araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 1-year-old male with acute myeloid leukemia; genetic feature: IDH1

Clinical trial: Biomarkers in Samples From Patients With Down Syndrome and Acute Megakaryoblastic Leukemia

Summary: RATIONALE: Studying samples of blood or tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer.
  PURPOSE: This research study is studying biomarkers in samples from patients with Down syndrome and acute megakaryoblastic leukemia.

Detailed description: OBJECTIVES:
  -  Determine whether megakaryocyte differentiation agents comprising a Rho kinase inhibitor and a JAK3 inhibitor can lead to proliferation arrest, polyploidization, and terminal differentiation of blasts in specimens from patients with Down syndrome and acute megakaryoblastic leukemia.
  OUTLINE: Cryopreserved specimens are cultured and treated in vivo (in mice) and in vitro with megakaryocytic differentiation agents comprising a Rho kinase inhibitor and a JAK3 inhibitor.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of acute megakaryoblastic leukemia
  -  Diagnosis of Down syndrome
  -  Cryopreserved specimens available
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 1-year-old male with acute myeloid leukemia; genetic feature: IDH1

Clinical trial: Biomarkers in DNA Samples From Younger Patients With Newly Diagnosed Acute Myeloid Leukemia Receiving Gemtuzumab Ozogamicin

Summary: RATIONALE: Studying samples of DNA from patients receiving gemtuzumab ozogamicin may help doctors learn more about the effects of gemtuzumab ozogamicin on cells. It may also help doctors understand how well patients respond to treatment.
  PURPOSE: This research study is studying biomarkers in DNA samples from younger patients with newly diagnosed with acute myeloid leukemia receiving gemtuzumab ozogamicin.

Detailed description: OBJECTIVES:
  -  To analyze candidate-coding polymorphisms in CD33 of DNA samples from children with newly diagnosed acute myeloid leukemia treated with gemtuzumab ozogamicin on COG-AAML03P1.
  -  To determine the association between these polymorphisms and clinical response of patients treated with this regimen.
  OUTLINE: Archived DNA samples are analyzed for candidate polymorphisms in CD33 by PCR-based sequencing.

Eligibility: DISEASE CHARACTERISTICS:
  -  Newly diagnosed acute myeloid leukemia
  -  Treated with gemtuzumab ozogamicin on COG-AAML03P1
  -  Genomic DNA samples available
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 1-year-old male with acute myeloid leukemia; genetic feature: IDH1

Clinical trial: Blood and Tumor Tissue Samples From Young Patients With Acute Myeloid Leukemia

Summary: RATIONALE: Studying samples of blood and tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer.
  PURPOSE: This research study is studying blood and tumor tissue samples from young patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  -  To evaluate Mer and Axl expression in samples from pediatric patients with acute myeloid leukemia (AML).
  -  To determine if abnormal expression of Mer and Axl is associated with poor clinical characteristics (e.g., induction failure or relapse) of AML in these patients.
  OUTLINE: This is a multicenter study.
  Archived samples from pediatric patients with acute myeloid leukemia are analyzed for Mer and Axl expression by flow cytometry and western blot assays.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of acute myeloid leukemia
  -  Children Oncology Group (COG) patient samples
  PATIENT CHARACTERISTICS:
  -  Available clinical data
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 1-year-old male with acute myeloid leukemia; genetic feature: IDH1

Clinical trial: Biomarker Changes in Samples From Young Patients With Acute Myeloid Leukemia

Summary: RATIONALE: Studying samples of blood or tumor tissue from patients with cancer in the laboratory may help doctors learn about changes that occur in DNA and identify biomarkers related to cancer.
  PURPOSE: This research study is studying biomarker changes in samples from young patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  -  Map key histone modifications and cytosine methylation in leukemia cell lines with defined oncogenic mutations.
  -  Acquire genome-wide maps of key histone modifications and cytosine methylation for primary leukemia in samples from patients with acute myeloid leukemia (AML).
  -  Investigate functional relationships between genetic and epigenetic landscapes in AML.
  OUTLINE: Archived samples are analyzed in vivo and in vitro (cell line) for histone modification and cytosine methylation. Genome-wide locations of 5 histone modifications are analyzed using chip-Seq, as well as DNA methylation analysis at nucleotide-resolution by high-throughput bisulfite sequencing. These epigenetic data are correlated with genomic data (sequence analysis, expression array, SNP array).

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of acute myeloid leukemia
  -  Primary leukemia samples from the Children Oncology Group (COG) bank with sufficient number of cells (500,000-1 million cells) with > 80% of leukemia blasts
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 1-year-old male with acute myeloid leukemia; genetic feature: IDH1

Clinical trial: Development of a Diagnostic Kit for FLT3-ITD in Acute Myeloid Leukemia

Summary: FLT3 overexpression in acute myeloid leukemia (AML) is often caused by mutations in this gene. These mutations cause constitutive phosphorylation of FLT3 proteins leading to increased proliferation and survival, decreased apoptosis and resistance to chemotherapeutic agents in AML cells. There are two major types of FLT3 mutations- internal tandem duplication (ITD) and point mutation at 835th amino residue. AMLs with FLT3 mutations have worse prognosis and are often resistant to conventional chemotherapy. Several small molecule compounds targeting FLT3 have been in the market or in clinical trials. Therefore, identification of these mutations at the time of diagnosis will provide a better prognostic prediction, might guide the treatment selection and follow-up strategies. In this study, the investigators will develop a sensitive molecular assay to detect FLT3 mutations for future clinical application. The investigators will collect 100 AML samples with at least 20 samples with known FLT3 mutations. The investigators will compare this assay with commonly used methods and standardize the procedure to meet the requirement of clinical pathology laboratory with reasonable cost.


Eligibility: Inclusion Criteria:
  -  Patients with confirmed diagnosis of acute myeloid leukemia
  Exclusion Criteria:
  -  non

Relevance to patient case: not relevant
Patient case: 1-year-old male with acute myeloid leukemia; genetic feature: IDH1

Clinical trial: Identification of de Novo Fanconi Anemia in Younger Patients With Newly Diagnosed Acute Myeloid Leukemia

Summary: This research study is studying identification of de novo Fanconi anemia in younger patients with newly diagnosed acute myeloid leukemia. Studying samples of tissue from patients with cancer in the laboratory may help doctors identify and learn more about biomarkers related to Fanconi anemia in patients with acute myeloid leukemia.

Detailed description: PRIMARY OBJECTIVES:
  I. Identify children with newly diagnosed acute myeloid leukemia (AML) treated on COG-2961 and COG-AAML03P1 who are at high risk of having de novo Fanconi anemia.
  II. Procure diagnostic samples from the COG AML Biology Repository and identify Fanconi anemia patients using western blot techniques.
  OUTLINE:
  Previously collected cryopreserved cells are analyzed via western blot to identify patients with Fanconi anemia.

Eligibility: Inclusion Criteria:
  -  Treated on COG-2961 or COG-AAML03P1
  -  At high risk of having Fanconi anemia, defined as meeting one the following groups of clinical criteria:
  -  Group 1: Prolonged neutropenia after induction, severe regimen-related toxicity (mucositis, veno-occlusive disease, end-organ damage)
  -  Group 2: Early non-relapse death (induction, consolidation)
  -  Group 3: Small-for-weight, secondary malignancies

Relevance to patient case: not relevant
Patient case: 1-year-old male with acute myeloid leukemia; genetic feature: IDH1

Clinical trial: Drug Biomarkers in Cell Samples From Patients With Acute Myeloid Leukemia

Summary: RATIONALE: Studying cell samples from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer
  PURPOSE: This research study is studying drug biomarkers in cell samples from patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  -  To determine, in vitro, the cytotoxic activity of novel CD33-targeting immunoconjugate agents in cell samples from patients with acute myeloid leukemia (AML).
  -  To define the characteristics of AML cells responding to or resisting these agents.
  OUTLINE: Cell samples are thawed and used for in vitro studies to determine the cytotoxic activity of novel CD33-targeting immunoconjugate agents, including gemtuzumab ozogamicin, for genotyping characterization by flow cytometry-based assays and/or western blot, and colony-forming cell assays.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of acute myeloid leukemia
  -  Cryopreserved samples available
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 1-year-old male with acute myeloid leukemia; genetic feature: IDH1

Clinical trial: Obatoclax Mesylate in Samples From Young Patients With Acute Myeloid Leukemia

Summary: RATIONALE: Studying the effects of obatoclax mesylate in cell samples from patients with cancer in the laboratory may help doctors learn more about the effects of obatoclax mesylate on cancer cells. It may also help doctors identify biomarkers related to cancer.
  PURPOSE: This research study is studying obatoclax mesylate in samples from young patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  -  Determine comprehensive gene and protein expression profiles of in vitro sensitivity and resistance to obatoclax mesylate in multiple-lineage leukemia (MLL)-rearranged cell lines and primary infant acute myeloid leukemia (AML) samples.
  -  Define optimum in vitro combinations of obatoclax mesylate targeting pro-survival BCL-2 family proteins with cytotoxic drugs in MLL-rearranged leukemia cell lines and primary infant AML samples.
  -  Identify synergistic combinations based on a pharmacodynamic modeling and simulation construct.
  -  Determine whether combinations of obatoclax mesylate targeting pro-survival BCL-2 family proteins with cytotoxic drugs improves survival in a xenograft model of MLL-rearranged infant AML.
  OUTLINE: This is a multicenter study.
  Obatoclax mesylate activity is assessed via the MTT assay. A priori features of acute myeloid leukemia (AML) blasts relating to the apoptosis and ATG cell death pathways and their execution are characterized using microarray analysis and quantitative real-time (Q-RT) PCR. Gene and protein expression is described and quantified using Q-RT PCR and western blot analysis at specific time points after obatoclax mesylate exposure to identify pharmacodynamic biomarkers of activity and characterize the cell death mechanism in multiple-lineage leukemia (MLL)+ AML. The MTT assay is performed using obatoclax mesylate-cytotoxic chemotherapy combinations to determine synergy focusing on common cytotoxic drugs employed in AML treatment regimens.
  Obatoclax mesylate efficacy is tested in a therapeutic NOG xenograft model of primary MLL+ infant AML.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of acute myeloid leukemia (AML)
  -  Cryopreserved samples from infants with AML available
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 1-year-old male with acute myeloid leukemia; genetic feature: IDH1

Clinical trial: Lestaurtinib With or Without Chemotherapy Agents in Samples From Young Patients With Leukemia

Summary: This research study is studying lestaurtinib with or with chemotherapy in samples from young patients with leukemia. Studying the effects of lestaurtinib with or without chemotherapy in cell samples from patients with cancer in the laboratory may help doctors learn more about the effects of this treatment on cancer cells. It may also help doctors identify biomarkers related to cancer.

Detailed description: PRIMARY OBJECTIVES:
  I. Determine the potential of lestaurtinib with or without chemotherapy agents in treating samples from infants with leukemia.
  II. Determine whether FLT3 protein expression level and/or activation and sensitivity to lestaurtinib differ between subgroups of infants with leukemia.
  III. Determine whether lestaurtinib activates STAT5, AKT, and RAS-MAPK and other pathways.
  IV. Determine whether lestaurtinib can synergize with other chemotherapy agents kill infant leukemia cells.
  OUTLINE: This is a multicenter study.
  Cryopreserved specimens are studied in vitro with lestaurtinib with or without chemotherapy agents. Samples are analyzed for FLT3 protein expression and/or activation; sensitivity to lestaurtinib with or without chemotherapy agents; and activation of STAT, AKT, and RAS-MAPK and other pathways by western blot. The most effective treatment from this study is then validated in vivo in a NOD/SCID xenograft model.

Eligibility: Inclusion Criteria:
  -  Cryopreserved samples from infants with leukemia available

Relevance to patient case: not relevant
Patient case: 1-year-old male with acute myeloid leukemia; genetic feature: IDH1

Clinical trial: Phase II Study for Safety and Efficacy Evaluation of Imatinib Mesylate in Children With Chronic Myeloid Leukemia (CML) Philadelphia Chromosome-positive (Ph+)

Summary: The purpose of this study is to evaluate the hematological, cytogenetic and molecular response to continuous-use of Imatinib in children with CML Ph+.


Eligibility: Inclusion Criteria:
  1. Diagnose: suspected CML (hematology and/or myelogram and/or immunophenotyping and/or Leukocyte alkaline phosphatase [LAP]) to be confirmed, after, by cytogenetic and/or molecular biology. OBS: only CML Ph+ newly-diagnose in chronic or accelerate phase; resistant CML Ph+ to Interferon α (INF-α), Hydroxyurea and/or low-dose ARA-C in chronic or accelerate phase; CML Ph+ with cytogenetic relapse after BMT, that didn't use Imatinib previously, in chronic or accelerate phase.
  2. Female patients of childbearing age, should have pregnancy test (blood βhCG) performed before treatment initiation. Effective contraception must be used. Pregnant women won't be included.
  3. Karnofsky and Lansky scale: ≥40.
  4. Life expectation > 8 weeks.
  5. Laboratory: renal function (serum creatinine ≤ 1,5 x ULN and/or Clearance ≥70 ml/min/1,73m2), hepatic function (total bilirubin ≤ 1,5 x ULN, TGP < 3 x ULN and albumin > 2 g/dl.
  6. CNS toxicity ≤ II
  7. Cardiac function: normal ejection fraction.
  8. Signed ICF by child legal responsible.
  Exclusion Criteria:
  1. Patient receiving any other tyrosine kinase inhibitor (TKI).
  2. Pregnant patient or breastfeeding.
  3. Patient considered incapable to follow purposed treatment.
  4. Patients with molecular relapsed.
  5. Medications:
  -  Colony stimulating: it cannot be administered at least 1 week before treatment.
  -  Anticonvulsants: Imatinib is metabolized by P-450 enzyme, thereby subject cannot receive drug that activates the P-450 system. The anticonvulsants allowed are valproic acid and benzodiazepines.
  -  Anticoagulants: The use of warfarin (Marevan) is not allowed. If anticoagulant is needed, low-molecular-weight heparin (LMWH) can be used. Avoid anticoagulants with platelets < 50000.
  -  INF-Α 48h before D1.
  -  Hydroxyurea 24h before D1.
  -  ARA-C doses >100 mg/m2 for 5-7 days, 14 days before D1.
  -  Anthracyclines, Mitoxantrone or Etoposide 21 days before D1.
  -  Any other chemotherapeutic agent 28 days before D1.
  -  Hematopoietic Cell Transplantation (HCT) 6 weeks before D1.

Relevance to patient case: not relevant
Patient case: 1-year-old male with acute myeloid leukemia; genetic feature: IDH1

Clinical trial: Biomarkers in Tissue Samples From Young Patients With Acute Myeloid Leukemia

Summary: RATIONALE: Studying samples of tissue from patients with cancer the in laboratory may help doctors identify and learn more about biomarkers related to cancer.
  PURPOSE: This research study is studying biomarkers in tissue samples from young patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  -  To determine whether the pattern of global and TSG-specific promoter CpG island hypermethylation and gene silencing that we have shown characterizes MLL-rearranged (MLL-r) infant bilineage ALL is also characteristic of other subsets of MLL-r leukemia.
  OUTLINE: Previously collected cryopreserved cells from diagnosis are analyzed for promoter methylation via HELP arrays, gene expression arrays, and RT-qPCR.
  PROJECTED ACCRUAL: A total of 32 samples (8 from each of 4 biologically defined cohorts) will be analyzed.

Eligibility: DISEASE CHARACTERISTICS:
  -  Available cryopreserved cells from diagnosis
  -  At least 2 x 10^7 viably cryopreserved cells
  -  One of the following biologically defined cytogenetics/molecular cohorts:
  -  t(9;11)
  -  t(11;19)
  -  Other 11q23 translocations
  -  Normal cytogenetics
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 1-year-old male with acute myeloid leukemia; genetic feature: IDH1

Clinical trial: Biomarkers in Tissue Samples From Patients With Acute Promyelocytic Leukemia

Summary: RATIONALE: Studying samples fo tissue from patients with cancer in the laboratory may help doctors identify and learn more about biomarkers related to cancer.
  PURPOSE: This research study is studying biomarkers in tissue samples from patients with acute promyelocytic leukemia.

Detailed description: OBJECTIVES:
  -  Demonstrate that S100A10 is expressed on APL cells and that levels of S100A10 correspond to the amount of fibrinolytic activity.
  -  Evaluate the impact of ATRA on S100A10 level and fibrinolytic activity in vitro.
  -  Evaluate the impact of S100A10 knockdown on fibrinolytic activity.
  -  Correlate in vitro findings in cell culture to primary patient samples both pre- and post-ATRA therapy.
  OUTLINE: This is a multicenter study.
  Previously collected samples are analyzed via flow cytometry and western blot analysis. Cell surface levels of S100A10 and annexin A2 are correlated to the promyelocyte population and total protein levels are examined to determine total annexin A2 and S100A10 in acute promyelocytic leukemia cells.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of acute promyelocytic leukemia
  -  Available cryopreserved cells from diagnosis or cryopreserved cells from remission (germline)
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 1-year-old male with acute myeloid leukemia; genetic feature: IDH1

Clinical trial: Prognostic Biomarkers in Samples From Young Patients With Acute Myeloid Leukemia

Summary: RATIONALE: Studying samples of blood or tumor tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer. It may also help doctors predict how patients will respond to treatment.
  PURPOSE: This research study is studying prognostic biomarkers in cell samples from young patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  Primary
  -  To determine the percentage of primary acute myeloid leukemia (AML) samples with increased Stat3 signaling pathway activity.
  -  To evaluate the presence of constitutive Stat3 activation and the sensitivity of Stat3 activation to low- and high-doses of cytokines.
  -  To evaluate the expression levels of Stat3 protein and the upstream and downstream regulators of Stat3 activation.
  Secondary
  -  To classify samples according to a Stat3 activation pattern and correlate this result with event-free survival (EFS) and overall survival (OS).
  OUTLINE: Cryopreserved AML specimens are analyzed for pStat3 and pStat5 levels, response to cytokine levels, and expression level of proteins known to influence stat activity by flow cytometry and western blot assays. Results are also compared with prognostic variables determined in CCG-291 study, including age, race, WBC, and cytogenetic risks.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of acute myeloid leukemia (AML)
  -  Cryopreserved AML specimens
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 1-year-old male with acute myeloid leukemia; genetic feature: IDH1

Clinical trial: Biomarkers in Samples From Young Patients With Acute Myeloid Leukemia

Summary: RATIONALE: Studying bone marrow samples from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer.
  PURPOSE: This research study is studying biomarkers in samples from young patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  -  To compare the frequency of germline telomerase mutations in pediatric patients with acute myeloid leukemia (AML) demonstrating prolonged myelosuppression, defined as ≥ 1 episode > 35 days of neutrophil count recovery after chemotherapy, to the pediatric patients with the expected myelosuppression, defined as consistently < 35 days of neutrophil count recovery after chemotherapy.
  -  To assess association between telomerase mutations and incidence of grade 3 or 4 mucositis, relapse, and death.
  -  To compare germline (remission) telomere length in pediatric AML patients demonstrating delayed bone marrow recovery with the pediatric patients with consistently expected recovery.
  -  To assess whether a correlation between telomere length and incidence of grade 3 or 4 mucositis, relapse, and death exist.
  OUTLINE: This is a multicenter study.
  Cryopreserved bone marrow samples are analyzed for DNA sequencing and mutation by Sanger-based sequencing methods, quantitative PCR, and SeqMan Pro (Lasergene from DNAStar). Results are then compared with previously published data and existing databases to determine the allele frequency in control populations.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of acute myeloid leukemia
  -  Enrolled on CCG-2961 and meeting 1 of the following criteria:
  -  More than 35 days to recover to an ANC > 500/mm³ after any course of chemotherapy
  -  Consistently recovered < 35 days to an ANC > 500/mm³ after all courses of chemotherapy
  -  Available cryopreserved cell from diagnostic and end-of-therapy samples
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant