araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 61-year-old male with melanoma; genetic feature: BRAF amplification

Clinical trial: An Observational Study of BRAF Inhibitors Effectiveness in Patients With Newly Diagnosed Metastatic Melanoma

Summary: This observational study will evaluate the effectiveness of BRAF inhibitors and current therapies in patients with newly diagnosed metastatic melanoma with or without BRAF V600 mutation. Patients will be treated per the locally approved therapeutic options in clinical practice. The observation period for each patient will be up to 24 months.


Eligibility: Inclusion Criteria:
  -  Adult patients, >/= 18 years of age at diagnosis
  -  Histologically confirmed new diagnosis of unresectable or metastatic melanoma
  -  Patients with tumor samples available for assessment of BRAF V600 mutation
  Exclusion Criteria:
  -  Prior systemic therapy for metastatic disease
  -  Participation in interventional clinical trials

Relevance to patient case: possibly relevant
Patient case: 61-year-old male with melanoma; genetic feature: BRAF amplification

Clinical trial: Study to Determine the Feasibility of Sentinel Node Biopsy in Patients With Anal Cancer

Summary: The purpose of this study is assess the technical and operational feasibility of a specialised biopsy technique, sentinel lymph node biopsy (SLNB), in patients with anal cancer.

Detailed description: SLNB is based on the premise that lymphatic dissemination from a tumour occurs in a stepwise fashion, with initial involvement of a primary node, called the sentinel node, before dissemination to the remainder of the lymphatic chain. If the sentinel node is histologically negative, then the remainder of the nodes in the same anatomic region will be at a lower (assumed to be minimal) risk of containing metastases. SLNB is part of standard care for patients with malignant melanoma and with breast cancer but has yet to be prospectively evaluated in patients with anal cancer.
  Currently, the standard way to treat patients with anal cancer is to deliver a combination of chemotherapy and radiation to the tumour at the anus together with 'preventative' (prophylactic) radiotherapy to the lymph glands of the groin and pelvis. There is a growing perception for the need to reduce the morbidity of radiotherapy i.e. current regimens over-treat the patient and one approach is to reduce radiotherapy volume and/or dose where there is an absence or very low risk of nodal metastases.
  This feasibility study is a vital first step in informing the design of a larger study examining the role of SLNB in clinical decision-making and outcomes for patients with anal cancer. In this trial eligible patients will attend for lymphoscintigraphy, to locate the lymph node, before sentinel lymph node removal by surgery. Detection rate of the sentinel node(s) will be the key outcome for the study.

Eligibility: Inclusion Criteria:
  -  Patients with squamous cell carcinoma (SCC) of the anus (any T size and/or those with recurrent disease)
  -  Equivocal lymph node involvement on standard CT staging or magnetic resonance (MR) staging or PET-CT scan, as determined by the anal cancer multidisciplinary team (MDT)
  -  Age >= 18 years
  -  Written informed consent provided by the patient
  Exclusion Criteria:
  -  Patients with unequivocal lymph node involvement on standard CT staging or MR staging, as determined by the anal cancer MDT.
  -  Unfit for surgical biopsy
  -  Patients undergoing palliative treatment
  -  Previous pelvic or inguinal area radiotherapy
  -  Other coincident cancers
  -  Previous inguinal surgery (e.g. hernia repair) with mesh insertion

Relevance to patient case: not relevant
Patient case: 61-year-old male with melanoma; genetic feature: BRAF amplification

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: 61-year-old male with melanoma; genetic feature: BRAF amplification

Clinical trial: Phase I-II Study With Tumor Molecular Pharmacodynamic (MPD) Evaluation and Pharmacokinetics of PD-0332991 in Patients Suffering Metastatic Melanoma

Summary: An open label multicentre, phase I-II study with tumour molecular pharmacodynamics (MPD) evaluation and pharmacokinetics of PD-0332991 added to vemurafenib in patients suffering metastatic melanoma with BR.
  The main objective is to establish the Maximum Tolerated Dose (MTD) of PD-0332991 when added to standard vemurafenib therapy (960 mg BID). The estimated MTD is defined as the dose of PD-0332991 combined with vemurafenib that will be associated with a prespecified proportion of patients experiencing a Dose-Limiting Toxicity (DLT), ie, 1/3.


Eligibility: Inclusion Criteria:
  -  Age > 18 years
  -  Stage IV or un-resectable stage III melanoma
  -  Presence of BRAF V600E/K mutation and CDNKN2A loss and expression of Rb using immunohistochemistry in a recent metastatic sample (< 6 months)
  -  A previous exposure to BRAF inhibitor or combination of BRAF and MEK inhibitors therapy is allowed unless it has been stopped more than 3 months before study enrolment(This will defined the two strata of the trial)
  -  No previous therapy by MEK inhibitor unless associated with BRAF inhibitors
  -  No previous therapy with the AKT/PI3K pathway inhibitor
  -  Patients should have a tumour available for repeated biopsies for pharmacodynamics evaluation
  -  Life expectancy of > 3 months
  -  ECOG performance status <2
  -  Signed informed consent
  -  Patient with health insurance coverage
  -  No patient under guardianship or curators
  Exclusion Criteria:
  -  Inadequate hepatic function defined as serum bilirubin>25 μmol/l, transaminases > 3.0 times the upper limit of normal (ULN) or 5ULN in cases of liver metastases;
  -  Inadequate bone marrow function defined as absolute neutrophil count<1500/mcl, platelets<150000/mcl and haemoglobin<8g/dL
  -  Inadequate renal function with serum creatinine>2.0mg/dl) and /or creatinine clearance< 60 ml/min
  -  Untreated brain metastases : Patients with brain metastases will be eligible if they have completed treatment 1 months prior to the start of study medication, have discontinued corticosteroid treatment for these metastases for at least 5 days, and are neurologically asymptomatic
  -  Myocardial infarct or unstable angina within the past 6 months
  -  Concomitant take of drugs known to be strong inhibitor or inducers of CYP314
  -  HIV positive.
  -  Chemotherapy, immunotherapy within 4 weeks
  -  Drugs interfering with PD-0332991 and vemurafenib metabolism
  -  Malabsorption syndrome or other condition that would interfere with enteral absorption
  -  Congenital long QT syndrome or screening QTc > 470 msec
  -  Need for chronic corticosteroid therapy of ≥10 mg of prednisone per day

Relevance to patient case: possibly relevant
Patient case: 61-year-old male with melanoma; genetic feature: BRAF amplification

Clinical trial: Pancreatic Cancer Early Detection Program

Summary: Early detection testing is recommended for individuals at elevated risk for the development of Pancreatic Cancer. This Protocol will define sufficiently elevated risk as either equal to or greater than five times the general population risk, or five times the average risk (1.5%) of developing pancreatic cancer by age 70; that is a 7.5% lifetime risk. Our inclusion criteria has a strong focus on the risk for pancreatic cancer imparted by the presence of hereditary cancer genes, as well as by family history. Enrolled subjects will undergo Endoscopic Ultrasound (EUS) alternating with Magnetic Resonance Imaging (MRI), every six to 12 months, for up to 5 years.

Detailed description: Interested individuals can be referred by physicians, or by family or friends.
  Individuals are informed that the purpose of this study is to collect outcome data following early detection testing based upon our criteria for elevated risk.
  Consent is obtained by any of the co-investigators. Consent is obtained for the primary PCEDP, and also obtained to allow for data to be used by our Cancer Program.
  We have a weekly review of all calls made and of all enrollments.
  We have a monthly meeting to review all proceeding regarding the study.
  Our IRB routinely reviews the proceedings of the study
  Our institution has a monthly Clinical research Committee meeting.

Eligibility: Inclusion Criteria: Any of the following:
  1. Known carrier of either the BRCA2 or CDKN2A mutation;
  2. Known carrier of any of the following mutations (BRCA1, MLH1, MSH2, PMS2, MSH6, EPCAM , P53, PALB2, APC, or ATM) PLUS first or second degree relative affected with pancreatic cancer;
  3. Individual with Peutz-Jeghers Syndrome;
  4. Familial Pancreatic Cancer, defined as at least two affected relatives with Pancreatic Cancer, who are first degree relatives with each other, and at least one of those affected must be first degree relative to the study subject;
  5. Both parents affected, any age:
  6. Any first degree relative diagnosed with pancreatic cancer under age 50;
  7. Chronic Pancreatitis Syndrome, defined by either PRSS1 or SPINK1 mutations AND appropriate clinical and family history
  Exclusion Criteria:
  1. Any medical condition that contraindicates endoscopy or biopsy
  2. Any medical condition that contraindicates MRI
  3. Status post partial or complete resection of the pancreas
  4. History of pancreatic cancer, either endocrine or exocrine
  5. Clinical suspicion of pancreatic cancer, or any previous radiographic or histologic diagnosis of a pre-malignant finding, including IPMN (Intraductal papillary mucinous neoplasm) and PanIN (Pancreatic intraepithelial Neoplasm).
  6. diagnosis of dementia
  7. Uncontrolled, current illness
  8. Renal insufficiency with serum creatinine greater than 2.0 mg/dl

Relevance to patient case: not relevant
Patient case: 61-year-old male with melanoma; genetic feature: BRAF amplification

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: 61-year-old male with melanoma; genetic feature: BRAF amplification

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: 61-year-old male with melanoma; genetic feature: BRAF amplification

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: 61-year-old male with melanoma; genetic feature: BRAF amplification

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: 61-year-old male with melanoma; genetic feature: BRAF amplification

Clinical trial: Study to Evaluate the Safety and Efficacy of Gefitinib, in Subjects With EFGR Amplification Refractory Solid Tumors

Summary: This study is a single-arm,phase II study of gefitinib in patient with epidermal growth factor receptor amplification Refractory solid tumors.
  Gefitinib 250 mg will be administered orally daily.
  To investigate the efficacy and safety of gefitinib in patient with epidermal growth factor receptor amplification Refractory solid tumors.


Eligibility: Inclusion Criteria:
  1. Provision of fully informed consent prior to any study specific procedures.
  2. Patients must be ≥20 years of age.
  3. Patient with Epidermal growth factor receptor amplification Refractory Solid Tumors and/or specific sensitivity to Gefitinib by Avatar scan that has recurred or progressed following standard therapy, or that has not responded to standard therapy, or for which there is no standard therapy.
  (EGFR amplification by cancer scan + EGFR IHC overexpression +2 or +3)
  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 ≤5 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. KRAS mutation (codon 12 or 13) or BRAF mutation (V600)
  7. Any previous treatment with Gefitinib
  8. Patients with a risk factor of interstitial lung disease

Relevance to patient case: not relevant