araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 4-year-old female with leukemia; genetic feature: ABL1

Clinical trial: LAL-Ph-2000: Treatment of Acute Lymphoblastic Leukemia Chromosome Philadelphia Positive

Summary: Due to ALL Ph+ patients should receive a different treatment, is proposed a therapeutical protocol with: intensification treatment of induction to increment the CR rate, allogenic transplantation in first CR, autologous transplantation follow by alfa interferon in patients cannot done allogenic transplantation.

Detailed description: Remission Induction:
  -  Vincristine (VCR): 1,5 mg/m2 i.v., days 1 and 8
  -  Daunorubicin (DNR): 60 mg/m2 i.v., days 1 and 8.
  -  Prednisone (PDN): 60 mg/m2/day, i.v. or p.o., days 1 to 14
  -  L-asparaginase (L-ASA): 10.000 UI/m2, i.v.days 5-7 and 11-13
  Results:
  1. Standard response: The induction treatment will be completed with the same drugs, changing L-ASA to ARA-C, during two more weeks
  2 Slow response. Chemotherapy with mitoxantrone and high dose ARA-C
  Intrathecal chemotherapy:
  Treatment with mitoxantrone, ARA-C e hydrocortisone, days 1 and 22
  CONSOLIDATION TREATMENT 1
  Start in two weeks after last dose of induction chemotherapy:
  -  Mercaptopurine (MP) 50 mg/m2, p.o., days 1-7, 28-35 and 56-63
  -  Mitoxantrone (MTX): 3g/m2, i.v., in 24 hours, day 1, 28 and 56.
  -  VM-26: 150 mg/m2 every 12 horas, i.v. (infusión 1 hora), días 14 y 42
  -  ARA-C: 500 mg/m2 cada 12 hours, i.v., in 3 hours, days 14-15 and 42-43
  -  Intrathecal treatment, days 28 and 56.
  6.4. CONSOLIDATION TREATMENT 2
  Start in a week after last dose of mercaptopurine of previous cycle
  -  Dexamethasone (DXM):
  -  10 mg/m2 day, p.o. or i.v. days 1-14
  -  5 mg/m2 day, p.o. or i.v., days 15-21
  -  Vincristine (VCR): 1,5 mg/m2 i.v., days 1 and 8 and 15
  -  Daunorubicin (DNR): 30 mg/m2 i.v., days 1, 2, 8 and 9.
  -  CFM 600 mg/m2 day, i.v., days 1 and 15
  -  L-asparaginase (L-ASA): 10.000 UI/m2, i.v.or im , days 1-3 and 15-17
  -  Intrathecal treatment days 1 and 15.
  TRANSPLANTATION
  Hematopoietic autologous transplantation with related donor, one or two months after last dose of consolidation treatment.
  Hematopoietic autologous transplantation with unrelated donor, in patients younger than 45, and with PS 0-1
  Hematopoietic autologous transplantation in patients without related donor and without unrelated donor after six months searching

Eligibility: Inclusion Criteria:
  ALL BCR/ABL+ patients Age < 65 years No previous treatment
  Exclusion Criteria:
  1. Other LLA variability
  2. Previous history of coronary valvular, hypertensive cardiopathy illness
  3. Chronic hepatic illness
  4. Chronic respiratory insufficiency
  5. Renal insufficiency not caused by LLA
  6. Severe neurological problems not caused by LLA
  7. Severe affection of the performance status (grade 3-4 OMS gradation) not caused by LLA

Relevance to patient case: definitely relevant
Patient case: 4-year-old female with leukemia; genetic feature: ABL1

Clinical trial: External-Beam Radiation Therapy With or Without Indinavir and Ritonavir in Treating Patients With Brain Metastases

Summary: RATIONALE: Radiation therapy uses high-energy x-rays to kill tumor cells. Indinavir and ritonavir may stop the growth of tumor cells by blocking some of the enzymes needed for cell growth. It is not yet known whether external-beam radiation therapy is more effective with or without indinavir and ritonavir in treating patients with brain metastases.
  PURPOSE: This randomized phase II trial is studying external-beam radiation therapy alone to see how well it works compared to external-beam radiation therapy given together with indinavir and ritonavir in treating patients with brain metastases.

Detailed description: OBJECTIVES:
  -  Compare the efficacy, in terms of time to treatment failure at CNS level and 4-months treatment failure rate, in patients with brain metastases treated with external-beam radiotherapy in combination with indinavir sulfate and ritonavir versus external-beam radiotherapy alone.
  -  Prospectively investigate the efficacy of a potentially antiangiogenic agent, indinavir sulfate.
  -  Investigate the antineoplastic activity of indinavir sulfate in combination with ionizing radiation in cancer patients with metastatic disease to the brain.
  OUTLINE: Patients are randomized to 1 of 2 treatment arms.
  -  Arm I: Patients undergo radiotherapy to the brain once daily, 5 days a week for 2 weeks (10 doses total). Patients also receive oral indinavir sulfate and oral ritonavir twice daily for 35 days beginning at day 1 of radiotherapy.
  -  Arm II: Patients undergo radiotherapy to the brain once daily, 5 days a week for 2 weeks (10 doses total).
  Patients complete quality of life questionnaires, including QOL-30 and the Mini Mental Status Examination, at baseline, 2 weeks after completion of radiotherapy, and at 1 and 3 months after completion of study treatment.
  After completion of study treatment, patients are followed periodically for at least 4 months.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically confirmed metastatic cancer with brain metastases
  -  Biopsy of brain metastases is not required
  -  All cancer types allowed, except for the following:
  -  Prostatic adenocarcinoma
  -  Sarcoma
  -  Melanoma
  -  Germ cell carcinoma,
  -  Small-cell lung cancer
  -  Measurable disease by MRI of the brain
  -  Not requiring immediate surgical decompression (may qualify after surgery, if remaining measurable brain lesions)
  PATIENT CHARACTERISTICS:
  -  ECOG performance status 0-2 (corresponds to recursive partitioning analysis groups I or II)
  -  Life expectancy > 4 months
  -  Able to understand the aim of trial and to comply with follow-up
  -  No HIV seropositivity
  PRIOR CONCURRENT THERAPY:
  -  Prior dexamethasone allowed provided it is tapered before initiation of study radiotherapy
  -  Not requiring cytotoxic treatment within 3 months after study radiotherapy
  -  At least 1 week since prior and no concurrent phenytoin

Relevance to patient case: not relevant
Patient case: 4-year-old female with leukemia; genetic feature: ABL1

Clinical trial: A Phase II Study of Dasatinib in Children and Adolescents With Newly Diagnosed Chronic Phase CML or With Ph+ Leukemias Resistant or Intolerant to Imatinib

Summary: The purpose of this study is to determine whether dasatinib is safe and effective in children and adolescents with newly diagnosed chronic myeloid leukemia (CML), or in children with Ph+ acute lymphoblastic leukemia (ALL), accelerated or blast phases CML who relapse after imatinib or who are resistant or intolerant to imatinib. The side effects of this oral investigational drug in children and adolescents will be evaluated

Detailed description: Cohort 2 is closed to enrollment

Eligibility: For more information regarding BMS clinical trial participation, please visit www.BMSStudyConnect.com.
  Inclusion Criteria:
  -  CP-CML who prove resistant or intolerant to imatinib (cohort #1)
  -  Ph+ ALL, AP-CML, or BP-CML who are resistant or intolerant to or who relapse after imatinib therapy (cohort #2)
  -  Newly diagnosed, treatment naive CP-CML (cohort #3)
  -  Lansky or Karnofsky scale >50
  -  Life expectancy ≥12 weeks
  -  Adequate hepatic and renal function
  -  Written informed consent
  Exclusion Criteria:
  -  Eligibility for potentially-curative therapy including hematopoietic stem-cell transplantation
  -  Symptomatic CNS involvement (other than signs and symptoms caused by leptomeningeal disease)
  -  Isolated extramedullary disease
  -  Prior therapy with Dasatinib

Relevance to patient case: definitely relevant
Patient case: 4-year-old female with leukemia; genetic feature: ABL1

Clinical trial: Collecting Tissue Samples From Patients With Leukemia or Other Blood Disorders Planning to Enroll in an ECOG Leukemia Treatment Clinical Trial

Summary: RATIONALE: Collecting and storing samples of blood and bone marrow from patients with cancer to study in the laboratory may help doctors learn more about diagnosing cancer and determine a patient's eligibility for a treatment clinical trial. It may also help the study of cancer in the future.
  PURPOSE: This laboratory study is collecting tissue samples from patients with leukemia or other blood disorders who are planning to enroll in an ECOG leukemia treatment clinical trial.

Detailed description: OBJECTIVES:
  -  To provide a mechanism for sample collection and submission for diagnostic review to determine eligibility of patients with suspected leukemia or related hematologic disorders for enrollment on ECOG leukemia clinical trials.
  -  To obtain baseline samples for correlative studies outlined in parent clinical trials.
  OUTLINE: This is a cohort, multicenter study.
  Patients submit bone marrow and/or blood samples. The samples are studied to determine patients' eligibility for ECOG leukemia treatment clinical trials. Samples may be stored for future correlative studies related to ECOG treatment clinical trials.

Eligibility: DISEASE CHARACTERISTICS:
  -  Candidate for enrollment on an ECOG treatment clinical trial for acute or chronic leukemia
  -  Suspected clinical diagnosis and protocol ID number of the treatment clinical trial under consideration must be submitted to ECOG's Leukemia Translational Studies Laboratory to ensure that the required antibody panels are used and functional assays are performed
  -  Chosen ECOG treatment clinical trial must be active and accruing
  -  Patient must not have begun treatment on the ECOG treatment clinical trial
  -  Patient may be concurrently enrolled on this laboratory study and a treatment clinical trial if immediate treatment is medically necessary
  -  If subsequent diagnostic review alters the original diagnosis, the patient will be removed from the treatment clinical trial
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 4-year-old female with leukemia; genetic feature: ABL1

Clinical trial: Collecting and Storing Malignant, Borderline Malignant Neoplasms, and Related Samples From Young Patients With Cancer

Summary: This study is collecting and storing malignant, borderline malignant neoplasms, and related biological samples from young patients with cancer. Collecting and storing samples of tumor tissue, blood, and bone marrow from patients with cancer to study in the laboratory may help the study of cancer in the future.

Detailed description: OBJECTIVES:
  I. Collect malignant, borderline malignant neoplasms, and related biological specimens from Children's Oncology Group institutions for cases in which there is no disease-specific biologic protocol.
  II. Provide a repository for long-term storage of malignant, borderline malignant neoplasms, and related biological specimens from these patients.
  III. Make specimens available to qualified researchers to understand the biology of cancer in these patients.
  OUTLINE:
  Tumor tissue samples, blood, and bone marrow aspirates are collected and stored for future analysis.

Eligibility: Inclusion Criteria:
  -  Meets any of the following criteria:
  -  Diagnosed with primary neoplasm
  -  Developed a second malignant neoplasm
  -  Any diagnoses having an ICD-O Morphology Code ending in 1, 2, or 3 as listed in the International Classification of Disease for Oncology, Third Edition
  -  Must have biological specimens including solid tumors and leukemias available
  -  Solid tumors meeting the following criteria:
  -  Snap frozen primary tumor OR OCT embedded primary tumor OR formalin fixed (block or tissue in formalin) primary tumor AND at least 10 unstained paraffin slides for NIH Mandated QC (tumors that have undergone central pathology review are allowed)
  -  Slides for pathology review (instead of slides for QC) are required for patients with rare tumors
  -  Pleural fluid or cytologic specimens meeting the following criteria:
  -  At least 1 mL of fluid and at least 2 unstained cytospin slides (or 2 unstained smears)
  -  Slides for pathology review (instead of slides for QC) are required for patients with rare tumors
  -  ALL/AML
  -  3-6 mL of bone marrow aspirate and 10 mL of whole blood
  -  Not eligible for disease-specific biology or banking protocol

Relevance to patient case: not relevant
Patient case: 4-year-old female with leukemia; genetic feature: ABL1

Clinical trial: Assessing Arsenic Trioxide in Young Patients With Leukemia or Lymphoma Who Were Treated on Clinical Trial NCI-00-C-0070J

Summary: RATIONALE: Studying bone marrow and blood samples from patients with leukemia or lymphoma treated with arsenic trioxide may help doctors learn more about cancer.
  PURPOSE: This research study is assessing arsenic trioxide in young patients with recurrent or refractory leukemia or lymphoma who were treated on clinical trial NCI-00-C-0070J.

Detailed description: OBJECTIVES:
  -  To assess the pharmacokinetic and pharmacodynamic profiles of arsenic trioxide in pediatric patients treated on protocol NCI-00-C-0070J.
  OUTLINE: Bone marrow or peripheral blood mononuclear cells collected during treatment on NCI-00-C-0070J are assessed for pharmacodynamics studies. Plasma cells collected during treatment are assessed for pharmacokinetics studies. Total arsenic (As), inorganic As forms (AsIII and AsV), and methylated metabolites of As are assessed.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically confirmed leukemia or lymphoma refractory to standard curative treatment regimens
  -  No meningeal leukemia or lymphoma
  -  No HIV-related lymphoma
  -  No lymphoproliferative diseases
  -  Received treatment on protocol NCI-00-C-0070J
  -  Bone marrow or peripheral blood and serum samples collected during treatment on NCI-00-C-0070J are available
  PATIENT CHARACTERISTICS:
  -  See NCI-00-C-0070J
  PRIOR CONCURRENT THERAPY:
  -  See NCI-00-C-0070J

Relevance to patient case: not relevant
Patient case: 4-year-old female with leukemia; genetic feature: ABL1

Clinical trial: DNA Analysis of Tissue From Patients With T-Cell Acute Lymphoblastic Leukemia

Summary: RATIONALE: Studying samples of 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 laboratory study is looking at tissue samples from patients with T-cell acute lymphoblastic leukemia.

Detailed description: OBJECTIVES:
  -  Identify the transcriptional signatures associated with the presence of NOTCH1 mutations in primary T-cell acute lymphoblastic leukemia (T-ALL) cells using oligonucleotide microarrays.
  -  Characterize the global changes on gene expression resulting from the inactivation of NOTCH signaling in human T-ALL lymphoblasts.
  OUTLINE: This is a multicenter study.
  Frozen lymphoblast samples from patients with T-cell acute lymphoblastic leukemia (NOTCH1-mutated and wild type) are assessed for genetic expression profiles and mutations by microarray analysis and activated NOTCH1 protein by western blot analysis.
  PROJECTED ACCRUAL: A total of 48 samples from patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Confirmed diagnosis of T-cell acute lymphoblastic leukemia
  -  Frozen lymphoblast samples available
  -  NOTCH1-mutated or wild type sample available
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 4-year-old female with leukemia; genetic feature: ABL1

Clinical trial: Resistance to Methotrexate in Patients With Acute Lymphoblastic Leukemia in Relapse or Remission

Summary: RATIONALE: Studying samples of blood from patients with cancer in the laboratory may help doctors learn more about cancer and the development of drug resistance in patients.
  PURPOSE: This laboratory study is looking at resistance to methotrexate in patients with acute lymphoblastic leukemia in relapse or remission.

Detailed description: OBJECTIVES:
  -  Determine the mechanisms of intrinsic and acquired methotrexate resistance using in vitro assays of matched initial diagnosis, relapsed, and nonrelapsed (control) leukemic blast samples from patients with acute lymphoblastic leukemia in relapse or remission.
  -  Determine if the mechanisms of acquired methotrexate resistance are related to dosage or timing of methotrexate administration or other clinical factors in these patients.
  OUTLINE: Random samples of frozen leukemic blasts from relapsing patients at initial diagnosis and relapse are selected. A corresponding sample from nonrelapsing patients (control) at initial diagnosis is also randomly selected.
  Reduced folate carrier (RFC) and dehydrofolate reductase (DHFR) expression is measured using a quantitative reverse transcriptase-polymerase chain reaction assay of prepared RNA. DHFR gene amplification is measured by a dot blot analysis of prepared DNA. Results of these assays are used to determine if a particular mechanism of acquired methotrexate resistance is associated with a particular subset of acute lymphoblastic leukemia patients. Data are collected regarding the actual timing and dosage of methotrexate received by each patient and are correlated with the mechanisms of resistance.
  PROJECTED ACCRUAL: A total of 135 paired samples will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Meets 1 of the following criteria:
  -  Acute lymphoblastic leukemia (ALL) in relapse, including all risk groups and leukemia subtypes, with frozen leukemic blast samples stored from the time of initial diagnosis and relapse
  -  Non-relapsing ALL (as control)
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 4-year-old female with leukemia; genetic feature: ABL1

Clinical trial: S9910, Collecting and Storing Blood and Bone Marrow Samples From Patients With Hematologic Cancer

Summary: RATIONALE: Collecting and storing samples of blood and bone marrow from patients with cancer to study in the laboratory may help doctors learn more about diagnosing cancer and how well patients will respond to treatment.
  PURPOSE: The purpose of this study is to collect and store blood and bone marrow samples from patients with hematologic cancer to be tested in the laboratory.

Detailed description: Primary objective:
  -  Maintain and expand tissue repositories of highly characterized samples from patients with acute lymphoblastic leukemia, chronic lymphocytic leukemia, acute myeloid leukemia, chronic myelogenous leukemia, or myelodysplastic syndromes.
  Other objectives as funding permits:
  -  Develop laboratory assays for rapid and precise diagnosis of leukemia using bone marrow and peripheral blood samples.
  -  Determine biologic, genetic, and molecular parameters that distinguish different subtypes of human leukemia with differing responses to therapy, and develop "risk-adapted" therapeutic approaches based on these parameters to tailor therapeutic regimens, randomize or stratify patients in clinical trials, or otherwise assist in therapeutic decision-making.
  -  Develop new automated and standardized laboratory methods for the detection and monitoring of therapeutic responsiveness and minimal residual disease in patients and use this information to design clinical trials.
  OUTLINE: Patients receive treatment as directed by the Southwest Oncology Group (SWOG) study to which they are registered.
  Patients undergo collection of peripheral blood (myeloid leukemia) or venous blood (lymphoid leukemia) and bone marrow at baseline, at the time of response or remission, and at the time of progression or relapse. Additional collections may take place according to the guidelines of the study in which the patient is registered.
  Specimens are stored for use in laboratory research.
  PROJECTED ACCRUAL: Samples from a maximum of 1,000 patients will be collected for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Currently registered on a Southwest Oncology Group (SWOG) treatment study for acute lymphoblastic leukemia, chronic lymphocytic leukemia, acute myeloid leukemia, chronic myelogenous leukemia, or myelodysplastic syndromes
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 4-year-old female with leukemia; genetic feature: ABL1

Clinical trial: Chronic Graft-Versus-Host Disease in Patients Who Have Undergone Donor Stem Cell Transplant

Summary: RATIONALE: Studying samples of tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to chronic graft-versus-host disease in patients who have undergone donor stem cell transplant.
  PURPOSE: This phase I trial is studying chronic graft-versus-host disease in patients who have undergone donor stem cell transplant.

Detailed description: OBJECTIVES:
  -  To determine and define the biological basis of different subtypes of chronic graft-vs-host disease using a targeted single nucleotide polymorphisms approach in patients who have undergone allogeneic stem cell transplantation.
  OUTLINE: Two important aspects of the methodologies that will be employed for the analysis of SNPs associated with GVHD are throughput efficiency to be able to perform the assays on a reasonable number of samples as well as having the ability to add or remove SNPs to the assay panel. While a genome-wide association study to identify variants associated with GVHD would offer an unbiased approach, our patient cohort size would not allow significant statistical power in the study. Therefore, a more targeted approach using two established technologies is proposed.
  The Sequenome assay uses the unique combination of a single-base primer extension assay incorporating one of four modified nucleotides. The four modified nucleotides each have a unique mass that allows them to be distinguished from one another using mass spectrometry. Each SNP is determined analyzing the primer extension product from a PCR amplicon that surrounds the SNP of interest. The development of each assay involves designing flanking PCR primers and an internal extension assay using web-based software provided by Sequenome. The assays can be designed to analyze up to 30 SNPs in a single reaction, providing a customizable, efficient and high-throughput assay for SNPs of interest.

Eligibility: DISEASE CHARACTERISTICS:
  -  Underwent prior matched related or unrelated allogeneic stem cell transplantation (SCT)
  -  Presence OR absence of chronic graft-vs-host disease after day 100 and alive after day 180 post-transplantation
  -  No T-cell depleted SCT, cord blood transplantation, mismatched allogeneic transplantation, or autologous transplantation
  -  Available recipient and donor DNA (samples collected from the Vanderbilt University or the Fred Hutchinson Cancer Center tissue bank)
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant