Refractory anemia with excess blasts (RAEB-1) Refractory anemia with excess blasts (RAEB-2) Patients with refractory anemia with excess blasts (RAEB)-2 who have not received myelosuppressive chemotherapy i.e. induction chemotherapy Men or women ?18 years who are candidates to receive IV decitabine, ie, subjects with MDS previously treated or untreated with de novo or secondary MDS, including all French-American-British subtypes (refractory anemia, refractory anemia with ringed sideroblasts, refractory anemia with excess blasts, refractory anemia with excess blasts in transformation, and chronic myelomonocytic leukemia [CMML]), and subjects with MDS International Prognostic Scoring System (IPSS) int-1, -2, or high-risk MDS. RAEB-2 per WHO MDS criteria (10% to <20% BM blasts) Myelodysplasia (MDS) International Prognostic Scoring System (IPSS) intermediate (Int)-2 or high risk (i.e., refractory anemia with excess blasts [RAEB], RAEB in transformation [RAEBt]) or refractory anemia with severe pancytopenia or high risk cytogenetics; blasts must be < 10% by a representative bone marrow aspirate morphology Subjects with a histologically confirmed diagnosis of MDS, including both MDS and refractory anemia with excess blasts in transformation (RAEB-T) (acute myeloid leukemia [AML] with 20-30% blasts and multilineage dysplasia by French-American-British [FAB] criteria) by World Health Organization (WHO), and chronic myelomonocytic leukemia (CMML) are eligible Patients with refractory anemia with excess blasts (RAEB) who have not received myelosuppressive chemotherapy i.e. induction chemotherapy and will receive conditioning Regimen C (fludarabine and total body irradiation [TBI]) will be excluded; patients with RAEB who have not received myelosuppressive chemotherapy but who will receive conditioning Regimen A or B are eligible for this study as long as other inclusion and exclusion criteria are met Subjects with a histologically confirmed diagnosis of MDS, including both MDS and refractory anemia with excess blasts (RAEB)-T (acute myeloid leukemia [AML] with 20-30% blasts and multilineage dysplasia by French-American-British [FAB] criteria) by World Health Organization (WHO) and chronic myelomonocytic leukemia (CMML) are eligible Myelodysplastic syndrome: any subtype including refractory anemia (RA) if severe pancytopenia or complex cytogenetics; blasts must be less than 5%. If 5% or more requires chemotherapy for cytoreduction to =< 5% prior to transplantation Myelodysplastic syndrome: International Prognostic Scoring System (IPSS) interleukin-2 (INT-2) or high risk; revised (R)-IPSS high or very high; World Health Organization (WHO) classification: refractory anemia with excess blasts (RAEB)-1, RAEB-2; severe cytopenias: absolute neutrophil count (ANC) < 0.8, anemia or thrombocytopenia requiring transfusion; poor or very poor risk cytogenetics based on IPSS or R-IPSS definitions; therapy-related MDS; blasts must be < 5% by bone marrow aspirate morphology; if >= 5% blasts, patient requires chemotherapy for cytoreduction to < 5% blasts prior to transplantation Patients treated on this study will have:\r\n* Acute myeloid leukemia in morphologic complete remission (CR) not requiring treatment for their disease for 4 weeks\r\n* A history of acute myeloid leukemia (AML) with < 10% residual blasts (use highest count on staging studies) after induction therapy and persisting with < 10% blasts for at least 8 weeks without reinduction and at the time of HSCT\r\n* Refractory anemia (RA) or refractory anemia with ring sideroblasts (RARS) or isolated 5q- \r\n* Refractory anemia with excess blasts (RAEB)-1, refractory cytopenia with multilineage dysplasia (RCMD)+/-ringed sideroblasts (RS), or myelodysplastic syndrome (MDS) not otherwise specified (NOS) with stable disease for at least 3 months\r\n* RAEB-2 must demonstrate chemo-responsiveness; chemo-responsiveness is defined as a persistent blast percentage decrease by at least 5 percentage points to therapy and there must be =< 10% blasts (use highest count on staging studies) after treatment and at the time of transplant\r\n* Hodgkin or Indolent non-Hodgkin’s lymphoma \r\n* Myeloma with < 5% plasma cells in the marrow\r\n* Myeloproliferative disorders (excludes chronic myelomonocytic leukemia [CMML])\r\n* Aplastic anemia\r\n* A hematological or oncological disease (not listed) in which allogeneic HSCT is thought to be beneficial, and the disease is chemoresponsive \r\n* Patients without clear manifestation of their disease status in terms of stage and/or responsiveness should be discussed with the principal investigator (PI) and enrollment analysis should be documented in the study records Myelodysplastic syndrome\r\n* Refractory anemia with excess blasts (RAEB) I or II\r\n* High-risk International Prognostic Scoring System (IPSS)\r\n* Secondary myelodysplastic syndrome (MDS) MDS classified as follows: refractory anemia with excess blasts (RAEB)-1 (5%-9% bone marrow [BM] blasts); RAEB-2 (10%-19% BM blasts); chronic myelomonocytic leukemia (CMML) (5%-19% BM blasts); refractory anemia with excess blasts in transformation (RAEB-t) (20%-29% BM blasts) AND/OR by International Prognostic Scoring System (IPSS): intermediate-1 and high risk patients PHASE I\r\n* Primary or secondary AML according to World Health Organization (WHO) classification, with relapsed or refractory disease or newly diagnosed older subjects (greater than or equal to 65 years of age), not candidates for intensive chemotherapy\r\n* Subjects with myelodysplastic syndrome (MDS), International Prognostic Scoring System (IPSS) intermediate (Int)-2 or high risk (refractory anemia with excess blasts [RAEB]-2 only, i.e. greater than or equal to 10% blast) who are resistant or intolerant to standard treatment and are not candidates for transplantation \r\n* Subjects with acute lymphoblastic leukemia (ALL), relapsed, refractory or intolerant to standard treatment and for whom no effective treatment options are available Myelodysplastic syndrome (MDS): refractory anemia (RA)/refractory cytopenia with multilineage dysplasia (RCMD) with high risk cytogenetic features or transfusion dependence, refractory anemia with excess blasts (RAEB)-1 and RAEB-2 and acute myelogenous leukemia (AML) evolved from MDS, who are not eligible for transplantation under protocol institutional review board (IRB) 08-008 Myelodysplastic syndrome (MDS): Refractory anemia (RA)/refractory anemia with ring sideroblasts (RARS)/refractory cytopenia with multilineage dysplasia (RCMD) with high risk cytogenetic features or transfusion dependence, as well as refractory anemia with excess blasts (RAEB)-1 and RAEB-2 and acute myelogenous leukemia (AML) evolved from MDS who are not eligible for transplantation under protocol institutional review board (IRB) 08-008 Patients must have untreated AML, or high-risk myelodysplastic syndromes (MDS) (refractory anemia with excess blasts, [RAEB], or RAEB \in transformation\ [RAEB-t]) characterized by t(8;21), inv(16), or t(16;16); the presence of additional abnormalities is irrelevant Myelodysplastic syndrome (MDS): Any 2001 World Health Organization (WHO) classification subtype; refractory anemia with excess blasts (RAEB)-2 patients may proceed directly to transplant, but may also be considered for induction chemotherapy before transplant; patients with >= 20% morphologic marrow blasts require induction therapy to reduce morphologic marrow blasts below 5% before transplant MDS International Prognostic Scoring System (IPSS) intermediate (Int)-2 or high risk (i.e. refractory anemia with excess blasts [RAEB], RAEB in transformation [RAEBt]) or refractory anemia with severe pancytopenia or high risk cytogenetics; blasts must be < 10% by a representative bone marrow aspirate morphology Refractory anemia with excess blasts, or leukemia Myelodysplasia (MDS) International Prostate Symptom Score (IPSS) Int-2 or High risk (i.e. refractory anemia with excess blasts [RAEB], refractory anemia with excess blasts in transformation [RAEBt]) or refractory anemia with severe pancytopenia or high risk cytogenetics; blasts must be < 10% by a representative bone marrow aspirate morphology Myelodysplastic syndrome: any subtype including refractory anemia (RA) if severe pancytopenia or complex cytogenetics; blasts must be less than 5%; if 5% or more requires induction therapy pre-transplant to reduce blast count to =< 5% Myelodysplasia (MDS) IPSS intermediate (INT)-2 or high risk (i.e. refractory anemia with excess blasts [RAEB], refractory anemia with excess blasts in transformation [RAEBt]) or refractory anemia with severe pancytopenia, transfusion dependence, or high risk cytogenetics or molecular features; blasts must be < 10% by a representative bone marrow aspirate morphology Patients with any of the following diagnoses are eligible: 1) high-risk MDS (i.e. refractory anemia with excess blasts [RAEB-1 or RAEB-2] by World Health Organization [WHO] classification, or any WHO subset with International Prognostic Scoring System [IPSS] intermediate-2 or high, or any patients that has failed prior therapy with hypomethylating agents); 2) chronic myelomonocytic leukemia (CMML); 3) acute myeloid leukemia (AML) by WHO classification; 4) chronic myeloid leukemia in blast phase (CML-BP); patients with myelofibrosis are also eligible Must have a pathologically confirmed diagnosis by World Health Organization (WHO) criteria of MDS, CMML, or acute myeloid leukemia (AML) (except acute promyelocytic leukemia) with < 30% bone marrow blasts (refractory anemia with excess blasts in transformation [RAEB-t] by French American British criteria) Myelodysplastic syndrome\r\n* Refractory anemia with excess blasts (RAEB)\r\n* RAEB-in transformation (T) (requires marrow and blood blasts < 10% after induction chemotherapy) MDS: MDS classifiable by the World Health Organization (WHO) system as RA, RARS, refractory cytopenia with multilineage dysplasia (RCMD), RCMD and ringed sideroblasts (RCMD-RS) or RAEB For a diagnosis of high-risk Myelodysplastic Syndrome RAEB 2 the patient must have 10-19% bone marrow blasts Refractory anemia with excess blasts (RAEB) - defined as having 5% to 20% myeloblasts in the bone marrow. Relapsed and/or primary refractory Acute Myeloid Leukemia (AML) or Myelodysplastic Syndrome (MDS) with subtype refractory anemia with excess blasts (RAEB)-2 defined as high or very high-risk that is recurrent or refractory, or the patient is intolerant to established therapy. Adults with pathologically confirmed acute myelogenous leukemia, in pathologically confirmed complete remission; patients with refractory anemia with excess blasts-2 (RAEB-2), who are in remission following therapy, can also be eligible Subjects with a histologically confirmed diagnosis of MDS by French American British (FAB) criteria, including both MDS and refractory anemia with excess blasts in transformation (RAEB-T) (AML with 20-30% blasts and multilineage dysplasia) and chronic myelomonocytic leukemia (CMML) with at least 10% bone marrow blasts by World Health Organization (WHO) classification are eligible Myelodysplasia (MDS) International Prognostic Scoring System (IPSS) intermediate (Int)-2 or high risk (i.e., refractory anemia with excess blasts [RAEB], refractory anemia with excess blasts in transformation [RAEBt]) or refractory anemia with severe pancytopenia or high risk cytogenetics; blasts must be < 10% by a representative bone marrow aspirate morphology MDS classified as follows: refractory anemia with excess blasts (RAEB)-1 (5%-9% bone marrow [BM] blasts); RAEB-2 (10%-19% BM blasts); chronic myelomonocytic leukemia (CMML) (5%-19% BM blasts); refractory anemia with excess blasts in transformation (RAEB-t) (20%-29% BM blasts) AND/OR by International Prognostic Scoring System (IPSS): intermediate-2 and high risk patients Myelodysplastic syndrome criteria:\r\n* Diagnosis of MDS classifiable by the World Health Organization (WHO) system as:\r\n** Refractory anemia\r\n** Refractory cytopenia with multilineage dysplasia \r\n** MDS-unclassified\r\n** Refractory cytopenias with multilineage dysplasia and ringed sideroblasts, refractory anemia with excess blasts-1\r\n** Refractory anemia with excess blasts-2\r\n** Chronic myelomonocytic leukemia (CMML)\r\n** MDS transformed to acute leukemia High risk MDS (refractory anemia with excess blasts [RAEB]-1, RAEB-2, treatment related MDS) not responsive to 2 lines of therapy (including hypomethylating agent and induction chemotherapy) Myelodysplastic syndrome refractory anemia with excess blasts (RAEB) 1 or 2; cytogenetics showing complex karyotype (3 or more abnormalities), monosomy 7/del(7q), or inv(3)/t(3q)/del(3q); or transfusion dependent Patients with refractory anemia with excess blasts (RAEB) who have not received myelosuppressive chemotherapy i.e. induction chemotherapy Patients with advanced AML or ALL defined as beyond first remission, primary refractory disease, or evolved from myelodysplastic or myeloproliferative syndromes; or patients with MDS expressed as refractory anemia with excess blasts (RAEB), refractory cytopenia with multilineage dysplasia (RCMD), RCMD with ringed sideroblasts (RCMD-RS), or chronic myelomonocytic leukemia (CMML) Myelodysplastic syndrome\r\n* Refractory anemia with excess blasts (RAEB) I or II\r\n* High-risk International Prognostic Scoring System (IPSS)\r\n* Secondary MDS Myelodysplastic syndrome (MDS): refractory anemia (RA)/refractory cytopenia with multilineage dysplasia (RCMD) with high risk cytogenetic features or transfusion dependence, refractory anemia with excess blasts (RAEB)-1 and RAEB-2 and AML evolved from MDS, who are not eligible for a higher priority protocol Pathologically confirmed diagnosis of myelodysplastic syndrome (including secondary MDS, refractory anemia with excess blasts in transformation [RAEB-T], and chronic myelomonocytic leukemia [CMML, if white blood cells count is < 13,000/mm^3]) as defined by World Health Organization or French-American-British classifications Myelodysplastic syndrome: any subtype including refractory anemia (RA) if severe pancytopenia or complex cytogenetics; blasts must be less than 5%; if 5% or more requires induction therapy pre-transplant to reduce blast count to =< 5% Myelodysplasia with any of the following features: \r\n* Refractory anemia with excess blasts type I (5-10% blasts) or II (11-20% blasts) in the bone marrow (RAEB I and II)\r\n* Refractory cytopenia with multilineage dysplasia (RCMD) and poor risk cytogenetics (i.e., chromosome 7 abnormalities or complex karyotype with at least 3 abnormalities per clone) Myelodysplastic syndrome: IPSS INT-2 or high risk; R-IPSS high or very high; World Health Organization (WHO) classification: RAEB-1, RAEB-2; severe cytopenias: absolute neutrophil count (ANC)0000 < 0.8, anemia or thrombocytopenia requiring transfusion; poor or very poor risk cytogenetics based on IPSS or R-IPSS definitions; therapy-related MDS; blasts must be < 5% by bone marrow aspirate morphology; if >= 5% blasts, patient requires chemotherapy for cytoreduction to < 5% blasts prior to transplantation Documented diagnosis of myelodysplastic syndrome (MDS), MDS/myeloproliferative neoplasm (MPN), chronic myelomonocytic leukemia (CMML) by World Health Organization (WHO) criteria or AML with 20-30% myeloblasts (refractory anemia with excess blasts in transformation [RAEB-T] by French-American-British [FAB)] criteria)