araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 13-year-old male with acute myeloid leukemia; genetic feature: FLT3

Clinical trial: Biomarkers in Bone Marrow Samples From Pediatric Patients With High-Risk Acute Myeloid Leukemia

Summary: This pilot research trial studies biomarkers in bone marrow samples from pediatric patients with high risk acute myeloid leukemia. Studying samples of bone marrow from patients with cancer in the laboratory may help doctors identify and learn more about biomarkers related to cancer.

Detailed description: PRIMARY OBJECTIVES:
  I. To provide a detailed, molecular map of pediatric high risk acute myeloid leukemia (AML).
  II. To identify mutations, expression profile, gene copy number, loss of heterozygosity (LOH) status and genomic methylation patterns in order to identify novel changes associated with pediatric AML.
  III. To generate fibroblast cell lines in order to obtain germline nucleic acids from marrow specimens from AML patients with induction failure.
  IV. To identify genomic alterations contributing to induction failure in childhood AML.
  OUTLINE:
  Banked bone marrow samples from diagnosis and remission are used to develop a detailed molecular map of pediatric high-risk acute myeloid leukemia. Analysis includes genome single nucleotide polymorphism (SNP) genotyping, expression, and methylation profiling.

Eligibility: Inclusion Criteria:
  -  Diagnosis of acute myeloid leukemia
  -  High-risk disease
  -  Treated on COG-AAML03P1 or COG-AAML0531
  -  Meets the following criteria:
  -  Initial remission with no known adverse risk factors
  -  High quantity and quality of ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) available
  -  Highly enriched specimens with >= 50% blast available

Relevance to patient case: not relevant
Patient case: 13-year-old male with acute myeloid leukemia; genetic feature: FLT3

Clinical trial: Biomarkers in Young Patients With Acute Myeloid Leukemia

Summary: RATIONALE: Studying samples of tissue from patients with cancer in the laboratory may help doctors 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:
  -  Determine the frequency of ligand-independent phosphorylation of Stat3 in a small cohort of samples from pediatric patients with acute myeloid leukemia including, but not limited to, samples known to express mutated c-kit.
  -  Measure the level of Stat3 phosphorylation in these samples after stimulation of three key cytokine receptors expressed on hematopoietic cells IL-6R, G-CSFR, and c-kit.
  OUTLINE: Cryopreserved samples are analyzed for levels of various components of the Stat3 pathway via western blotting.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of acute myeloid leukemia
  -  One of the following karyotypes:
  -  t(8;21) and WT c-kit
  -  t(8;21) and mutant c-kit
  -  Normal karyotype
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 13-year-old male with acute myeloid leukemia; genetic feature: FLT3

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: 13-year-old male with acute myeloid leukemia; genetic feature: FLT3

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: 13-year-old male with acute myeloid leukemia; genetic feature: FLT3

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: 13-year-old male with acute myeloid leukemia; genetic feature: FLT3

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
Patient case: 13-year-old male with acute myeloid leukemia; genetic feature: FLT3

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: 13-year-old male with acute myeloid leukemia; genetic feature: FLT3

Clinical trial: Selecting a Favorable KIR Donor in Unrelated HCT for AML

Summary: Donors with favorable KIR B haplotype gene content have yielded reduced relapse risk and improved leukemia free survival (LFS) in retrospective analyses of unrelated donor (URD) hematopoietic cell transplantation (HCT) for acute myelogenous leukemia (AML). Specifically, donors with more KIR B gene content and those who are homozygous for the centromeric (Cen) B haplotype genes (as opposed to the telomeric (Tel) genes confer the most protective effect. This study proposes to prospectively test and validate the utility and effectiveness of further informing URD identification and selection by KIR genotyping as a supplement to HLA matching and the other variables known or suspected to indicate the best URD for a patient.
  Hypotheses:
  1. Favorable KIR donors will improve protection against relapse and improve leukemia free survival (LFS) after URD HCT for AML.
  2. Directed study procedures for rapid KIR genotyping and reporting to searching Transplant Centers (TC) can inform donor search and selection without delay in donor availability for HCT.

Detailed description: Transplant Centers will select the best HLA matched, and as appropriate, preferred KIR donor.

Eligibility: Inclusion Criteria:
  -  Patient with acute myeloid leukemia (AML) undergoing screening for potential URD HCT
  -  Potential URD undergoing screening to provide a HCT graft to a patient with acute myeloid leukemia (AML) at a participating institution
  -  Provides written consent
  Exclusion Criteria:
  Transplant Centers will select the best HLA matched, and as appropriate, preferred KIR donor. In situations where the preferred (best > better > neutral) KIR donor is not selected in favor of a less favorable KIR genotype donor, the center will report one or more defined reasons (donor age; gender; parity; CMV status; ABO status; availability/logistics; other) for the choice (among equivalently HLA matched donors).

Relevance to patient case: not relevant
Patient case: 13-year-old male with acute myeloid leukemia; genetic feature: FLT3

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: not relevant
Patient case: 13-year-old male with acute myeloid leukemia; genetic feature: FLT3

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: not relevant
Patient case: 13-year-old male with acute myeloid leukemia; genetic feature: FLT3

Clinical trial: Cell Samples From Patients With Leukemia

Summary: RATIONALE: Studying samples of blood and tissue from patients with cancer in the laboratory may help doctors learn more about cancer and the development of drug resistance in patients. It may also help doctors find better ways to treat cancer.
  PURPOSE: This research trial is studying samples from patients with leukemia.

Detailed description: OBJECTIVES:
  -  Demonstrate the capability of primary human leukemia samples to survive and proliferate in the zebrafish embryo.
  -  Confirm the anti-proliferative or toxic effects of known chemotherapeutics on the transplanted cells in vivo.
  -  Evaluate the effect of novel anticancer drugs and/or their combinations on individual samples.
  OUTLINE: This is a multicenter study.
  Cryopreserved specimens are injected into the yolk sac of zebrafish embryos under anesthesia. After 1 hour of recovery at 28° C, embryos are maintained at 38° C and screened for fluorescence at the injection site. Within 48 hours post-injection, some embryos are treated with various chemotherapeutic drugs or dimethyl sulfoxide and incubated in protease solution. Proliferation of leukemia cells are monitored by live-cell microscopy. Cells with or without drug treatment are then extracted at 24 and 72 hours post-injection. Leukemia cells are counted and tested with imatinib mesylate, all-trans retinoic acid (tretinoin), cytosine arabinose, and known bioactive chemical compounds from promising drug families, such as tyrosine kinase inhibitors, antiapoptotic agents, channel modulators, and prostaglandin agonists.

Eligibility: DISEASE CHARACTERISTICS:
  -  Samples of blood and tissue cells from patients diagnosed with myeloid disease including the following subtypes:
  -  Chronic phase chronic myeloid leukemia (CML), to complement initial studies in the K562 CML cell line
  -  Acute promyelocytic leukemia (APL), to complement initial studies in the NB4 APL cell line
  -  Acute myeloid leukemia (AML) expressing the t(8;21)(q22;q22) translocation, which occurs in approximately 12% of pediatric AML and is associated with good prognosis
  -  AML expressing 5q- or monosomy 7, associated with a poor prognosis
  -  AML expressing the fms-like tyrosine kinase 3 internal tandem duplication (FLT3-ITD), associated with a poor prognosis
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: definitely relevant
Patient case: 13-year-old male with acute myeloid leukemia; genetic feature: FLT3

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