araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 54-year-old male with melanoma; genetic feature: BRAF (V600K)

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: possibly relevant
Patient case: 54-year-old male with melanoma; genetic feature: BRAF (V600K)

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: possibly relevant
Patient case: 54-year-old male with melanoma; genetic feature: BRAF (V600K)

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: 54-year-old male with melanoma; genetic feature: BRAF (V600K)

Clinical trial: Clinical Research on the Treatments on Advanced Malignant Melanoma by Combining in Situ Immunotherapy and Laser Therapy

Summary: To evaluate the therapeutic efficacy and the safety for the treatments on malignant melanoma by combining semiantigen dinitrophenyl (DNP) in situ immunotherapy and laser therapy, and carry out monitoring on related immunological parameters of the patients.
  72 patients with stage III (b or c) or stage IV skin (which could not be excised by operations) malignant melanoma were treated by combining simple semiantigen DNP in situ immunotherapy and laser therapy respectively. The changes in peripheral blood CD4+CD25+Treg regulatory T cells (Treg), CD8+T, CD4+ T effector cells, IL-10, TGF-β and other inhibitory cytokines of the patients were detected, the changes in anti-DNP IgG antibody titer was monitored, the relationship between delayed-type hypersensitivity (DTH) and survival was observed, and results of clinical follow-ups were also examined.


Eligibility: Inclusion Criteria:
  -  pathologically diagnosed as malignant melanoma, HMB45 (+～++++), S100 (+～++++);
  -  Basically normal hepatic and renal functions as well as results for blood routine examinations;
  -  Karnofsky score ≥ 60;
  -  Anticipated life span for more than three months;
  -  They were all malignant melanoma patients suffering from skin malignant melanoma of local or distal metastasis unsuitable for operations in their skin;
  -  The therapeutic efficacy was objectively evaluated with reference to the criteria from WHO;
  -  All of the subjects had signed the informed consent and had been submitted and approved by the ethic committee of the hospital, the compliance was good and follow-ups can be easily carried out.

Relevance to patient case: not relevant
Patient case: 54-year-old male with melanoma; genetic feature: BRAF (V600K)

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: 54-year-old male with melanoma; genetic feature: BRAF (V600K)

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: 54-year-old male with melanoma; genetic feature: BRAF (V600K)

Clinical trial: Detection of BRAF Mutation on FNAB From Papillary Thyroid Carcinoma

Summary: Immunohistochemical detection of the BRAF-V600E mutation on pre-operative fine needle aspiration biopsy (FNAB) from patients suspected for papillary thyroid carcinoma, using the mutation specific antibody VE1.

Detailed description: The BRAF mutation is reported to be present in approximately 50% of papillary thyroid carcinomas (PTC). The mutation has been associated with poor prognosis and more advanced disease stage. Therefore, pre-operative detection of the BRAF-V600E mutation may be of clinical interest in order to individualize treatment of patients with BRAF positive PTC.
  FNABs are performed immediately before the thyroid operation, and BRAF-V600E detection using VE1 is performed on clots. The VE1 stain is compared to the mutation status of the removed cancer or control tissue using the Cobas test.

Eligibility: Inclusion Criteria:
  -  Bethesda system of reporting thyroid cytology (BSRTC) group 5-6 on pre-operative FNAB from the nodule (>1cm)
  -  Undergoing thyroid surgery (histology of index nodule)
  Exclusion Criteria:
  -  Not undergoing thyroid surgery

Relevance to patient case: possibly relevant
Patient case: 54-year-old male with melanoma; genetic feature: BRAF (V600K)

Clinical trial: A Study to Investigate the Effect of Itraconazole and Rifampin on Pharmacokinetics (PK) of Vemurafenib at Steady State

Summary: This is a two-part, Phase 1, open-label, multicenter, two-period, one-sequence study to investigate the effect of itraconazole and rifampin on the PK of vemurafenib following multiple 960 milligrams (mg) twice daily (BID) dosing in adult participants with unresectable Stage IIIC or Stage IV metastatic melanoma positive for the BRAF V600 mutation, or other malignant tumor types that harbor a V600-activating mutation of BRAF where the participant has no acceptable standard treatment options.


Eligibility: Inclusion Criteria:
  -  Participants with age greater than or equal to (>=) 18 years with either unresectable Stage IIIC or Stage IV metastatic melanoma positive for the BRAF V600 mutation, or other malignant tumor types that harbor a V600-activating mutation of BRAF
  -  Eastern Cooperative Oncology Group Performance Status 0 to 2
  -  Life expectancy >=12 weeks
  -  Adequate hematologic and end organ function obtained within 2 weeks prior to first dose of study drug
  -  Female participants of childbearing potential and male participants with partners of childbearing potential must agree to always use two effective methods of contraception including at least one method with a failure rate of <1% per year during the course of the study and for at least 6 months after completion of study treatment
  -  Negative serum pregnancy test within 7 days prior to commencement of dosing in women of childbearing potential
  -  Absence of any psychological, familial, sociological, or geographical condition potentially hampering compliance with the study protocol and follow-up schedule
  Exclusion Criteria:
  -  Prior treatment with vemurafenib or other BRAF inhibitor within 42 days of Study Day 1 of Period A
  -  Allergy or hypersensitivity to components of the vemurafenib formulation
  -  Experimental therapy within 4 weeks prior to first dose of study drug treatment on Study Day 1 of Period A
  -  Major surgical procedure or significant traumatic injury within 14 days prior to first dose of study drug treatment on Study Day 1 of Period A, or anticipation of the need for major surgery during study treatment
  -  Prior anti-cancer therapy (e.g., biologic or other targeted therapy, chemotherapy) within 28 days (6 weeks for nitrosoureas or mitomycin C, and 14 days for hormonal therapy or kinase inhibitors) before the first dose of study treatment on Study Day 1 of Period A.

Relevance to patient case: possibly relevant
Patient case: 54-year-old male with melanoma; genetic feature: BRAF (V600K)

Clinical trial: Study to Analyze Mutations in V600 BRAF Oncogen in Participants With Metastatic Melanoma

Summary: This is a national, multicenter, cross-sectional epidemiological study in adult Spanish participants diagnosed with advanced or metastatic melanoma.


Eligibility: Inclusion Criteria:
  -  Valid tumor samples from participants diagnosed with Stage IIIc or IV melanoma
  -  Written informed consent granted
  Exclusion Criteria:
  - Do not fulfill one or more inclusion criteria

Relevance to patient case: possibly relevant
Patient case: 54-year-old male with melanoma; genetic feature: BRAF (V600K)

Clinical trial: Study of Efficacy and Safety of Dabrafenib and Trametinib Combination Therapy in Japanese Patients With BRAF V600E Stage IV NSCLC

Summary: This is an open-label, multicenter, non-randomized, single arm, phase II study to assess efficacy and safety of the dabrafenib and trametinib combination in Japanese patients with any line, stage IV NSCLC harboring a confirmed BRAF V600E mutation.
  Patients will receive oral dabrafenib twice daily and oral trametinib once daily combination therapy. Patients may continue study treatment until disease progression, unacceptable adverse events, start of a new anti-cancer therapy, consent withdrawal, death, or end of the study. Patients who have met the criteria for disease progression (PD) according to RECIST v1.1 may continue to receive study treatment if the investigator believes the patient is receiving clinical benefit and the patient is willing to continue on study treatment. After discontinuation of study treatment, all patients will be followed for survival until death, lost to follow-up, withdrawal of consent, or end of study.


Eligibility: Inclusion Criteria:
  -  Histologically- or cytologically-confirmed diagnosis of NSCLC stage IV (according to AJCC Staging 7th Edition)
  -  Presence of a BRAF V600E mutation in lung cancer tissue. BRAF V600E mutation tested by local laboratory (e.g. study center laboratory, local laboratory company) with proper quality control and license to operation by local health authority is allowed.
  -  Measurable disease according to RECIST v1.1.
  Exclusion Criteria:
  -  Previous treatment with a BRAF inhibitor (including but not limited to dabrafenib, vemurafenib, encorafenib, and XL281/BMS-908662) or MEK inhibitor (including but not limited to trametinib, cobimetinib, binimetinib, AZD6244, and RDEA119) prior to start of study treatment
  -  Patients with brain metastases are excluded if their brain metastases are:
  -  Symptomatic OR
  -  Treated (surgery, radiation therapy) but not clinically and radiographically stable 3 weeks after local therapy (as assessed by contrast enhanced magnetic resonance imaging [MRI] or computed tomography [CT]), OR
  -  Asymptomatic and untreated but >1 cm in the longest dimension
  -  History of malignancy with confirmed activating RAS mutation at any time.
  -  History of interstitial lung disease or pneumonitis
  -  A history or current evidence of retinal vein occlusion (RVO)
  -  Current evidence of unstable aneurysm or one that needs treatment
  Other protocol-defined inclusion/exclusion may apply.

Relevance to patient case: possibly relevant
Patient case: 54-year-old male with melanoma; genetic feature: BRAF (V600K)

Clinical trial: A Study to Detect V-Raf Murine Sarcoma Viral Oncogene Homolog B1 (BRAF) V600 Mutation on Cell-Free Deoxyribonucleic Acid (cfDNA) From Plasma in Participants With Advanced Melanoma

Summary: This is a single arm, multicenter, open label, and non-randomized clinical study on adult participants with unresectable or metastatic melanoma. The study will be conducted in two phases. Pre-screening phase will assess the BRAF V600 mutation in a new mutation analysis triggered by a mutant plasma cfDNA test result. Treatment phase will assess the clinical outcome for the participants treated with vemurafenib plus cobimetinib. The length of the study will be approximately 36 months.


Eligibility: Inclusion Criteria:
  Pre-screening phase:
  -  Participants with histologically confirmed melanoma, either unresectable Stage IIIc or Stage IV metastatic melanoma, as defined by American Joint Committee on Cancer (AJCC) 7th edition
  -  Documentation of BRAF V600 test result mutation-positive status on melanoma tumor tissue using a validated tissue test
  Treatment Phase:
  -  Eastern cooperative oncology group (ECOG) performance status of 0-2
  -  Adequate hematologic and end organ function obtained within 14 days prior to first dose of study drug treatment
  -  Negative serum pregnancy test prior to commencement of dosing in women of childbearing potential
  -  Absence of any psychological, familial, sociological, or geographical condition that potentially hampers compliance with the study protocol and treatment regimen and follow-up after treatment discontinuation schedule
  -  Female participants of childbearing potential and male participants with partners of childbearing potential must agree to always use 2 effective forms of contraception during the course of this study and for at least 3 months after completion of study therapy
  -  Participants should be able to swallow tablets
  -  Documentation of BRAF mutation positive status in melanoma tissue (archival or new)
  Exclusion Criteria:
  Treatment Phase:
  -  History of prior rapidly accelerated fibrosarcoma (RAF) or mitogen-activated protein kinase (MEK) pathway inhibitor treatment
  -  Palliative radiotherapy within 14 days prior to the first dose of study treatment
  -  Evidence of retinal pathology on ophthalmologic examination
  -  Systemic risk factors for retinal vein occlusion (RVO)
  -  History of clinically significant cardiac dysfunction
  -  Current severe, uncontrolled systemic disease
  -  Pregnancy, lactating or breast feeding
  -  Intake of potent cytochrome P450 3A4 (CYP3A4) enzyme inducer and potent CYP3A4 enzyme inhibitor at least 7 days prior to initiation of and during the study treatment

Relevance to patient case: possibly relevant