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

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

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

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

Clinical trial: HLA-mismatched Microtransplantation for High Risk Acute Myeloid Leukemia

Summary: To compare the antitumor efficacy and toxicity of Idarubicin and cytarabine in combination with or not with infusions of granulocyte colony-stimulating factor-mobilized HLA-mismatched donor peripheral blood stem cells in patients with newly diagnosed high-risk acute myeloid leukemia (AML).


Eligibility: Inclusion Criteria:
  1. Having signed informed consent
  2. Diagnosis was based on the French-American-British (FAB) and WHO criteria.
  3. Age ≥ 7 years old
  4. Age ＜ 60 years old
  Exclusion Criteria:
  1.Patients with a blast crisis of chronic myeloid leukemia or acute promyelocytic leukemia

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

Clinical trial: S0106B Studying Bone Marrow Samples From Women With Acute Myeloid Leukemia

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

Detailed description: OBJECTIVES:
  -  Estimate the proportion of acute myeloid leukemia (AMLs) that originate in CD33+ precursors or in which uncontrolled growth is limited to CD33+ precursors.
  -  Explore whether there is an association between the cellular origin of AML (i.e., origination in CD33+ precursors or not) and cytogenetic, molecular, and other patient characteristics.
  -  Explore whether overall survival (OS), event-free survival (EFS), disease-free survival (DFS), response rate (RR), or relapse rate is improved for patients with AMLs that originate in CD33+ precursors or in which uncontrolled growth is limited to CD33+ precursors compared to patients with clonally involved cells not detected.
  OUTLINE: Archived bone marrow samples are analyzed for CD33+ progenitors, X-chromosome inactivation, and somatic mutations (t(8;21), inv(16), FLT3/ITD, NPM1, CEBPA, KIT) by fluorescence-activated cell sorting, long-term culture in hypoxic condition in cytokine-containing liquid media, and flow cytometry. Results are then compared with each patient clinical data.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnostic bone marrow specimens from female patients with untreated AML undergoing intensive ("3+7"-like) induction chemotherapy
  -  Specimens from the South Western Oncology Group (SWOG) protocols S0106 (age 18 to 60 years), excluding patients who received gemtuzumab ozogamicin (GO), and S9333 (age > 60 years)
  PATIENT CHARACTERISTICS:
  -  See Disease Characteristics
  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: Developing and Treating a Mouse Model of Acute Myeloid Leukemia Using Tissue Samples From Younger Patients With Acute Myeloid Leukemia

Summary: These laboratory trial studies the development and treatment of a mouse model for acute myeloid leukemia (AML) using samples from younger patients with AML. Studying tissue samples from patients with cancer in the laboratory may help doctors learn more about cancer and how well patients will respond to treatment.

Detailed description: PRIMARY OBJECTIVES:
  I. To determine the rate of engraftment of pediatric FMS-Like Tyrosine Kinase-3 (FLT3)-internal tandem duplication (ITD) acute myeloid leukemia (AML) samples in NOD scid gamma (NSG) mice.
  II. To determine the efficacy of treatment of FLT3-ITD xenografts with tyrosine kinase inhibitors.
  OUTLINE:
  Human acute myeloid leukemia cells are injected into NSG mice. Mice are then treated with sorafenib or quizartinib via gavage once daily for 28 days. Peripheral blood and tissue samples are collected biweekly or weekly and analyzed for the presence of human CD45+ and CD33+ cells by quantitative flow cytometry.

Eligibility: Inclusion Criteria:
  -  Cryopreserved human AML samples
  -  FLT3-ITD samples with high allelic ratios

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

Clinical trial: Trial to Assess the Efficacy of Midostaurin (PKC412) in Patients With c-KIT or FLT3-ITD Mutated t(8;21) AML

Summary: To assess the efficacy of tyrosine-kinase inhibitor midostaurin in c-KIT or FLT3-ITD mutated t(8;21) AML. To assess the efficacy of midostaurin depending on the type of c-KIT mutation

Detailed description: AML patients displaying t(8;21) have a relatively favourable outcome. Nevertheless, only approximately 50% of patients carrying this cytogenetic aberration are alive at 5 years. This suggests that some patients have more aggressive leukemic phenotypes and indicates the need for treatment optimization with novel therapies.
  The mutated KIT gene as well as the FLT3-ITD mutation have recently been identified as factors most likely to explain the heterogeneous clinical outcomes within the group of t(8;21) AML. The FLT3 and c-KIT genes encode type III receptor tyrosine kinases (RTK) with important and partly redundant functions in early hematopoietic stem cells. Various activating mutations have been described for both genes. For c-KIT, the incidence ranges from 17 to 48% depending on the source population and type of mutations determined. It has been consistently shown that in AMLs with t(8;21), mutated c-KIT is associated with a dramatically increased risk of relapse and reduced overall survival compared to their unmutated counterparts. The FLT3-ITD mutation has a similar negative effect on prognosis in the patient group of t(8;21) mutated AMLs as c-KIT.
  PKC412 (midostaurin) is known to inhibit the c-KIT RTK activity as well as the FLT3 kinase, both in patients with ITD and TKD mutations. It should therefore be possible to abrogate the negative impact of pathologically increased c-KIT or FLT3-ITD activity on relapse and overall survival by using midostaurin in this patient population. Aim of the proposed clinical trial is to prove the efficacy of midostaurin in c-KIT or FLT3-ITD mutated t(8;21)- AMLs in an open-label one-arm design.

Eligibility: Inclusion Criteria:
  -  Diagnosis of c-KIT mutated t(8;21) AML i.e.
  1. >20% myeloid blasts in bone marrow and/or peripheral blood at initial diagnosis
  2. Plus cytogenetic diagnosis of aberration t(8;21)/AML1-ETO
  3. Plus mutation of c-KIT gene (mut-KIT17 or mut-KIT8) or FLT3-ITD mutation or both c-KIT and FLT3-ITD mutations
  -  Chemoresponsive disease as determined by early bone marrow assessment on day 14-16 after first cycle of induction therapy with cytarabine in combination with daunorubicine or idarubicine, or mitoxantrone- Fit for further intensive chemotherapy
  -  Age 18-65 years
  -  ECOG performance status of 0-2
  -  Life expectancy of at least 12 weeks
  Exclusion Criteria:
  -  Primary refractory or previously relapsed AML
  -  Non-eligibility for high-dose cytarabine based consolidation, e.g. intolerance to cytarabine
  -  Inability to swallow oral medications
  -  Symptomatic congestive heart failure
  -  Bilirubin >2.5 x upper limit of normal

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

Clinical trial: Bioelectrical Impedance Measurement for Predicting Treatment Outcome in Patients With Newly Diagnosed Acute Leukemia

Summary: This clinical trial studies bioelectrical impedance measurement for predicting treatment outcome in patients with newly diagnosed acute leukemia. Diagnostic procedures, such as bioelectrical impedance measurement, may help predict a patient's response to treatment for acute leukemia.

Detailed description: PRIMARY OBJECTIVES:
  I: To determine the feasibility of obtaining standardized phase angle measurements (bioelectrical impedance measurement) on patients hospitalized for treatment of newly diagnosed acute leukemia.
  II. To evaluate the association between standardized phase angle measured at the start of therapy and treatment-related outcomes including treatment related mortality (defined as 60-day mortality) III. Evaluate the association of the day 14 standardized phase angle and treatment related outcomes, 30-day mortality, length of hospitalization, transfer to intensive care unit during induction, treatment response (14 day bone marrow response, complete remission), receipt of post-remission therapy, overall survival.
  IV. An exploratory analysis investigating associations with the primary and secondary outcomes using different ways to categorize the baseline standardized phase angle and, for acute myeloid leukemia (AML) patients, the standardized phase angle measure obtained just prior to the nadir marrow.
  OUTLINE:
  Patients undergo bioelectrical impedance phase angle measurement on day 1 of treatment. Patients with AML undergo a second measurement prior to the nadir marrow. Patients also undergo bioelectrical impedance measurements prior to any invasive procedures (bone marrow biopsy, leukapheresis, peripherally inserted central catheter [PICC] line placement, etc.).
  After completion of study treatment, patients are followed up for two years.

Eligibility: Inclusion Criteria:
  -  Hospitalized for newly diagnosed acute leukemia
  -  Receiving induction treatment while hospitalized
  -  Willing and able to provide written informed consent
  Exclusion Criteria:
  -  Presence of a pacemaker or defibrillator
  -  Patients pregnant at the time of enrollment
  -  Any condition or abnormality which may, in the opinion of the investigator, compromise the safety of patients
  -  Unable/unwilling to follow protocol requirements

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

Clinical trial: Maintenance Low Dose 5'-Azacitidine Post T Cell Depleted Allogeneic Stem Cell Transplantation for Patients With Myelodysplastic Syndrome and Acute Myelogenous Leukemia With High Risk for Post-Transplant Relapse

Summary: The purpose of this study is to learn if 5'-Azacitidine will help to lower the risk of the disease coming back after a stem cell transplant in patients with MDS and AML. This study will also be looking at the side effects of this medicine.
  5'-Azacitidine is an FDA approved drug for treatment of MDS and AML, as well as patients whose disease came back after transplant, where it helped going into remission. It is unclear if 5'-Azacitidine can prevent the disease from coming back after transplant. This study will help show if getting 5'-Azacitidine soon after transplant can lower the risk of your disease coming back.


Eligibility: Inclusion Criteria:
  Patients who have undergone T cell depleted allogeneic hematopoietic stem cell transplantation at MSKCC for:
  -  De novo myelodysplastic syndromes (MDS): IPSS-1 with poor risk cytogenetics or higher IPSS.
  -  Acute myelogenous leukemia (AML) in first remission that required more than 1 cycle of treatment to achieve remission or with the following cytogenetic abnormalities: FLT3 mutation, deletion/monosomy of chromosome 5 or 7, MLL gene rearrangement, or more than or equal to 3 cytogenetics abnormalities. Also patients in second or greater remission.
  -  Patients with Secondary MDS/AML.
  -  Patients will be considered eligible for the study if after transplant they achieved hematologic (<5% blasts) and cytogenetic remission.
  -  Patients will be eligible to enter the study between 60-120 days post transplant.
  -  Age: pediatrics and adults patients - 1 year old-75 years old.
  -  Karnofsky performance status >=60% for patients >16yo and Lansky performance status >=60% for patients ≤16yo
  -  Stable blood counts (ANC>1000/uL, Hb>8gr/dL, Plt>50,000/ uL) not supported by transfusions.
  -  Renal: Serum creatinine <1.5 ULN
  -  Hepatic: <3xULN ALT and <1.5 total serum bilirubin, unless there is congenital benign hyperbilirubinemia.
  -  Cardiac: Adequate cardiac function measured by LVEF>50%. If asymptomatic, pretransplant echocardiogram is adequate. If symptomatic, echocardiogram needs to be repeated.
  -  Each patient must be willing to participate as a research subject and must sign an informed consent form.
  Exclusion Criteria:
  Patients will be excluded from the trial if at time of enrollment:
  -  Active uncontrolled bacterial, fungal or viral infection.
  -  Evidence of uncontrolled graft-versus-host disease.
  -  Pulmonary: new onset hypoxia
  -  Known or suspected hypersensitivity to 5'-azacitadine or mannitol.
  -  Evidence of residual disease either by increased blasts count (>5%) or persistence of previous known cytogenetics abnormalities.
  -  Peripheral blood neutrophil chimerism: less than 95% donor.

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

Clinical trial: Interferon for the Intervention of Molecular Relapse in t (8; 21) AML After Allo-HSCT

Summary: molecular relapse in t (8; 21) acute myeloid leukemia (AML) after allogeneic stem cell transplantation (allo-SCT) is still a problem even after donor lymphocyte infusion.
  Interferon seemed to augment graft-versus-leukemia (GVL) effect in this part of patients.
  the study is to evaluate the safety and efficacy of interferon for the intervention of molecular relapse in t (8; 21) acute myeloid leukemia (AML) after allogeneic stem cell transplantation (allo-SCT)


Eligibility: Inclusion Criteria:
  -  high risk t (8; 21) AML
  -  molecular relapse after allo-SCT
  Exclusion Criteria:
  -  active graft-versus-host disease
  -  uncontrolled severe infection
  -  organ function failure

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

Clinical trial: Early Response Assessment of Induction Chemotherapy in Acute Myeloid Leukemia Patients Using F-18 FLT PET/CT

Summary: The purpose of this study is to investigate whether F-18 FLT PET/CT is useful in early response assessment of induction chemotherapy in acute myeloid leukemia patients.

Detailed description: Assessment of treatment response in AML is very important to determine the next treatment. Standard treatment of AML begins with induction chemotherapy. NCCN guideline recommend to assess the treatment response via bone marrow examination approximately 7-10 days after completion of induction chemotherapy. However, the possibility of sampling error and risks of infection and bleeding are the limitation of bone marrow biopsy.
  F-18 fluorodeoxythymidine (FLT) is a radiopharmaceutical for PET, reflecting the proliferation of the cell. F-18 FLT is trapped after phosphorylation by thymidine kinase1, whose expression is increased in replicating cells. There have been several studies that reported F-18 FLT PET could measure health and proliferation of the bone marrow.
  The aim of this study is to evaluate if F-18 FLT PET/CT is suitable for early response assessment of induction chemotherapy in acute myeloid leukemia patients.

Eligibility: Inclusion Criteria:
  -  acute myeloid leukemia
  -  must receive induction chemotherapy
  -  19 years old and over
  Exclusion Criteria:
  -  no standard therapy
  -  pregnancy

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

Clinical trial: Metabolism Des LAM

Summary: In this study, the investigators study the prognostic role of oxidative stress metabolism and iron in Acute myeloid leukemia.

Detailed description: Primary goal of this study is to Evaluate the characteristics of regulatory networks of iron and redox balance in leukemic cells, to study the correlations between the prognosis of AML patients (in terms of response to induction chemotherapy and survival i) and metabolism of these markers. Secondary ones areto assess the impact of induction therapy on markers of oxidative stress and to correlate biological iron and redox metabolism with the molecular status of patients (eg Flt3/IDH/CEBPA/NPM...).
  Eligibility criteria are patients at diagnostic of de novo acute myeloid leukemia (promyelocytic excluded) aged from 18 to 100 years.

Eligibility: Inclusion Criteria:
  de novo acute myeloid leukemic patient from 18 years to 99 years at diagnosis
  Exclusion Criteria:
  age under 18 years promelocytic leukemia secondary leukemia

Relevance to patient case: not relevant