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

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

Summary: RATIONALE: Studying samples of bone marrow 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 laboratory study is studying bone marrow samples from patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  -  To rigorously examine fractionated hematopoietic stem and progenitor cells from patients with acute myeloid leukemia (AML).
  -  To define somatic mutations occurring in de novo AML, including the FLT3-ITD, CEBPA, NPM1, TET2, ASXL1, IDH1, and IDH2 mutations.
  -  To examine what cellular compartments (LT-HSC, ST-HSC, CMP, GMP, and MEP) contain the selected mutations and in what order those mutations occur.
  OUTLINE: Archived bone marrow specimens are analyzed for sequencing and detection of mutations by Sanger-based resequencing of PCR amplicons. Results are then compared with the results of age-matched healthy controls.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of acute myeloid leukemia
  -  Bone marrow samples must meet 1 of the following criteria:
  -  Normal karyotype from patients enrolled on ECOG-1900 archived at the ECOG Leukemia Tissue Bank
  -  Live, sortable mononuclear cells prepared at the time of initial diagnosis (slow-frozen in media with 10% DMSO OR fresh cells shipped immediately
  -  Age-matched healthy control samples from commercial providers
  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 of Bone Marrow From Patients With Acute Myeloid Leukemia

Summary: RATIONALE: Studying samples of bone marrow 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 looking at bone marrow samples from patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  -  To successfully transplant human acute myeloid leukemia (AML) cells into immunocompromised mice for the purpose of expansion of the cells.
  -  To harvest the cells and use chromatin immunoprecipitation (ChIP) methods to identify the locations of the protein complexes on the genome.
  -  To study the interactions of the Super Elongation Complex (SEC) and Dot1 Complex (DotCom) complexes in human leukemia samples.
  -  To compare the genomic targets of the complexes formed by MLL-ENL chimeras to non-MLL-rearranged leukemia samples to normal controls.
  OUTLINE: Cryopreserved cells are implanted into NOD SCID gamma mice, expanded, harvested, and studied by chromatin immunoprecipitation (ChIP) methods (using antibodies to ENL, Af9, and AF10). Results are then analyzed by PCR, DNA sequencing, and/or microarray analysis.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of acute myeloid leukemia (AML)
  -  Cryopreserved mixed-lineage leukemia (MLL) ENL AML rearrangement cells, normal karyotype and non-MLL rearrangement AML cells, and non-leukemic bone marrow samples from the COG tissue bank
  -  3 specimens of each type
  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: Pharmacokinetic, Safety and Efficacy of Intermittent Application of Caspofungin for Antifungal Prophylaxis

Summary: The study is a pilot phase II, prospective, non-comparative, single center trial aimed to evaluate pharmacokinetic and safety of an intermittent dosing schedule for antifungal prophylaxis in high risk patients.

Detailed description: Pharmacokinetic and safety of caspofungin, in an intermittent dosing schedule, for prophylaxis of invasive fungal (IFI) infections will be evaluated in patients receiving induction chemotherapy for treatment of acute myeloid leukemia, myelodysplastic syndrome with blast crisis or acute lymphatic leukemia.
  For prophylaxis caspofungin once daily will be given three times a week after a loading phase of three days. For drug monitoring serum samples will be collected from the first day of trial medication till one day after end of therapy (EOT). Invasive fungal infections will be diagnosed analog the criteria defined by the European organization for Research and Treatment of Cancer and the Mycosis Study Group (EORTC/MSG), revised in 2008.
  Caspofungin prophylaxis will be stopped after the end of neutropenia, in case of documented proven or probable invasive fungal disease and in case of a serious adverse event attributable to the study drug, for which in view of the investigator further usage of the study drug should be avoided.

Eligibility: Inclusion Criteria:
  -  acute myeloid leukemia or myelodysplastic syndrome and blast crisis or acute lymphatic leukemia
  -  receiving induction chemotherapy
  Exclusion Criteria:
  -  current or need of systemic antifungal therapy
  -  history of proven or probable invasive aspergillus infection
  -  pregnant or breastfeeding women
  -  weight more than 100 kg
  -  history of allergy, hypersensitivity or any serious reaction to caspofungin

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

Clinical trial: Biomarkers in Predicting Response to Treatment in Bone Marrow Samples From Young Patients With Acute Myeloid Leukemia

Summary: RATIONALE: Studying samples of bone marrow from patients with cancer in the laboratory may help doctors predict how well patients will respond to treatment.
  PURPOSE: This research trial is studying biomarkers in predicting response to treatment in bone marrow samples from young patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  Primary
  -  To validate the accuracy of a pre-specified acute myeloid leukemia (AML) induction response classifier or the My Profile™ AML Induction Therapy Assay (run in a Good Laboratory Practice [GLP] laboratory using Good Manufacturing Practice [GMP] reagents) in predicting response to cytarabine-based induction chemotherapy in pediatric patients with non-M3 AML.
  Secondary
  -  To validate the continuous score from the pre-specified induction response classifier as a predictor of response to induction chemotherapy, after controlling for the simultaneous effects of clinical variables at base-line and/or pre-induction therapy (e.g., age, WBC, and percentage [%] of blasts), and tests commonly available after the start of induction therapy (e.g., cytogenetics and molecular markers).
  -  To validate the accuracy of the pre-specified induction response classifier as a binary predictor of induction response using a pre-specified cutpoint to assign patients to no response (NR) or complete response (CR) groups.
  -  To validate the accuracy of the pre-specified induction response classifier as a binary predictor of induction response using a pre-specified cutpoint to assign patients to NR or CR groups, after controlling for the simultaneous effects of clinical variables at base-line (pre-induction therapy) (e.g., age, WBC, % blasts) and clinical variables, including tests commonly available after start of induction therapy (e.g., age, WBC, cytogenetics).
  OUTLINE: Cryopreserved bone marrow mononuclear cell specimens are analyzed by cell networking profiling assays. Results are then compared with patient outcomes and demographics from COG-AAML03P1 and COG-AAML0531 studies.
  Molecular markers analyzed include Flt3ITD, NPM1, CEBPA, and MRA.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of acute myeloid leukemia (AML)
  -  Non-M3 AML
  -  Cryopreserved bone marrow mononuclear cell specimens from patients enrolled on COG-AAML03P1 and COG-AAML0531 collected prior to cytarabine-based induction therapy
  -  Patient samples from COG-AAML0531 must come from the control arm (i.e., no gemtuzumab ozogamicin induction therapy)
  PATIENT CHARACTERISTICS:
  -  No Down syndrome
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: definitely relevant
Patient case: 1-year-old male with acute myeloid leukemia; genetic feature: IDH1

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

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

Detailed description: OBJECTIVES:
  Primary
  -  To determine if serum 2-hydroxyglutarate (2HG) is only detected in acute myeloid leukemia (AML) patients with isocitrate dehydrogenase (IDH) mutations.
  Secondary
  -  To determine if the level of serum 2HG impacts leukemia-free survival (LFS).
  -  To determine if the level of serum 2HG impacts overall survival (OS).
  -  To determine if serum 2HG is undetectable at the time of documented clinical remission (CR) in IDH-mutated patients.
  OUTLINE: Archived serum samples are analyzed for 2-hydroxyglutarate expression by reverse-phase liquid chromatography coupled to mass spectrometry. Results are then compared with presence or absence of an IDH mutation, patients' clinical outcome, as well as age, sex, white blood cell count at diagnosis, platelet count, bone marrow blast percentage at diagnosis, circulating (serum) percentage at diagnosis, cytogenetic risk group, presence of FLT3, NPMN1, and/or TET2 mutations, specific IDH mutation, and randomization treatment group allocation.

Eligibility: DISEASE CHARACTERISTICS:
  -  Morphologically confirmed acute myeloid leukemia (AML)
  -  Newly diagnosed with AML
  -  Serum samples from patients enrolled on the ECOG-1900 clinical trial between 2002 and 2008
  -  Patients with or without isocitrate dehydrogenase (IDH) mutations
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Received 2 different doses of standard induction chemotherapy on ECOG-1900

Relevance to patient case: definitely relevant
Patient case: 1-year-old male with acute myeloid leukemia; genetic feature: IDH1

Clinical trial: Study of Gemtuzumab Ozogamicin Therapy in DNA Samples From Patients With Acute Myeloid Leukemia Treated on COG-AAML0531

Summary: RATIONALE: DNA analysis of blood and tissue samples may help doctors predict how well patients will respond to treatment. It may also help doctors learn more about how gemtuzumab ozogamicin works in the body.
  PURPOSE: This research study is looking at gemtuzumab ozogamicin in DNA samples from patients with acute myeloid leukemia treated on COG-AAML0531.

Detailed description: OBJECTIVES:
  -  To genotype the genomic DNA from acute myeloid leukemia (AML) patients treated on COG-AAML0531 clinical trial for CD33 (and PgP and SOC3) single nucleotide polymorphisms (SNPs).
  OUTLINE: Archived DNA samples are analyzed for single nucleotide polymorphisms in CD33, PgP, and SOC3 genes by Sequenome platform. Results are then compared with patients clinical outcomes, including minimal-residual disease levels post induction I (chemotherapy and gemtuzumab ozogamicin), complete remission rates, refractory disease with various levels of bone marrow blasts, development of CNS/persistent disease, event-free survival, overall survival, and toxicity.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosed with acute myeloid leukemia
  -  DNA samples from patients treated on COG-AAML0531
  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: Study of Proteins in Promoting Chemotherapy Resistance in Samples From Patients With Acute Myeloid Leukemia

Summary: RATIONALE: Studying samples of tissue from patients with cancer in the laboratory may help doctors learn more about cancer and development of drug resistance in patients.
  PURPOSE: This research trial is studying proteins that may promote chemotherapy resistance in samples from patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  -  Investigate whether changes in prosurvival signaling occur by comparing activation of the signal transducer and activator of transcription-3 (Stat3) and Stat5 pathways in paired diagnostic and relapse samples.
  -  Investigate changes in leukemia cell responses to extrinsic cues from the environment change, using a bone marrow stromal-cell co-culture model of chemotherapy resistance.
  OUTLINE: Cryopreserved samples are analyzed for Stat3 and Stat5 expression by flow cytometry and in vitro chemotherapy sensitivity.

Eligibility: DISEASE CHARACTERISTICS:
  -  Paired diagnostic and relapsed cryopreserved samples from patients with acute myeloid leukemia
  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 Adult Patients With Acute Myeloid Leukemia Who Failed Existing Standard-of-Care Treatment

Summary: RATIONALE: Studying samples of bone marrow and blood from patients with cancer who failed treatment may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer resistance. It may also help doctors find better ways to treat cancer.
  PURPOSE: This research trial studies biomarkers in samples from adult patients with acute myeloid leukemia who failed standard-of-care treatment.

Detailed description: OBJECTIVES:
  -  Define a "non-response" signature that will help up-front identification of cases of intermediate-risk acute myeloid leukemia (AML) destined to fail existing standard-of-care therapy.
  -  Identify biological pathways in the "non-response" group that can provide targets for novel therapeutics.
  OUTLINE: DNA and RNA extracted from cryopreserved bone marrow cells and/or blood cells are analyzed for mutations and gene expression signatures (genome-wide methylation, mRNA and miRNA expression, and single nucleotide polymorphism (SNP) analysis) by microarray assays.

Eligibility: DISEASE CHARACTERISTICS:
  -  Samples from previously untreated non-M3 acute myeloid leukemia (AML)
  -  Normal karyotype (NK) intermediate-risk disease
  -  Two or more vials of cryopreserved pretreatment bone marrow cells and/or two or more vials of cryopreserved pretreatment blood cells available from the Intergroup AML Repository
  -  Blast count ≥ 60%
  -  Eligible and evaluable for the patient's clinical trial, and did not have fatal induction toxicity
  -  Response to protocol induction chemotherapy:
  -  Non-response: AML with failure to achieve a complete remission (CR) after induction chemotherapy ("7 & 3"-based therapy using cytatabine and/or daunorobicin hydrochloride (DNR) OR idarubicin and/or DNR
  -  Responders: continued complete remission (CCR) > 2 years
  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: Biomarker Study of Chemotherapy Resistance and Outcomes in Samples From Older Patients With Acute Myeloid Leukemia

Summary: RATIONALE: Studying blood 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 trial studies biomarkers related to chemotherapy resistance and outcomes in samples from older patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  -  Delineate the spectrum of genetic and epigenetic lesions occurring in elderly patients with acute myeloid leukemia (AML).
  -  Determine the biological functions perturbed by these lesions.
  -  Identify and validate lesions or pathways that are most highly associated with chemo-sensitive and chemo-refractory disease, and with adverse outcome in elderly AML.
  -  Identify potential classifiers and biomarker lesions that we can then evaluate prospectively in the E2906 trial which is about to begin enrollment.
  OUTLINE: DNA and RNA extracted from cell samples are analyzed for genetic and epigenetic expression by Agilent SureSelect sequencing, Illumina HiSeq2000 platform coding and sequencing, DNA methylation, and microarray assays. Results are then associated with patients' overall survival, progression-free survival, and complete response rate. Results are also analyzed assessing the prognostic relevance of known mutations and epigenetic alterations that have shown to have an impact on overall survival and response to therapy in younger patients with acute myeloid leukemia (AML) in E1900 including, but not limited to, FLT3, DNMT3A, IDH1, IDH2, TET2, ASXL1, WT1, and MLL, and 15-gene DNA methylation classifier, and with novel recurrent mutations identified by other AML-profiling efforts.

Eligibility: DISEASE CHARACTERISTICS:
  -  Subset of patients diagnosed with acute myeloid leukemia (AML) enrolled on E3999
  -  AML resistant or sensitive to chemotherapy
  -  Mononuclear cell 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: Study to Predict Risk of Relapse in Bone Marrow Cell Samples From Younger Patients With Acute Myeloid Leukemia

Summary: RATIONALE: A screening test, such as My Profile Pediatric Assay, may help doctors predict a patient's risk of relapse and plan better treatment for acute myeloid leukemia.
  PURPOSE: This clinical trial is studying using the My Profile Pediatric Assay to see how well it works in predicting risk of relapse in bone marrow cell samples from younger patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  Primary
  -  To validate the accuracy of the My Profile Pediatric Assay to predict risk of relapse in pediatric patients with non-M3 acute myeloid leukemia (AML) who responded to cytarabine-based induction chemotherapy.
  Secondary
  -  To validate the continuous score from the pre-specified classifier as a predictor of relapse after response to induction chemotherapy, while controlling for the simultaneous effects of the following clinical and laboratory variables: age, WBC, ethnicity, cytogenetics, Flt3-ITD, NPM1, MRD, and bone marrow (BM) donor availability.
  -  To validate the accuracy of the prespecified low versus high relapse indicator variable (I_L/H) as a predictor of relapse after induction therapy.
  -  To validate the accuracy of the prespecified I_L/H as a predictor of relapse after induction therapy, while controlling for the simultaneous effects of the following clinical and laboratory variables: MRD, age, WBC, ethnicity, cytogenetics, Flt3-ITD, NPM1, and BM donor availability.
  OUTLINE: Archived bone marrow mononuclear cells are analyzed by single cell network profile assay, the My Profile™ AML Risk of Relapse Assay. Molecular markers analyzed include Flt3-ITD, NPM1, and MRA. Results are then correlated with each patient's clinical data including patient's age, race/ethnic background, gender, treatment received, and outcomes.

Eligibility: DISEASE CHARACTERISTICS:
  -  Patients with confirmed non-M3 acute myeloid leukemia
  -  Treated on COG-AAML03P1 or COG- AAML0531 protocols
  -  Samples from COG-AAML0531 can come from either treatment arm, but these samples need to be independent from any patients who donated samples assayed in study COG-AAML11B2
  -  Patients with Down syndrome are excluded
  -  Cryopreserved bone marrow mononuclear cell (BMMC) samples collected at diagnosis, prior to start induction therapy
  -  Samples must have been cryopreserved at central lab within 3 days of draw at clinical site
  -  Target of 10 X 10^6 cells frozen
  -  Patients' clinical annotations required after unblinding
  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: Comparison of Laboratory Test Results of Minimal-Residual Disease in Samples From Patients With Acute Myeloid Leukemia

Summary: RATIONALE: Diagnostic procedures that find residual disease may help predict if the disease will come back in patients diagnosed with acute myeloid leukemia.
  PURPOSE: This research trial studies the comparison of laboratory test results for minimal residual disease in samples from patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  -  To promote harmonization between Cooperative Group Reference Laboratories conducting minimal-residual disease (MRD) evaluation of acute myeloid leukemia by flow cytometry.
  OUTLINE: Archived bone marrow and blood samples, distributed to the Eastern Cooperative Oncology Group, Southwest Oncology Group, and Cancer and Leukemia Group B laboratories, are analyzed for leukemia-associated immunophenotype (LAIP) assays and minimal residual disease studies by flow cytometry. Results are then provided to the National Cancer Institute for assessment and comparability of test results.

Eligibility: DISEASE CHARACTERISTICS:
  -  Non-identified cryopreserved samples of bone marrow and/or peripheral blood from patients with acute myeloid leukemia (AML) from the Children Oncology Group (COG) studies
  -  Baseline/diagnostic AML samples
  -  Samples collected after initial treatment and representing varying levels of residual blast counts
  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: Role of Biomarkers in Disease Progression in Samples From Patients With Acute Myeloid Leukemia

Summary: RATIONALE: Studying samples of blood, tissue, and bone marrow 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 trial studies the role of biomarkers in disease progression in samples from patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  -  To determine the subcellular localization of the MLL-AF1q fusion protein in leukemia cells.
  OUTLINE: Cryopreserved specimens are analyzed for MLL-AF1q fusion protein and AF1 gene expression by mass spectrometry, western blot analysis, semi-quantitative PCR, and qPCR.

Eligibility: DISEASE CHARACTERISTICS:
  -  Cryopreserved acute myeloid leukemia specimens
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant