araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: A Study of R1507 in Participants With Recurrent or Refractory Sarcoma

Summary: This study will evaluate the efficacy and safety of R1507 in participants with recurrent or refractory sarcoma. Eight cohorts of sarcoma participants will be studied in parallel. Cohort 1: Ewing's sarcoma primary cohort defined as participants who have relapsed less than or equal to (<=) 24 months from diagnosis, received at least two prior chemotherapy programs and are unresectable. Cohort 2: Ewing's sarcoma non-primary (secondary) cohort defined as participants who have relapsed greater than or equal to (>=) 24 months from diagnosis or have only received one prior chemotherapy program. Cohort 3: Expanded Ewing's sarcoma defined as participants with recurrent or relapse regardless of prior number of salvage regimens and regardless of time of relapse. Cohort 4: participants with osteosarcoma. Cohort 5: Participants with synovial sarcoma. Cohort 6: Participants with rhabdomyosarcoma Cohort 7: Participants with alveolar soft part sarcoma (7a), desmoplastic small round cell tumors (7b), extraskeletal myxoid chondrosarcoma (7c), clear cell sarcoma (7d), myxoid liposarcoma (7e). Cohort 8: Participants with unspecified sarcoma diagnosis. Participants in the expanded Ewing's sarcoma Cohort 3 will receive 27 milligrams (mg)/kilogram (kg) every 3 weeks intravenously (IV). All other participants will receive R1507 9 mg/kg IV weekly. The anticipated time on study treatment is until disease progression or unacceptable adverse events, withdrawal or death.


Eligibility: Inclusion Criteria:
  -  progressive, recurrent or refractory Ewing's sarcoma, or recurrent or refractory osteosarcoma, synovial sarcoma, rhabdomyosarcoma, or other sarcomas of the following sub-types: alveolar soft part sarcoma, desmoplastic small round cell tumor, extraskeletal myxoid chondrosarcoma, clear cell sarcoma and myxoid liposarcoma;
  -  Cohort 3 only: age must be >= 2 and <= 21 years
  Exclusion Criteria:
  -  clinically significant unrelated systemic illness which would compromise the participant's ability to tolerate the investigational agent, or interfere with the study procedures or results;
  -  known hypersensitivity to any of the components of R1507 or prior hypersensitivity reactions to monoclonal antibodies;
  -  treatment (within the past 2 weeks) with pharmacologic doses of corticosteroids or other immunosuppressive agents;
  -  current or prior therapy with insulin-like growth factor (IGF) inhibitor (monoclonal or specific kinase inhibitor);
  -  history of solid organ transplant;
  -  other malignant disease diagnosed within the previous 5 years, excluding intra-epithelial cervical neoplasia or non-melanoma skin cancer;
  -  active central nervous system disease

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: GENSARC 2008 : Medical Economic Evaluation of the Molecular Detection by FISH (Fluorescent in Situ Hybridization) and by PCR (Polymerase Chain Reaction) of Sarcomas Specific Translocations and Amplifications .

Summary: The clinical and histological diagnosis of sarcomas is often very difficult. The identification of chromosomal and molecular anomalies, such as amplifications, deletions or fusion genes is a powerful help for establishing a correct diagnosis of sarcomas and their benign counterparts. However, the cost of the cytogenetic and molecular techniques for the detection of these alterations is often a limitation to their use. The aim of our study is to evaluate the direct cost of the molecular techniques in comparison to the cost that would be generated by an appropriate therapy and care management of the patient in case of an erroneous diagnosis.


Eligibility: Inclusion Criteria:
  -  patients with biopsy or excision of sarcoma (suspected or diagnosed)
  -  sampling reviewed by pathologists
  -  frozen sampling
  -  clinical data available
  Exclusion Criteria:
  -  opposition of patient

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: Initiative for Molecular Profiling in Advanced Cancer Therapy (IMPACT) Trial, An Umbrella Protocol

Summary: Primary Objective The primary objective of this study is to establish a program for the molecular profiling of patients with advanced cancer, with the goals of (1) providing a comprehensive characterization of the molecular profiles of individual patients and (2) correlating molecular profile with response to phase I therapies.
  Specimens will be received from the LAB07-0817 (Tissue Bank) protocol in the Department of Investigational Cancer Therapeutics. Note that this study is considered an umbrella protocol to systematically enroll phase I patients for molecular profiling analysis and correlate the results with treatment outcomes. The IMPACT trial is not a treatment protocol.
  Secondary Objectives
  1. To characterize advanced cancer by delineating genetic mutations, amplifications, translocations, and other defining molecular patient characteristics.
  2. To assess the antitumor effects of treatments by tumor responses using the World Health Organization (WHO) or Response Evaluation Criteria in Solid Tumors (RECIST) criteria and/or any other clinical benefits, including progression-free survival and overall survival, demonstrated in phase I clinical trials.
  3. To correlate molecular profiles of patients with evidence of antitumor activity (complete remission, partial remission, prolonged stable disease, or overall survival) to define subsets of patients who will respond to specific therapies in clinical trials of novel agents.
  4. To correlate molecular profiles with toxicities induced by investigational agents to define subsets of patients who may or may not be candidates for treatment with these agents in the future.

Detailed description: The prognosis of patients with advanced metastatic malignancies is poor, and their median survival, irrespective of diagnosis, is approximately 8.8 months (95% confidence interval, 7.4 to 10.9 months). In recent years there has been increased interest in novel agents.
  Elucidating the molecular basis of advanced cancer will lead to the development of potentially curative strategies for these diseases aimed at the specific molecular and genetic aberrations characteristic of specific tumors.
  This study is a molecular profiling analyses of the patients' stored samples and will not involve more than minimal risk to the subjects. Subjects are at no more than minimal risk because only leftover blood, tissue, and patient data will be used for this study, and all patient data will be kept confidential.

Eligibility: Inclusion Criteria:
  1) Any patient seen in the department of Investigational Cancer Therapeutics is eligible. Patients who have blood or tissue samples collected must be registered on the tissue bank protocol (LAB07-0817).
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: Level of HER2-neu Gene Amplification an Response to Trastuzumab

Summary: Primary objective of the study is to evaluate the correlation between level of HER2-neu gene amplification evalued by dual-color Fluorescent in-situ hybridization (FISH) test and time to progression (TTP) in patients with HER2-positive advanced breast cancer treated with trastuzumab-containing regimens.


Eligibility: Inclusion Criteria:
  -  HER2-positive breast cancer Trastuzumab-containing regimen delivered for advanced disease Tumor sample available at Pathology Archive
  Exclusion Criteria:
  -  HER2-negative advanced breast cancer Pretreatment with trastuzumab

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: Molecular Mechanisms of Clinical Resistance to Targeted Therapy Among Patients With Breast Cancer

Summary: The purpose of this study is to learn why certain drugs stop working in patients.In lab studies, tumors become resistant in several ways. Specific molecules seem to change and this may be why therapy stops working. However, we do not know if the same molecules change in patients. This study is being done to see if they do change. If we learn more about how patients become resistant, we may be able to offer better treatment in the future.


Eligibility: Inclusion Criteria:
  All patients:
  -  Diagnosed with progressive, recurrent or metastatic HER2+ or ER+ breast cancer.
  Cohort 1
  -  Patients who previously received treatment with anti-HER2 therapy (including trastuzumab, pertuzumab, TDM1, or lapatinib) as part of adjuvant chemotherapy and now have progressive or recurrent breast cancer or, patients who previously (or currently) received anti-HER2 therapy as part of a regimen for metastatic breast cancer and subsequently experienced.
  -  Evidence of disease progression or recurrence after prior therapy (e.g. radiologic progression by RECIST criteria or new metastasis).
  -  Prior tumor biopsy (may be original) defined as HER2+ by amplification by FISH (>1.9 gene copy number) or IHC 3+.
  Cohort 2
  -  Patients who previously received treatment with hormonal therapy (including tamoxifen, toremifene, raloxifene, anastrozole, letrozole, exemestane, fulvestrant, ARN-810) as a part of adjuvant therapy and now have progressive or recurrent breast cancer or patients who previously (or currently) receive hormonal therapy as part of a regimen for metastatic breast cancer and subsequently experienced evidence of disease progression.
  Cohort 3
  -  Patients not eligible for Cohorts 1 or 2, but previously received treatment of any other kind for breast cancer.
  Exclusion Criteria:
  -  Patients who are unable to consent to a biopsy.
  -  Patients for whom a repeat biopsy would be medically unsafe

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: Study of DNA in Blood Samples From Patients With Neuroblastoma

Summary: This research trial studies is deoxyribonucleic acid (DNA) in blood samples from patients with neuroblastoma. Studying samples of blood 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.

Detailed description: OBJECTIVES:
  I. Perform in a blind study a multicentric study by analyzing serum from patients at diagnosis (with a known tumor v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog (MYCN) status determined in the Children's Oncology Group [COG] reference lab), in order to confirm our previous data and to define the most appropriate MYCN/control ratio cutoff capable of determining positive and negative cases.
  II. Define the limits of the procedure in non-metastatic patients and in those with reduced tumor burden (International Neuroblastoma Staging System [INSS] stage 1 and 2).
  OUTLINE:
  Circulating DNA is extracted from serum. Polymerase chain reaction (PCR) amplification of MYCN is performed and analyzed by agarose gel electrophoresis. Real-time quantitative PCR is also performed.

Eligibility: Inclusion Criteria:
  -  Serum samples from neuroblastoma (NB) patients obtained through the COG (and legacy Children's Cancer Group [CCG]/Pediatric Oncology Group [POG] Biology Studies)
  -  The MYCN status on corresponding tumors have been determined using standard techniques; the panel of samples must be obtained from NB patients with and without MYCN amplification tumors
  -  Cases will be drawn from clinical subsets at greatest likelihood to benefit from this testing ability, stage 1 and 2 NBs (both infants and toddlers), stage 4 patients under 18 months of age, and 4S patients

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: Study Evaluating the Efficacy and Safety of IPI 504 in Patients With Advanced Dedifferentiated Liposarcoma

Summary: The primary objective of the study is to determine the safety profile and overall response rate of IPI 504 in patients with advanced dedifferentiated liposarcoma.


Eligibility: Inclusion Criteria:
  -  At least 18 years of age at the time of signing informed consent.
  -  Histologic diagnosis of dedifferentiated liposarcoma.
  -  Available archival pathology specimen or tissue sample from a new biopsy for confirmation of diagnosis by central pathology reading.
  -  At least one prior chemotherapy regimen for dedifferentiated liposarcoma.
  -  No more than 2 prior chemotherapy regimens for dedifferentiated liposarcoma. Note: Any number of non-chemotherapy regimens is permitted.
  -  Measurable disease on computed tomography (CT) or magnetic resonance imaging (MRI) as defined by RECIST (version 1.1) with at least one measurable lesion.
  -  Eastern Cooperative Oncology Group (ECOG) performance status: 0 or 1.
  -  Life expectancy ≥6 months.
  Exclusion Criteria:
  -  Prior treatment with any heat shock protein 90 (Hsp90) inhibitor.
  -  Surgery, radiotherapy, or lesion ablative procedure to the only area of measurable disease
  -  Patients with prior hepatic resections or hepatic-directed therapy
  -  Use of a medication or food that is a clinically relevant CYP3A inhibitor or inducer within 2 weeks prior to dosing.

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: A Study of RO5045337 in Patients With Liposarcomas Prior to Debulking Surgery

Summary: This open-label study will evaluate efficacy, safety and tolerability of RO5045337 in patients with liposarcoma who are eligible for debulking surgery. Prior to surgery, patients will receive 2-3 cycles of RO5045337, orally for 10 days followed by 18 days of rest per cycle. Anticipated time on study treatment is 3 months. Patients with an incomplete resection may be treated for an additional 3 cycles with RO5045337.


Eligibility: Inclusion Criteria:
  -  adult patients, >/=18 years of age
  -  well differentiated and/or dedifferentiated liposarcoma eligible for tumor debulking surgery
  -  willing to undergo tumor biopsies before, during and after treatment
  -  ECOG performance status 0-1
  Exclusion Criteria:
  -  previous chemotherapy and/or radiation for liposarcoma; previous debulking surgery is acceptable
  -  patients receiving any other agent or therapy to treat their malignancy
  -  patients requiring anticoagulant therapy and/or anti-platelet therapy
  -  pre-existing gastrointestinal disorders which may interfere with absorption of drugs
  -  history of seizure disorders or unstable CNS metastases
  -  clinically significant cardiovascular disease
  -  history of long QT syndrome

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: Biomarkers in Tissue Samples From Patients With Breast Cancer Treated With Bevacizumab

Summary: RATIONALE: DNA analysis of tumor tissue may help doctors predict how well patients will respond to treatment.
  PURPOSE: This research study is studying biomarkers in tissue samples from patients with breast cancer treated with bevacizumab.

Detailed description: OBJECTIVES:
  Primary
  -  To demonstrate that vascular endothelial growth factor-A (VEGFA) haplotypes that are associated with an increased VEGFA expression will predict superior outcome for patients with metastatic breast cancer receiving bevacizumab in ECOG-E2100 (but not for the control arm).
  -  To demonstrate that candidate single nucleotide polymorphisms (SNPs) will further improve the predictive capacity of outcome (efficacy and toxicity) in patients enrolled in ECOG-E2100.
  -  To demonstrate that tumor VEGFA amplification or borderline amplification (estimated 14% frequency) will predict superior outcome for patients with metastatic breast cancer receiving bevacizumab on ECOG-E2100 whereas those with VEGFA deletion (estimated 11% frequency) will predict inferior outcome.
  -  To demonstrate that VEGFA amplification/deletion will not predict outcome in the control arm of ECOG-E2100.
  Secondary
  -  To demonstrate that tumor VEGFA amplification will predict increased protein expression as ascertained by IHC.
  -  To demonstrate that a combined algorithm calculated from tumor-specific variability (VEGFA amplification/deletion) and host-specific variability (SNPs) will optimally predict outcome (efficacy) with bevacizumab in patients enrolled on ECOG-E2100.
  OUTLINE: This is a multicenter study.
  Previously collected tumor-derived DNA is analyzed for VEGFA amplification/deletion and haplotype as biomarkers for outcome after bevacizumab treatment. Gene expression, polymorphism, protein expression analysis, and IHC are performed on the samples.

Eligibility: DISEASE CHARACTERISTICS:
  -  Enrolled on ECOG-E2100
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: Study to Assess the Incidence of Intussusception in Children < 2 Years of Age in Singapore

Summary: This prospective study aims to estimate the incidence of intussusception among children < 2 years old through hospital-based surveillance in Singapore.


Eligibility: Inclusion Criteria:
  -  A male or female infant aged < 24months at the time of diagnosis of intussusception.
  -  Subject is diagnosed with definite, probable, possible, suspected intussusception during the period of at least one year beginning at study start.
  -  Written informed consent obtained from the parent or guardian of the subject.
  Exclusion Criteria:
  -  A male or female infant ≥ 24 months of age at the time of intussusception diagnosis.
  -  The subject has had a radiographically or surgically confirmed case of intussusception prior to the current episode.

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: High-Dose 3F8/GM-CSF Immunotherapy Plus 13-Cis-Retinoic Acid for Consolidation of First Remission After Myeloablative Therapy and Autologous Stem-Cell Transplantation

Summary: The purpose of this study is to see if high-dose 3F8 combined with GM-CSF is better than standard dose 3F8 in treating neuroblastoma. Another purpose of the study is to find out what effects, good and/or bad, 3F8 has on cancer. The investigators also want to see if the antibody works against a very small amount of neuroblastoma (minimal residual disease) that is left in the bone marrow.


Eligibility: Inclusion Criteria:
  -  Diagnosis of NB as defined by a) histopathology (confirmed by the MSKCC Department of Pathology), or b) BM metastases or MIBG-avid lesion(s) plus high urine catecholamine levels.
  -  High-risk NB as defined by risk-related treatment guidelines1 and the International NB Staging System,89 i.e., stage 4 with (any age) or without (> or = to 18 months of age) MYCN amplification, MYCN-amplified stage 2 or stage 3 (any age), or MYCN-amplified stage 4S.
  -  The patients are post-stem cell transplantation and in first CR/VGPR, including no measurable MIBG-avid soft tissue tumor assessable for response.
  -  Signed informed consent indicating awareness of the investigational nature of this program.
  Exclusion Criteria:
  -  Creatinine > 3.0 mg/dL
  -  ALT, AST and Alkaline Phosphatase > 5.0 times the upper limit of normal
  -  Bilirubin > 3.0 mg/dL
  -  Patients with grade 3 or higher toxicities (using the CTCAE v3.0) related to cardiac, neurological, pulmonary or gastrointestinal function as determined by physical exam. Patients must have normal blood pressure for age.
  -  Progressive disease
  -  History of allergy to mouse proteins.
  -  Active life-threatening infection.
  -  Human anti-mouse antibody (HAMA) titer >1000 Elisa units/ml.
  -  Inability to comply with protocol requirements

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: 3F8/GM-CSF Immunotherapy Plus 13-Cis-Retinoic Acid for Consolidation of First Remission After Non-Myeloablative Therapy in Patients With High-Risk Neuroblastoma

Summary: The purpose of this study is to find out what effects, good and/or bad, the combination of 3F8 and GM-CSF has on the patient and the cancer.
  Antibodies are made by the body to attack tumors and to fight infections. 3F8 is the name of one kind of antibody. It is made by mice, and it can attack neuroblastoma in people. 3F8 has been used safely in many patients, and it has killed cancer cells in some patients. One way it can kill cancer cells is by causing the patient's own white blood cells to attack the cancer. Granulocytes are one kind of white blood cell. GM-CSF increases the number of granulocytes in people, and it makes the granulocytes better able to kill the cancer cells.


Eligibility: Inclusion Criteria:
  -  Diagnosis of NB as defined by a) histopathology (confirmed by the MSKCC Department of Pathology), or b) BM metastases or MIBG-avid lesion(s) plus high urine catecholamine levels.
  -  High-risk NB as defined by risk-related treatment guidelines1 and the International NB Staging System,89 i.e., stage 4 with (any age) or without (≥18 months of age) MYCN amplification, MYCN-amplified stage 2 or stage 3 (any age), or MYCN-amplified stage 4S.
  -  The patients are in first CR/VGPR after conventional therapy. They have no measurable MIBG-avid soft tissue tumor assessable for response.
  -  Signed informed consent indicating awareness of the investigational nature of this program.
  Exclusion Criteria:
  -  Creatinine > 3.0 mg/dL
  -  ALT, AST and Alkaline Phosphatase > 5.0 times the upper limit of normal
  -  Bilirubin > 3.0 mg/dL
  -  Patients with grade 3 or higher toxicities (using the CTCAE v3.0) related to cardiac, neurological, pulmonary or gastrointestinal function as determined by physical exam. Patients must have normal blood pressure for age.
  -  Progressive disease
  -  History of allergy to mouse proteins.
  -  Active life-threatening infection.
  -  Human anti-mouse antibody (HAMA) titer >1000 Elisa units/ml.
  -  Inability to comply with protocol requirements

Relevance to patient case: not relevant