fungal disease during induction therapy may proceed if they have a significant response to antifungal therapy with no or minimal evidence of disease remaining by CT evaluation. 3. Patients with active CNS leukemia or any other active site of extramedullary disease at the time of enrollment are not permitted. Note: Those with prior history of CNS or extramedullary disease, but with no active disease at the time of pre-transplant workup, are eligible. 4. Patients with genetic disorders (generally marrow failure syndromes) prone to secondary AML/ALL with known poor outcome are not eligible (Fanconi Anemia, Kostmann Syndrome, Dyskeratosis Congenita, etc).