araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 82-year-old male with glioma; genetic feature: BRAF

Clinical trial: The Oncopanel Pilot (TOP) Study

Summary: The BCCA Oncopanel is a clinical assay being developed to determine genotype status of a prospectively defined set of genes.
  The purpose of this pilot study is to assess the feasibility and effect on clinical-decision-making of the Oncopanel test. Eligible patients are those with advanced lung, colorectal, melanoma and GIST cancers and patients with diagnosed malignancies being considered for clinical trials.

Detailed description: Somatic mutations in solid tumors represent an established means of characterizing malignancies for prognostic, diagnostic and therapeutic purposes. Mutations in EGFR, KRAS, BRAF, and KIT and PDGFRA genes direct therapy in patients with advanced lung, colorectal, melanoma, and GIST tumors, respectively. Known or novel mutations in other genes may also be of clinical significance but are not identified by current genotyping offered to BC Cancer Agency (BCCA) patients. Furthermore, numerous candidate genes have been implicated as potential prognostic and predictive biomarkers in patients with solid tumours. As such, the Oncopanel is a clinical assay being developed to determine genotype status of a prospectively defined set of genes. The following clinically relevant set of genes and exons are included in the Oncpanel: KRAS, EGFR, BRAF, NRAS and HRAS, PIK3CA Signal Transduction Pathway Genes, RAS-RAF-MEK-MAPK Pathway, HER2, IDH1 and IDH2, ALK, TP53, c-KIT, STAT1&3 and PDGFRA. Additional testing on the tumour material will also include analysis of specific gene variants associated with adverse events or response to therapy.
  Numerous studies have documented the presence of circulating tumour DNA (ctDNA) among patients with advanced and early stage malignancies (20-22). The ability to diagnose standard cancer mutations with a blood-based assay (a "liquid biopsy") has not yet been established but presents obvious advantages. The emergence of "resistance" mutations arising in the metastatic tumor or throughout the course of therapy is well documented (21, 22). A blood biopsy may represent more accurate determination of the tumor's genetic features than archival DNA specimen. Adequate tissue specimens can be difficult to obtain from some patients with diagnosed malignancies, particularly lung cancer. A blood biopsy may represent a less invasive and timelier means of diagnosing both standard and translational cancer mutations.

Eligibility: Patients with archival tumor tissue and a known history of invasive malignancies are eligible if they meet one or more of the following criteria:
  -  Advanced colorectal cancer and eligible for standard KRAS testing,
  -  Advanced non-small cell lung cancer and eligible for standard EGFR testing,
  -  Advanced melanoma and eligible for standard BRAF testing,
  -  Gastrointestinal stromal tumors (GISTs) eligible for standard c-KIT and PDGFRA testing,
  -  Being considered for potential eligibility in clinical trial.

Relevance to patient case: not relevant
Patient case: 82-year-old male with glioma; genetic feature: BRAF

Clinical trial: Interdisciplinary Specialised Rehabilitation Among Glioma Patients

Summary: The results of the present RCT study will add to the growing body of literature investigating the potential role of exercise as a supportive therapeutic intervention for patient with glioma.

Detailed description: Gliomas are the most frequent primary neoplasm in the CNS and according to the World Health Organization histologically categorized into low-grade glioma (LGG) (WHO grades I/II) or high-grade glioma (HGG) (WHO grades III/IV). Gliomas are among the biggest challenges within the field of neuro-rehabilitation and oncology, and optimising treatment by improving QoL, function and cognition is of major clinical importance in this population. Because the majority of patients cannot be cured, clinical cancer research traditionally have focused on prolonging survival, exposing relapse or optimising the response to the medical treatment. Today there is a general consensus that health-related quality of life (HRQoL) is important in the evaluation of new treatments. However, research in HRQoL among patients with gliomas is scarce compared to the other categories of patients with tumors. In recent years have exercise become an important part of cancer treatment. The effects is well documented in studies among other cancer patients than gliomas and includes improvements of quality of life, physical function, reduce fatigue and thereby supports daily activities among cancer patients'. Inpatient rehabilitation studies among glioma patients have also indicated improved HRQoL and functional measurements such as activity of daily life, mobility and cognition. Despite of this rehabilitation efforts is still not emphasized in this population and recent literature concludes that there are no well-designed clinical studies examining the effect of multidisciplinary rehabilitation among Glioma patients. This study is the first to investigate the effect of an intensive specialised interdisciplinary outpatient rehabilitation program among gliomas patients.

Eligibility: Inclusion Criteria:
  -  Diagnosis of primary glioma (WHO grades I-IV)
  -  Age ≥ 18
  -  Reference with diagnosis or treatment at Odense University Hospital
  -  Karnofsky performance score (KPS) ≥70
  -  Ability to understand Danish.
  Exclusion Criteria:
  -  Pregnancy
  -  Known psychiatric diagnosis or substance abuse
  -  Heart problems excluding intense exercise (NYHA group III and IV)
  -  Pronounced impressive/expressive aphasia

Relevance to patient case: not relevant
Patient case: 82-year-old male with glioma; genetic feature: BRAF

Clinical trial: Use of Exome Sequence Analysis and Circulating Tumour in Assessing Tumour Heterogeneity in BRAF Mutant Melanoma

Summary: Despite recent advances in cancer treatment, little impact has been made on curing as opposed to controlling cancers over the last several decades. Part of the problem is that investigators have an incomplete understanding of how tumours behave as they evolve and in response to treatment. In this trial, the investigators hope to better understand the evolution of BRAF melanoma in response to drugs a patient may have received such as vemurafenib or dabrafenib. Importantly, the investigators want to understand how the tumours evolve resistance to these drugs and whether this can be predicted through blood tests, in particular of the circulating tumour DNA.

Detailed description: Study population: BRAF mutant melanoma patients
  Pre-mortem bloods will be taken from the patient on three occasions at one to thirty days apart from each other, with the first blood draw taking place on the patient's first clinic visit. Six 7 ml EDTA and one 6 ml SST vacutainers of blood (a total of approx. 50 ml of blood) will be taken from the patient.
  When death is expected within the next 48-72 hours, the Medical Oncologist/ Radiation Oncologist/ Hematologist OR delegate will revisit the RAP process with the patient and/or family/substitute decision maker to ensure that they are still in agreement. The patient and the families will also be provided with an additional consent form for participation including blood sampling.

Eligibility: Inclusion Criteria:
  UHN adult patient with BRAF mutant melanoma
  Exclusion Criteria:
  Non BRAF mutant melanoma patient Pediatric patient Non-UHN patient

Relevance to patient case: not relevant
Patient case: 82-year-old male with glioma; genetic feature: BRAF

Clinical trial: Study of Trametinib and Nab-paclitaxel in Patients With Melanoma

Summary: This study will investigate the combination of two drugs, trametinib and nab-paclitaxel, in patients with advanced unresectable or metastatic melanoma. Each drug has shown activity in trials of patients with melanoma. However, the combination of these two drugs has not been studied. In this trial the investigators will determine the maximum dose of the drug combination to be administered to patients with advanced unresectable or metastatic melanoma and examine the safety profile of the drug combination.

Detailed description: While treatment for melanoma has evolved in the last few years, advanced/metastatic melanoma remains an aggressive disease with poor prognosis. Trametinib and nab-paclitaxel have demonstrated single-agent activity in Phase III trials of patients with melanoma. The investigators propose to investigate this drug combination in patients with advanced unresectable or metastatic melanoma. This open-label Phase I study is designed to determine the maximum tolerated dose (MTD), recommended Phase II dose (RP2D), and safety profile of trametinib and nab-paclitaxel given in combination. Patients with melanoma and known BRAF mutation status will receive escalating doses of trametinib and nab-paclitaxel to determine the MTD. Once the MTD is determined an additional 6 patients will be treated at the MTD to establish the dose for future studies.

Eligibility: Inclusion Criteria:
  -  Adults (≥18 years) with histologically or cytologically-confirmed advanced unresectable or metastatic melanoma. BRAF mutation-positive and wild-type tumors are allowed.
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1
  -  Adequate hematologic, renal, and hepatic function
  -  Life expectancy ≥12 weeks
  -  Any pre-existing neuropathy must be <grade 2 per Common Technology Criteria for Adverse Events (CTCAE) version 4.0
  Exclusion Criteria:
  -  More than 1 prior cytotoxic chemotherapy regimen in the metastatic setting
  -  Prior MEK inhibitor therapy (prior BRAF inhibitor allowed)
  -  Prior nab-paclitaxel (prior taxane allowed)
  -  Use of an investigational anti-cancer drug within 21 days or 5 half-lives (whichever is shorter) prior to first dose. A minimum of 10 days after termination of investigational drug is required. Any drug-related toxicity should have resolved to Grade 1 or baseline.
  -  Symptomatic or untreated brain metastases
  -  History of retinal vein occlusion (RVO)

Relevance to patient case: possibly relevant
Patient case: 82-year-old male with glioma; genetic feature: BRAF

Clinical trial: Low-dose Aspirin Therapy for Esophageal Cancer

Summary: The aim of this study is to evaluate the survival benefit of low-dose aspirin use for stage II-III esophageal cancer patients.

Detailed description: The investigators aimed to evaluate the hypothesis that low-dose aspirin can improve survival in stage II-III esophageal cancer patients, and to evaluate whether this effect is influenced by PIK3CA, KRAS, BRAF mutation and COX-2 expression. Eligible participants will be randomized to either aspirin treatment arm (100 mg aspirin OD for 3 years), or non-aspirin user arm in 1:1 ratio. After randomization, participants will receive 3 monthly assessments during treatment and follow-up.

Eligibility: Inclusion Criteria:
  1. Male or female subjects with an age of 18 years or older.
  2. Subjects with Stage II-III histological proven esophageal cancer.
  3. Subjects with performance status (PS) of 0-1 or ECOG performance status 0-2.
  4. Subjects must have signed an approved informed consent prior to any study procedures.
  5. Subjects with adequate bone marrow, hepatic and renal functions, with a) neutrophils ≥ 1.5x109/ L; platelets ≥ 100x109/L; hemoglobin ≥ 9g/dL; b) Total bilirubin ≤ 2.0 x the upper limit normal; ALT and AST ≤ 2.5 x ULN (≤ 5 x ULN in case of liver metastasis); c) creatinine clearance > 50 ml/min;
  6. Subjects undergone complete resection of primary tumor;
  7. Subjects with life expectancy ≥ 3 months.
  8. Completed standard therapy ( at least 3 months of chemotherapy ± radiotherapy )
  9. Within 120 days of completion of standard therapy (surgery, chemotherapy ± radiotherapy)
  Exclusion Criteria:
  1. Subjects with haemorrhagic diathesis (i.e. haemophilia).
  2. Subjects with prior malignant tumors except for esophageal cancers in the past 5 years.
  3. Subjects with documented or suspected central nervous system metastases.
  4. Subjects with serious, nonhealing wound, ulcer, or bone fracture.
  5. Subjects with a history of stroke, coronary arterial disease, angina, or vascular disease.
  6. Subjects who are pregnant, lactating, or not using adequate contraception.
  7. Subjects who have known allergy to NSAID or Aspirin.
  8. Subjects receiving other antiplatelet agents (i.e. clopidogrel, ticlopidine) or anticoagulants (i.e. warfarin, low molecular weight heparins).
  9. Subjects receiving current long term treatment (≥ 1 month) with Aspirin or other NSAIDs.
  10. Subject unwilling or unable to comply with study requirements.

Relevance to patient case: not relevant
Patient case: 82-year-old male with glioma; genetic feature: BRAF

Clinical trial: 68Ga-NOTA-NFB: Radiation Dosimetry in Healthy Volunteers and Applications in Glioma Patients or Breast Cancer Patients

Summary: The purpose of this study is to assess the safety, biodistribution, dosimetric properties of the positron emission tomography (PET) radiopharmaceutical agent 68Ga-NOTA-NFB. To preliminarily evaluate its application in glioma diagnosis.
  To assess the application of 68Ga-NOTA-NFB PET/CT in the evaluation of the neoadjuvant chemotherapy in patients with breast cancer before and after the therapy.

Detailed description: 6 healthy volunteers with whole-body PET/CT scans 0, 0.5, 1.0, 2.0, and 3.0 hours after tracer injection (mean dose, 4.93 ± 0.10 mCi) will be performed. During the imaging period, 1 mL blood samples will be obtained specifically at 1, 3, 5, 10, 30,60, 90, 120, 150, and 180 minutes after the injection, for time-activity curve calculations. The estimated radiation doses will be calculated by using OLINDA/EXM software.
  8-10 patients with glioma will be enrolled for the clinical study of diagnosing glioma, they will be performed with both 68Ga-NOTA-NFB PET/CT and18F-FDG PET/CT scans before surgery. The preoperative images are compared and correlated with the pathologically report. Next, the expression of CXCR4 will be determined by immunohistochemical staining of the resected brain tumor tissues.
  30 patients with breast cancer will be underwent 68Ga-NOTA-NFB PET/CT and18F-FDG PET/CT scans before and after the neoadjuvant chemotherapy. SUV of lesions before and after therapy will be contrasted.

Eligibility: Inclusion Criteria:
  -  volunteers : healthy patients with glioma: diagnosed by MR and ready for surgery patients with breast: cancer appropritate of neoadjuvant chemotherapy.
  Exclusion Criteria:
  -  patients with glioma: refuse or cannot endure surgery. patients with breast: refuse neoadjuvant chemotherapy.

Relevance to patient case: not relevant
Patient case: 82-year-old male with glioma; genetic feature: BRAF

Clinical trial: A Trial of Trametinib and Panitumumab in RAS/RAF Wild Type Advanced Colorectal Cancer

Summary: This is a phase 2 study (the second phase in testing a new drug or drug combination) to see how useful the combination of two drugs, panitumumab and trametinib, are in patients with advanced colorectal cancer with KRAS, NRAS, or BRAF wild type (genes that are not mutated).
  Panitumumab is a drug that is approved by Health Canada for the treatment of advanced colorectal cancer with KRAS wild type. Panitumumab works by binding to and blocking the protein, epidermal growth factor receptor (EGFR) from working.
  Trametinib is a drug that is approved by Health Canada for the treatment of melanoma with a mutation in the BRAF gene. Trametinib works by binding to and blocking mitogen-activated protein kinase kinase (MEK) 1 and MEK2 from working.
  Previous studies have shown that the combination of panitumumab and trametinib may be more useful in KRAS, NRAS, or BRAF wild type colorectal cancer.


Eligibility: Inclusion Criteria:
  -  18 years of age or older
  -  KRAS/NRAS/BRAF wild type colorectal cancer, not responsive to standard therapies, no approved or curative therapy, refuse standard therapy
  -  Prior 5-FU, oxaliplatin and irinotecan
  -  ECOG Performance Status of 0 or 1
  -  Able to swallow/retain oral drugs
  -  Able and agree to have provide tumor tissue/have biopsies
  -  Agree to use contraception
  -  Not pregnant
  -  Adequate organ system function
  Exclusion Criteria:
  -  Chemotherapy, radiotherapy, immunotherapy, or other anti-cancer therapies <28 days or 5 half lives
  -  Prior EGFR, MEK, or RAF inhibitor or regorafenib
  -  Current use of prohibited medications
  -  Unresolved side effects
  -  GI disease or other condition affecting GI absorption
  -  Mucosal or internal bleeding
  -  Any major surgery <four weeks
  -  HIV, HBV, or HCV positive
  -  Active infection
  -  Leptomeningeal disease
  -  Brain metastases
  -  Unacceptable QTcF interval
  -  Significant uncontrolled arrhythmias
  -  Acute coronary syndromes, myocardial infarction, coronary angioplasty, or stenting or bypass grafting < 6 mos.
  -  Class II, III, or IV heart failure
  -  Other clinically significant ECGs
  -  Intra - cardiac defibrillators
  -  Cardiac metastases
  -  Condition that may interfere with patient safety
  -  Hypersensitivity to study drugs
  -  Severe or uncontrolled systemic diseases
  -  Pregnant or lactating
  -  Retinal vein occlusion
  -  Interstitial lung disease or pneumonitis
  -  Active liver or biliary disease

Relevance to patient case: possibly relevant
Patient case: 82-year-old male with glioma; genetic feature: BRAF

Clinical trial: Trial of Vemurafenib and Cobimetinib in Patients With Advanced BRAFV600 Mutant Melanoma

Summary: This trial explores the immunologic effects of vemurafenib (BRAF inhibitor) and cobimetinib (MEK inhibitor), administered alone and in combination, to patients with advanced BRAF V600E/K mutant melanoma.


Eligibility: Inclusion Criteria:
  -  Signed informed consent
  -  Signed HIV testing consent
  -  Life expectancy ≥ 12 weeks
  -  Able to swallow pills
  -  ECOG performance status 2 or less
  -  Adequate bone marrow function
  -  Adequate renal function
  -  Adequate liver function
  -  Negative urine pregnancy test within 7 days prior to commencement of dosing in premenopausal women
  -  Histological diagnosis of unresectable AJCC stage III or stage IV, BRAFV600E/K mutant melanoma
  -  Measurable disease
  -  Accessible tumor that can be biopsied
  -  Naive to targeted therapy (Prior immune-based therapy in the adjuvant setting or for advanced disease will be allowed if >2 weeks from study entry)
  Exclusion Criteria:
  -  Active systemic infection
  -  Active autoimmune disease or history of known or suspected autoimmune disease
  -  Active brain metastases or leptomeningeal metastases
  -  Treatment with any immunomodulatory medication within 4 weeks of initiation of study therapy.
  -  Positive test for hepatitis B virus
  -  Positive test for hepatitis C virus
  -  Positive test for human immunodeficiency virus (HIV)
  -  Pregnant, lactating or breast feeding women
  -  Localized radiation therapy within the last 14 days
  -  History of malabsorption
  -  No consumption of the following within 7 days prior to start of treatment:
  -  St. John's wort or hyperforin (potent cytochrome P450 CYP3A4 enzyme inducer)
  -  Grapefruit juice (potent cytochrome P450 CYP3A4 enzyme inhibitor
  -  History or evidence of cardiovascular risk
  -  History or evidence of retinal pathology

Relevance to patient case: possibly relevant
Patient case: 82-year-old male with glioma; genetic feature: BRAF

Clinical trial: Circulating Cell-free Tumor DNA in the Plasma of Patients With Gastrointestinal Stromal Tumors (GIST)

Summary: This observational study is proposed to evaluate if the trend in the levels of cf-DNA evaluated on a sample of peripheral blood may be related to different clinical behaviors of the disease monitored by radiological investigations conducted.

Detailed description: Demetri and colleagues presented, at the AACR and ASCO Annual Meeting 2013, an exploratory analysis to assess GIST genotypes on patients in the GRID study. Mutations in the KIT gene were detected in 58 percent of the blood samples compared with 66 percent of the tumor tissue samples (31). However, when focusing their analysis on secondary KIT mutations, which are the mutations that drive resistance to targeted therapies like imatinib and sunitinib, the researchers found mutations in 47 percent of blood samples compared with only 12 percent of tissue samples. In addition, nearly half of blood samples in which secondary KIT mutations were found, harbored multiple secondary mutations. Therefore, cf-DNA may become an efficient marker of mutational GIST status and disease itself.
  On this basis, this trial aims to evaluate whether tumor DNA carrying mutations (for KIT, PDGFRα, BRAF, RAS, SDH) can be detected and quantified in the plasma of patients with GISTs, either with active disease or during follow-up, and whether detection can be correlated with the disease status.

Eligibility: -  Male or female patients aged >= 18 years
  -  Histologically confirmed diagnosis of GIST of any anatomical location either by biopsy or surgical specimen
  -  Available archival tumor tissue
  -  Signed informed consent form
  Exclusion Criteria:
  -  Impossibility to ensure adequate clinical and serum sample follow-up
  -  Serious psychiatric disease that precludes informed consent or limits compliance

Relevance to patient case: not relevant
Patient case: 82-year-old male with glioma; genetic feature: BRAF

Clinical trial: Single-arm Study to Evaluate the Safety and Efficacy of Sorafenib, in Subjects With BRAF Mutation Refractory Solid Tumors

Summary: This is a pilot study of sorafenib in patients with BRAF Mutation Refractory Solid Tumors.
  This study is a single-arm, pilot study of sorafenib in patients with Refractory Solid Tumors harboring BRAF Mutation Sorafenib 400 mg will be administered orally twice a day for 28 days.
  To investigate the efficacy of sorafenib in patients with Refractory Solid Tumors harboring BRAF Mutation.


Eligibility: Inclusion Criteria:
  1. Provision of fully informed consent prior to any study specific procedures.
  2. Patients must be ≥20 years of age.
  3. BRAF mutation Refractory Solid Tumors that has recurred or progressed following standard therapy, or that has not responded to standard therapy, or for which there is no standard therapy.
  4. ECOG performance status 0-2.
  5. Have measurable or evaluated disease based on RECIST1.1. as determined by investigator.
  6. Adequate Organ Function Laboratory Values
  -  Absolute neutrophil count ≥ 1.5 x 109/L, Hemoglobin ≥ 9g/dL, Platelets ≥ 100 x 109/L
  -  bilirubin ≤ 1.5 x upper limit of normal AST/ALT ≤ 2.5 x upper limit of normal (5.0 X upper limit of normal , for subjects with liver metastases)
  -  creatinine ≤1.5 x UNL
  7. Patients of child-bearing potential should be using adequate contraceptive measures (two forms of highly reliable methods) should not be breast feeding and must have a negative pregnancy test prior to start of dosing.
  8. Adequate heart function.
  Exclusion Criteria:
  1. Patients with second primary cancer, except: adequately treated non-melanoma skin cancer, curatively treated in-situ cancer of the cervix, or other solid tumours curatively treated with no evidence of disease for ≤3 years.
  2. Has known active central nervous system (CNS) metastases.
  3. Has an active infection requiring systemic therapy.
  4. Pregnancy or breast feeding
  5. Patients with cardiac problem.
  6. Any previous treatment with sorafenib

Relevance to patient case: possibly relevant