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

Clinical trial: Biomarkers in Tissue Samples From Patients With Ewing Sarcoma

Summary: RATIONALE: Studying samples of tissue 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 understand how well patients respond to treatment.
  PURPOSE: This research study is studying biomarkers in tissue samples from patients with Ewing sarcoma.

Detailed description: OBJECTIVES:
  -  To describe the spectrum of GGAA-microsatellite polymorphisms at specific loci in genomic DNA prepared from Ewing sarcoma tumor specimens.
  -  To determine if there are differences in GGAA-microsatellite polymorphisms in genomic DNA prepared from Ewing sarcoma tumor specimens as compared to non-afflicted European and African normal genomic DNA.
  -  To determine if GGAA-microsatellite polymorphisms at specific loci in genomic DNA prepared from Ewing's sarcoma tumor specimens correlates with disease outcome in patients treated on COG protocol AEWS0031.
  -  To determine whether whole-genome amplification introduces alterations in GGAA-microsatellites as compared to non-amplified genomic DNA.
  OUTLINE: Genomic PCR is used to amplify the microsatellites in the NR0B1 and GSTM4 promoters. In addition to determining microsatellite size, each microsatellite is sequenced following cloning into the pCR4 vector (Invitrogen) using standard topoisomerase cloning protocols.

Eligibility: DISEASE CHARACTERISTICS:
  -  Specimens from patients with Ewing sarcoma used for protocol COG-AEWS08B1
  -  Obtained from patient samples taken from patients enrolled on COG-AEWS0031
  -  Whole genome-amplified DNA will be used
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

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

Clinical trial: A Prospective Observational Study Evaluating c-MET Expression and EGFR Gene Mutation Correlation With Erlotinib Response

Summary: 1. Trial design: Prospective observational study
  2. Target population: 200 NSCLC patients with histologically or cytologically confirmed stage IV or recurrent NSCLC who have progressive disease after 1st line chemotherapy who consent for study participation and meet the study selection criteria
  3. Primary objective: To investigate C-met expression/amplification and EGFR gene mutations in NSCLC patients treated with Erlotinib
  -  C-met expression by IHC C-met amplification by SISH EGFR mutation by real time PCR
  4. We will also assess the correlation of EGFR mutations and c-MET with clinical outcome (Overall Response Rate, Progression Free survival )
  5. Duration of Trial Recruitment: 2 years


Eligibility: Inclusion Criteria:
  -  Informed consent
  -  19~80 year old male or female
  -  Histologically proven advanced or metastatic NSCLC
  -  Failed to 1st line chemotherapy
  -  Tumor tissue for genetic analysis
  -  Evaluable target lesion by RECIST v1.1
  -  ECOG performance from 0 to 3
  -  Expected survival more than 12 weeks
  Exclusion Criteria:
  -  Previous treatment of EGFR-tyrosine kinase inhibitors
  -  Severe hypersensitivity to erlotinib
  -  Residual toxicities (above grade 2) after previous chemotherapy
  -  Total bilirubin more than 1.5x of upper normal limit Liver function tests more than 2.5x of upper normal limits

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

Clinical trial: Studying Genes in Tissue Samples From Younger and Adolescent Patients With Soft Tissue Sarcomas

Summary: This research trial studies genes in tissue samples from younger and adolescent patients with soft tissue sarcomas. Studying samples of 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 find better ways to treat cancer

Detailed description: Study Subtype: Ancillary/Correlative Observational Study Model: Cohort Time Perspective: Retrospective Biospecimen Retention: Samples With DNA Biospecimen Description: Tissue Study Population Description: Existing NRSTS samples from the COG D9902/ARST0332 studies Sampling Method: Non-Probability Sample
  OBJECTIVES:
  I. To determine the frequency with which actionable mutations are found in archived non-rhabdomyosarcoma soft tissue sarcoma (NRSTS) tumor specimens using mass spectrometry (MS) analysis of tumor-derived deoxyribonucleic acid (DNA).
  OUTLINE:
  Archived DNA tissue samples are analyzed for frequency of genetic mutations, including single nucleotide polymorphisms (SNPs), single nucleotide variants (SNVs), and small deletions and/or insertions, by polymerase chain reaction (PCR) and mass spectometry (Sequenom MassARRAY). Results are then analyzed to determine whether specific mutations correlate with patient or disease features such as tumor stage, histological grade, or outcome.

Eligibility: Inclusion Criteria:
  -  Archived non-rhabdomyosarcoma soft tissue sarcoma (NRSTS) tumor-derived DNA
  -  Synovial sarcoma, malignant peripheral nerve sheath tumor (MPNST), soft tissue sarcoma not otherwise specified (NOS), or other less common pediatric NRSTS
  -  Formalin-fixed, paraffin-embedded (FFPE) tissue from patients enrolled on:
  -  COG-D9902 Soft Tissue Sarcoma (STS) Biology and Banking Protocol
  -  COG-ARST0332 A Risk-Based Treatment for Pediatric NRSTS Study
  -  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: A Study of RO5045337 in Combination With Doxorubicin in Patients With Soft Tissue Sarcoma

Summary: This multicenter, open-label, Phase 1b study will evaluate the safety, pharmacokinetics and efficacy of RO5045337 in combination with doxorubicin in patients with soft tissue sarcoma. Cohorts of patients will receive escalating doses of RO5045337 orally on Days 1-5 (1-3) of each 28-day cycle in combination with doxorubicin 60 mg/m2 intravenously on Day 1 of each cycle for up to 6 cycles.


Eligibility: Inclusion Criteria:
  -  Adult patients, >/= 18 years of age
  -  Histologically or cytologically confirmed soft tissue sarcoma
  -  Evaluable disease according to RECIST version 1.1 criteria
  -  Eastern Cooperative Oncology Group (ECOG) performance status 0 to 1
  -  Eligible for doxorubicin therapy
  -  Acute toxicities from prior anti-tumor therapy, surgery or radiotherapy must have resolved to NCI-CTCAE Grade </= 1 prior to start of study
  -  Adequate bone marrow, hepatic and renal function
  -  Patients with stable CNS metastases are eligible
  Exclusion Criteria:
  -  Previous treatment with limiting doses of doxorubicin
  -  Patients receiving any other investigational or commercial agents or therapies administered with the intention to treat their malignancy or other ailment </= 28 days from Day 1 dosing on study treatment
  -  History of seizure disorders or unstable CNS metastases
  -  Severe and/or uncontrolled medical conditions or other conditions that could affect the participation in the study
  -  Pregnant or breastfeeding women
  -  HIV positive patients who are currently receiving combination anti-retroviral therapy
  -  Patients with known coagulopathy, platelet disorder or history of non-drug induced thrombocytopenia
  -  Patients receiving oral or parenteral anti-coagulants/anti-platelet agents

Relevance to patient case: possibly relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: Uncovering Potential Breast Cancer Biomarkers Amp; Possible Drug Targets Using Advanced Quantitative Mass Spectrometry

Summary: The purpose of this study is to evaluate the use of advanced quantitative mass spectometry (Super SILAC) as a discovery platform to uncover novel protein biomarkers in tumor and to compare the protein profile between different subtypes of breast cancer (ER positive, HER2 positive, triple negative). A maximum of 100 breast tumor specimens will be obtained from the NUHS Tissue repository, comprising approximately equal proportion of ER positive, HER2 positive, and triple negative tumors. Samples will be analyzed using advanced Mass Spectrometry (Super SILAC) as a discovery platform to identify novel protein biomarkers that may be important in cancer. DNA and RNA will also be extracted from tumor samples for correlative analysis with the proteomics data. Genomics and proteomics data will be correlated with clinical data including treatment response and survival data. Importance of proposed research to science or medicine:Identification of tumor biomarkers may allow better prognostication, follow-up, and selection of treatment for cancer patients in the future. Potential benefits and risks: No direct benefit to the patient. Risk to the subjects is minimal as there is no direct patient contact, and analysis is done on previously donated tumor samples. Patients have previously provided consent to donate their samples for research into the NUHS Tissue Repository.
  Novel tumor biomarkers that determine tumor biology, including prognosis and treatment sensitivity, may be detectable using the novel advanced quantitative mass spectromy method (Super SILAC). Different subtypes of breast cancers will have different proteomic profiles analyzed using super SILAC.


Eligibility: Inclusion Criteria:
  -  Patients with breast cancer

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

Clinical trial: An Extension Study of RO5045337 in Participants Participating in Previous Roche-sponsored Cancer Studies

Summary: This open-label, extension study is designed to provide continuing treatment with RO5045337 to participants who have completed parent studies NO21279 (NCT00623870), NO21280 (NCT00559533), NP25299 (NCT01164033), NP28021 (NCT01605526) or NP28023 (NCT01635296). Participants are eligible to participate in this study if they have completed required Phase 1 study assessments for primary objectives of respective parent protocol and are having evidence of clinical benefit (as defined by the parent protocol). Participants will continue the most similar dose and formulation available (which does not exceed the maximum tolerated dose [MTD] or the maximum safely administered dose for that formulation during Phase 1) and the same schedule of RO5045337 treatment that they were receiving at the time of transitioning from the parent clinical study protocol.


Eligibility: Inclusion Criteria:
  -  Participants must meet the inclusion criteria outlined in the respective parent protocols: NO21279 (NCT00623870), NO21280 (NCT00559533), NP25299 (NCT01164033), NP28021 (NCT01605526) or NP28023 (NCT01635296)
  -  Participants must have completed one of the following clinical study protocols and have been determined to have clinical benefit on treatment at the conclusion of required study analyses as defined in the respective parent protocols: NO21279 (NCT00623870), NO21280 (NCT00559533), NP25299 (NCT01164033), NP28021 (NCT01605526) or NP28023 (NCT01635296)
  Exclusion Criteria:
  -  Participants must meet the exclusion criteria outlined in the respective parent protocols: NO21279 (NCT00623870), NO21280 (NCT00559533), NP25299 (NCT01164033), NP28021 (NCT01605526) or NP28023 (NCT01635296)
  -  Participants who developed disease progression/ requiring other anti-tumor therapy while in the parent protocol
  -  Participants who have stopped study drug dosing for greater than 56 days
  -  Participants continuing to require dose modifications
  -  Participants with worsening adverse events
  -  Participants with unrelated adverse events, medical illnesses, or changes in performance status that, per investigator discretion, put them at high risk for continuing participation in the clinical study

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

Clinical trial: A Phase 1 Study Evaluating AMG 232 in Advanced Solid Tumors or Multiple Myeloma

Summary: First in human, open-label, sequential dose escalation and expansion study of AMG 232 in subjects with advanced solid tumors or multiple myeloma

Detailed description: Study Design: This is an open-label, dose exploration study evaluating AMG 232 in subjects with advanced p53WT solid tumors or multiple myeloma. The study will be conducted in 2 parts: Part 1 - Dose Exploration (parts 1a, 1b and 1c) and Part 2 - Dose Expansion. Part 1a is aimed at evaluating the safety, tolerability, PK and PD of AMG 232 and determining the MTD of a 7-day once daily (QD) dosing schedule in subjects with advanced solid tumors using a practical continuous reassessment method (CRM). Part 1b will evaluate the safety and tolerability of 3-day QD dosing schedule (or alternate dosing schedule based upon emerging data) with a particular emphasis on evaluating the tolerability of daily doses equal to or higher than the part 1a MTD in subjects with solid tumors or multiple myeloma. Part 1c will evaluate the safety and tolerability of 7-day twice daily (BID) dosing schedule with daily cumulative doses equal to or higher than the part 1a MTD in subjects with solid tumors. The dose expansion part of the study (Part 2) can open once the MTD has been determined in Part 1a. Part 2, part 1b and part 1c can be explored in parallel. The dose expansion part will consist of up to 85 additional subjects with specific tumors harboring MDM2 amplification (liposarcoma [LPS], gliobastoma [ GBM ] and all other solid tumors) or potentially harboring MDM2 overexpression (ER+ metastatic breast cancer) and a group of subjects with multiple myeloma.

Eligibility: Inclusion Criteria:
  -  Men or women > 18 years old
  -  Pathologically documented, definitively diagnosed, advanced solid tumor that is refractory to standard treatment, or which no standard therapy is available, or the subject refuses standard therapy or multiple myeloma
  -  Willing to undergo pre-dose core needle tumor biopsies or bone marrow aspirate for subjects with multiple myeloma.
  -  Ability to take oral medications and willing to record daily adherance to investigational product
  -  Adequate hematological, renal, hepatic, and coagulation laboratory assessments
  Exclusion Criteria:
  -  Active brain metastases
  -  For solid tumor-History or presence of hematological malignancies unless curatively treated with no evidence of disease for greater than or equal to 5 years
  -  Active infection requiring intravenous (IV) antibiotics
  -  Anti-tumor therapy
  -  Therapeutic or palliative radiation therapy within 30 days of starting treatment
  -  Currently enrolled in another investigational device or drug study

Relevance to patient case: possibly relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: A Phase I Dose Escalation Study of CGM097 in Adult Patients With Selected Advanced Solid Tumors

Summary: This is a first in human phase I study of single agent CGM097 in patients with advanced solid tumors who have progressed despite standard therapy or for whom no standard therapy exists. The tumor must be characterized by p53wt status. The study consists of a dose escalation part where patients will receive escalating doses of CGM097, and a dose expansion part in which patients are given CGM097 at the maximum tolerated dose (MTD) or Recommended Phase 2 Dose (RP2D). Each dose escalation step will be decided based on the recommendation from an adaptive Bayesian logistic regression model (BLRM).

Detailed description: This is a multi-center, open-label, dose finding, phase I study of single agent CGM097, administered in patients with advanced solid tumors who have progressed despite standard therapy or for whom no standard therapy exists. Patients' tumors must be characterized by p53wt status.
  The study consists of a dose escalation part, where cohorts of three to six newly enrolled patients will receive escalating doses of CGM097, and a dose expansion part, in which patients are given CGM097 the maximum tolerated dose (MTD) or Recommended Phase 2 Dose (RP2D). Novartis and the site investigators will jointly decide on each dose escalation step based on the recommendation from an adaptive Bayesian logistic regression model (BLRM). If safety data should indicate a lower increment than suggested by the BLRM, the next dose level (DL) will be adjusted accordingly.

Eligibility: Inclusion Criteria:
  -  Patient has advanced solid malignancy that has progressed despite standard therapy, or for which no effective standard therapy exists
  -  Tumor of the patient is p53wt
  -  Evaluable disease as determined by RECIST 1.1
  -  WHO performance status 0-2
  Exclusion criteria:
  -  Prior treatment with CGM097 or other p53/HDM2-interaction inhibitor
  -  Patient with symptomatic or growing CNS metastatic lesions
  -  Concurrent other malignancy
  -  Clinically significant cardiac disease as defined in the protocol
  -  Diagnosis of acute or chronic pancreatitis
  -  Concomitant therapy that precludes enrollment, as defined in the protocol
  -  Women of child-bearing potential, unless they are using highly effective methods of contraception during dosing and for 2 weeks after study drug discontinuation
  -  Pregnant or nursing women
  Other protocol-defined inclusion/exclusion criteria may apply.

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

Clinical trial: Genomic Profiling in Cancer Patients

Summary: The purpose of this study is to determine whether certain genes in cancer may be abnormal. When a gene is abnormal this is called a mutation. Most mutations in cancer cells are not inherited (passed down from parents) but happen after birth in the cancer itself. Most cancers have many mutations. Some of these mutations are important for the cancer cells to survive while others are not. The goal of this study is test cancer for certain mutations using leftover tumor tissue from a previous surgery or biopsy. Participants will also be asked to provide a tube of blood cheek (also known as a buccal) swab, or a saliva sample that contains normal genes for comparison.
  The purpose of Part B of this study is to:
  Understand how genetic changes in tumor effect the chance of responding to experimental cancer treatment. Understand how the genes in the tumor change overtime in response to targeted cancer treatment.


Eligibility: Inclusion Criteria:
  Part A:
  -  Patients with cancer or other related disorders
  Part B:
  -  Patients successfully registered to Part A of (MSKCC IRB # 12-245)
  -  Prior written approval for patient consent obtained from Director of the Center fo Molecular Oncology, or a Principal/Co-Principal Investigator of MSKCC IRB # 12-245.
  Part C:
  -  Patient must be receiving ongoing care at MSK. Treatment at an MSK Alliance Site does not qualify.
  -  Patient must have successfully consented to Part A of this study.
  Exclusion Criteria:
  -  Unwilling or unable to provide informed consent.

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

Clinical trial: Autologous Dendritic Cell Vaccine Loaded With Allogeneic Tumor Lysate Expression of Cancer Testis Antigens in Patients With Soft Tissue Sarcoma

Summary: The purpose of this study is to achieving a six-month progression free survival (PFS) of patients receiving autologous dendritic cell vaccine (ADKV) loaded with allogeneic tumor lysate expression of cancer-testis antigens (CTA) in patients with soft tissue sarcomas


Eligibility: Inclusion Criteria:
  -  age of 18 or older
  -  ECOG performance score 0 or 1
  -  Histologically proven soft tissue sarcoma
  -  Unresectable or metastatic soft tissue sarcoma
  -  Ability to give written informed consent
  -  Objective measured and measurable tumor lesions
  -  The failure of standard therapy
  -  Adequate amount of material for genetic research
  -  No active or chronic infection with HIV, Hepatitis B or Hepatitis C
  -  Men/Women of childbearing potential must use adequate contraception
  -  Hematology, liver function and renal function lab tests within required parameters
  Exclusion Criteria:
  -  Untreated or uncontrolled brain metastases.
  -  History of other active malignancy within last 2 years, except adequately treated other soft tissue sarcoma.
  -  Autoimmune disease (vitiligo is not a basis for exclusion).
  -  Serious uncontrolled medical disorder or active infection that would impede treatment.
  -  Underlying medical or psychiatric condition that would cause administration vaccine
  -  Any non-oncology vaccine therapy up to 1 month before or after any dose of vaccine
  -  Concomitant therapy with IL-2, interferon, other non-study immunotherapy, or cytotoxic chemotherapy; immune-suppressive agents within 30 days of registration; other investigational therapies; chronic use of systemic corticosteroids (however, a low stable dose steroid for mild brain edema or adrenal insufficiency is allowed; topical and inhaled standard dose corticosteroids are allowed).
  -  Dementia or significantly altered mental status that would prohibit understanding or rendering of informed consent and compliance with protocol requirements.
  -  Pregnant or breastfeeding women.
  -  Prisoners or subjects who are compulsorily detained (involuntarily incarcerated) for treatment of either a psychiatric or physical (e.g. infectious) illness.

Relevance to patient case: not relevant