araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

Clinical trial: Comprehensive Genomic Analysis in Tissue and Blood Samples From Young Patients With Lung Cancer

Summary: This research trial studies genomic analysis in tissue and blood samples from young patients with lung cancer. Identifying specific gene mutations (changes in deoxyribonucleic acid [DNA]) may help doctors tailor treatment to target the specific mutations and help plan effective treatment.

Detailed description: PRIMARY OBJECTIVES:
  I. To perform comprehensive genomic analysis of young lung cancer patients' samples to facilitate delivery of targeted therapies and clinical trial enrollment.
  II. To characterize the impact of young age at lung cancer diagnosis on the genomic landscape of primary lung cancer.
  III. To establish a prospective registry of young lung cancer patients for both tumor and germline next generation sequencing.
  OUTLINE:
  Tissue and blood samples are analyzed via next generation sequencing and whole exome sequencing.
  After completion of study, patients are followed up every 3 months for up to 3 years.

Eligibility: Inclusion Criteria:
  -  COHORT 1: LUNG CANCER PATIENTS
  -  Pathologically confirmed bronchogenic lung carcinoma (small cell lung cancer [SCLC] or non-small cell lung cancer [NSCLC] of any stage) at any treatment time point
  -  For individuals diagnosed with advanced disease (stage IV or recurrent) enrollment must occur within 2 years of diagnosis
  -  For appropriate patients (stage IV non-squamous NSCLC) epidermal growth factor receptor (EGFR ) and anaplastic lymphoma kinase (ALK) genotyping performed by a Clinical Laboratory Improvement Amendments (CLIA) certified laboratory is recommended prior to participation
  -  Provision of written informed consent
  -  Willingness to undergo a single blood draw
  -  Individuals who are under 18 are eligible for study if they meet the defined criteria for cohort 1; in addition, consent for participation must be given by a legal guardian or parent
  -  NOTE: to be eligible for genomics, availability of 10 unstained slides (plus hematoxylin and eosin [H&E] slide) or an adequate formalin-fixed paraffin-embedded (FFPE) tumor block from clinically indicated interventional procedures is required
  -  COHORT 2: DECEASED INDIVIDUALS
  -  Deceased individuals diagnosed with lung cancer at any age less than 40 may be studied on a case by case basis depending upon Institutional Review Board (IRB) approval at a participating institution; inclusion will require availability of adequate archived FFPE tissue and release of tissue and records by next of kin, if available
  Exclusion Criteria:
  -  Compromise of patient diagnosis or staging if tissue is used for research

Relevance to patient case: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

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: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

Clinical trial: Automatic Early Melanoma Detection by Ultrahigh Resolution Three Dimensional Optical Coherence Tomography

Summary: The investigators will use optical coherence tomography to detect the ex-vivo tissue image of surgical removed melanoma or other benign pigmented lesions of skin.

Detailed description: The investigators will use an advanced high resolution 3D optical coherence tomography (OCT) technology to observe skin tissue images in ex vivo culture. Parts of melanoma or benign pigmented lesions specimens derived from biopsy or surgical excision specimen will be observed by 3D optical tomography. A tiny tissue fragment of melanoma or benign pigmented lesions will be taken from surgical specimen without interference normal pathological evaluation. The location of melanocytic cells in melanoma or benign tissue fragments will be mapped by the 3D optical coherence tomography (OCT). The 3D optic tomography system utilize a Ce:YAG optical fiber as light source and also combined with confocal microscopy. Taken together, these features made the 3D optic tomography system have very high resolution and suitable for single cell imaging. This study will not interfere with the normal medical practice and had no impact on patient's safety and health. All of the materials will be destroyed once the experiments are done. The enrollment criteria will be dermatological patients who need to surgical intervention.

Eligibility: Inclusion Criteria:
  -  Patients aged older than 20 years old
  -  Patients who had melanoma, melanoma in situ, and/or other benign pigmented lesions,
  -  Patients who had non-melanoma skin cancers (basal cell carcinoma, or squamous cell carcinoma).
  -  Patients who had precancerous skin lesions (Bowen's disease, actinicc keratosis)
  Exclusion Criteria:
  • Pregnant women.

Relevance to patient case: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

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: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

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: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

Clinical trial: FLuorescence Identification of Melanoma by a Multicenter Based Algorithm (FLIMMA)

Summary: All patients will undergo dermoscopic diagnosis and be documented with a video image storing. The diagnosis based on dermoscopy will be immediately documented. Then, as a second diagnostic procedure, fluorescence diagnostics based on the two photon excitation from a dye-laser will be performed. The classification as non-melanoma or malignant melanoma by the medical device LIMES will also be documented immediately. Afterwards, the lesion will be excised and undergo histopathologic examination by the respective histopathologist of the participating centers. The histopathologic diagnosis will serve as gold standard for subsequent evaluations of the diagnostic accuracy.


Eligibility: Inclusion Criteria:
  -  Patients ≥ 18 years of age
  -  Male or female
  -  Patients having pigmented lesions with suspicion of dysplastic nevus or melanoma, in whom an excision is performed in order to exclude or diagnose malignant melanoma
  -  Patients who gave their written informed consent.
  Exclusion Criteria:
  -  Patients with skin type V and VI according to Fitzpatrick's scale;
  -  Where there is a risk that the scanning head is torn off be-cause the patient cannot be placed at rest (e.g. due to motoric disorders like tremor, convulsions, tics, compulsive acts
  -  Patients who cannot understand the patient information and provide informed consent
  -  Deep dermal lesions ≥ 5 mm beneath the stratum corneum
  -  Clinically or reflected-light microscopically obviously non-melanocytic lesions
  -  Peri- and subungual lesions
  -  Mucosal lesions
  -  Lesions with trauma, erosion (superficial defect), excoriation (defect down to the basement membrane) or ulceration (deep substantial defect) on more than 50 % of the lesion area (measurements must in any case not be carried out directly on the trauma, erosion, excoriation or ulceration)
  -  Tattooed lesions
  -  Pregnant or breast feeding women
  -  Patients suffering from albinism
  -  Lesions with dominant (>50%) regression
  -  Lesions which are not suitable to fix the scanning cap

Relevance to patient case: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

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: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

Clinical trial: Complete Lymph Node Dissection vs Watchful Waiting in Patients With Malignant Melanoma (Thickness of 1,0mm+ and Evidence of Metastases in the Sentinel Node)

Summary: Sentinel lymph node biopsy (SLNB) is considered as standard diagnostic procedure in melanoma patients carrying a reasonable risk for metastases. In numerous studies the prognostic role of micro metastases in the sentinel node (SN) was described. However, the prognostic value of a complete lymph node dissection in patients with a positive SN is still unclear.
  This study was planned to analyse the survival outcome of patients with a positive SN receiving complete lymphadenectomy versus watchful waiting.


Eligibility: Inclusion Criteria:
  -  Cutaneous melanoma with a tumour thickness of at least 1,00mm
  -  Positive sentinel node with micro metastases of max. 2mm in diameter
  Exclusion Criteria:
  -  Mucosal or ocular melanoma
  -  Cutaneous melanoma located in the head/neck region
  -  Evidence of satellite, in transit or local metastases / recurrences
  -  Macro metastases of the SN or micro metastases of >2mm in diameter
  -  Additional immune-suppressive therapy
  -  Pregnant of lactating women

Relevance to patient case: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

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: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

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: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

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: not relevant
Patient case: 38-year-old male with melanoma; genetic feature: BRAF (K601E)

Clinical trial: Employment and Quality of Life in Patients With Malignant Melanoma

Summary: Within the first year after diagnosis, data on employment and quality of life will be collected and evaluated in patients with malignant melanoma


Eligibility: Inclusion Criteria:
  -  first diagnosis of malignant melanoma stage 0 to stage IIIC within the last 6 weeks
  -  written informed consent
  Exclusion Criteria:
  -  diagnosis of malignant melanoma stage IV
  -  inability to follow the protocol

Relevance to patient case: not relevant