araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Detection of Choroidal Nevus Cells in Vitrectomy Fluid

Summary: The purpose of this study is to determine if the investigators can detect the presence of choroidal nevi cells in the vitreous fluid of humans, as this may improve the diagnosis and classification of choroidal nevi and melanomas in the future.

Detailed description: Approximately 7% of the population has a choroidal nevus, or "freckle," in the back of the eye. Like a nevus on the skin, there is potential for malignant change to a melanoma. Dermatologists have the ability to quickly and easily biopsy suspicious skin lesions while ophthalmologists currently have no way of determining the malignant potential of choroidal nevi other than a fine needle aspiration (which is invasive and has the potential complications of bleeding and retinal detachment). This study's sole aim is to see if choroidal nevi cells are present in the inside fluid of the eye. The investigators plan to analyze the fluid of the eye, which is routinely removed during retina surgery, to detect any nevus cells. If the investigators are able to detect these cells, then future studies may allow us to better classify choroidal nevi for potential malignant change.

Eligibility: Inclusion Criteria:
  -  Patients with a choroidal nevus who are undergoing routine vitrectomy surgery for another indication (such as epiretinal membrane or macular hole repair).
  Exclusion Criteria:
  -  Patients without a choroidal nevus
  -  Children under the age of 18
  -  Pregnant and nursing females

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Efficacy and Safety Study of GSK1120212, a MEK Inhibitor, in Subjects With Uveal Melanoma

Summary: The purpose of this study is to determine whether GSK1120212, a MEK inhibitor, is an effective and safe treatment for cancer subjects with metastatic uveal melanoma and mutation-positive GNAQ or GNA11 metastatic melanoma.


Eligibility: Inclusion Criteria:
  -  Histologically or cytologically confirmed diagnosis of metastatic uveal melanoma or previously documented mutation-positive GNAQ or GNA11 metastatic melanoma not previously treated with a MEK inhibitor.
  -  Provide archival tumor tissue or, if tissue blocks are not available, undergo fresh tumor biopsy prior to enrollment.
  -  The patient has a radiographically measurable tumor.
  -  ECOG performance status 0, 1, or 2.
  -  The patient is able to swallow and retain oral medication.
  -  Life expectancy of at least 4 months.
  -  Toxicities from previous anti-cancer therapy (except alopecia) are recovered (Grade 1 or less) at the time of enrollment.
  -  The patient has adequate organ and bone marrow function.
  -  Sexually active patients must use medically acceptable methods of contraception during the course of the study.
  -  Female patients of childbearing potential must have a negative serum pregnancy test at screening.
  Exclusion Criteria:
  -  The patient has had any of the following within 21 days of starting study drug or anticipates the need for any of the following during the course of study treatment: chemotherapy, immunotherapy, biologic therapy, hormone therapy, major surgery, or tumor embolization.
  -  The patient has received experimental therapy within 21 days of starting study drug.
  -  The patient has received nitrosourea or mitomycin C within 42 days of starting study drug.
  -  The patient has received any herbal medications or palliative radiotherapy within 14 days of starting study drug.
  -  The patient is currently receiving anticoagulation therapy that is not well controlled.
  -  Ongoing or newly diagnosed eye abnormality other than symptoms due to uveal melanoma.
  -  History of retinal vein occlusion or central serous retinopathy.
  -  Current severe, uncontrolled systemic disease.
  -  History of leptomeningeal disease or spinal cord compression secondary to metastasis.
  -  Brain metastasis, unless previously treated with surgery, whole-brain radiation or stereotactic radiosurgery and the disease has been stable for at least 3 months without steroid use or on a stable dose of steroids for at least 1 month prior to starting study drug. Stability of brain metastases must be confirmed with imaging.
  -  The patient has a concurrent, active hematological malignancy or other solid tumor malignancy.
  -  History of clinically significant cardiac or pulmonary dysfunction.
  -  Allergy or hypersensitivity to components of the GSK1120212 formulation.
  -  The patient is pregnant or breastfeeding.

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Study of Circulating Tumoral DNA in Metastatic Choroidal Melanoma

Summary: Circulating tumor DNA detection and quantification in patients with metastatic choroidal melanoma.

Detailed description: Technique development: In first step, the different available techniques will be evaluated for specificity and sensibility using serial dilutions of cell lines with or without GNAQ mutation.
  Validation: The tumor DNA detection rate will be estimated from metastatic uveal patient's blood. The investigators will study 40 patients to obtain at least 15 patients bearing a GNAQ mutation in the primitive tumor or in metastasis. With those 15 patients, the investigators will determinate the most sensitive technique and the best cost/efficiency ratio.

Eligibility: Inclusion Criteria:
  -  Age > or = 18 years.
  -  Patient with a metastatic choroidal melanoma.
  -  Patient with tumor or metastasis available for GNAQ (Guanine nucleotide blinding protein) status characterization.
  -  Patient able to stand a blood collection.
  -  Signed written informed consent approved by competent authority and ethic committee.
  Exclusion Criteria:
  -  Patient without social protection/insurance.
  -  Current pregnancy and lactation.
  -  All social, medical, psychological, situations making the study impossible.
  -  Person deprived of liberty.

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: A Study of LGK974 in Patients With Malignancies Dependent on Wnt Ligands

Summary: This primary purpose of this study is to find the recommended dose of LGK974 as a single agent and in combination with PDR001 that can be safely given to adult patients with selected solid malignancies for whom no effective standard treatment is available.


Eligibility: Inclusion Criteria:
  Diagnosis of locally advanced or metastatic cancer that has progressed despite standard therapy or for which no effective standard therapy exists and histological confirmation of one of the following diseases indicated below:
  Single Agent Dose escalation part:documented B-RAF mutant colorectal cancer or pancreatic adenocarcinoma. In addition, tumors of any histological origin with documented genetic alterations upstream in the Wnt signaling pathway are eligible with prior agreement with Novartis.
  Single Agent Dose expansion part: documented B-RAF mutant colorectal cancer with documented RNF43 mutation and/or RSPO fusion or pancreatic adenocarcinoma with documented RNF43 mutation. In addition, patients with tumors of any histological origin with documented genetic alterations upstream in the Wnt signaling pathway (e.g. RNF43 or RSPO fusion) are eligible with prior agreement with Novartis
  LGK974 with PDR001: Dose escalation: melanoma patients primary refractory to anti-PD-1 inhibitor. Dose expansion: patients with pancreatic cancer, or TNBC, or melanoma, or head and neck cancer.
  Exclusion Criteria:
  -  Impaired cardiac function
  -  Impairment of gastrointestinal function or gastrointestinal disease that may significantly alter the absorption of oral LGK974 (e.g., ulcerative diseases, uncontrolled nausea, vomiting, diarrhea, malabsorption syndrome, small bowel resection)
  -  Brain metastases that have not been adequately treated
  -  Malignant disease other than that being treated in this study
  -  Laboratory abnormalities as specified in the protocol
  -  Osteoporosis, severe or untreated osteopenia
  -  Bone fractures within the past year
  -  Pathologic bone fracture
  -  Active, known or suspected autoimmune disease or severe hypersensitivity reactions to other monoclonal antibodies
  Other protocol-defined inclusion/exclusion criteria may apply

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: A Study of Vemurafenib in Metastatic Melanoma Participants With Brain Metastases

Summary: This open-label, single-arm, multicenter study will evaluate the efficacy and safety in participants with metastatic melanoma who developed brain metastases. Participants may or may not have received prior systemic treatment for metastatic melanoma [except treatment with v-raf murine sarcoma viral oncogene homolog B (BRAF) or mitogen-activated protein kinase (MEK) inhibitors]. Participants will receive oral doses of 960 mg vemurafenib twice daily until disease progression, unacceptable toxicity or consent withdrawal.


Eligibility: Inclusion Criteria:
  -  Adult participants, >/= 18 years of age
  -  Histologically confirmed metastatic melanoma (Stage IV, American Joint Committee on Cancer) with BRAF V600 mutation (cobas 4800 BRAF V600 Mutation Test)
  -  Measurable brain metastases, defined as lesions that were accurately measured in at least one dimension (longest diameter to be recorded) as ≥0.5 cm in the brain MRI with contrast, treated or untreated
  -  Participants may or may not have received prior systemic therapy for metastatic melanoma and either a) have received no prior treatment for brain metastases or b) have received prior treatment for brain metastases and have progressed
  -  Participants may or may not have symptoms related to their brain metastases
  -  Eastern Cooperative Oncology Group (ECOG) performance status 0-1
  -  Participants must have recovered from all side effects of their most recent systemic or local treatment for metastatic melanoma
  Exclusion Criteria:
  -  Increasing corticosteroid dose during the 7 days prior to first dose of study drug
  -  Leptomeningeal involvement in participants with no prior treatment for brain metastases
  -  Previous malignancy requiring active treatment within the past 2 years, except for treated and controlled basal or squamous cell carcinoma of the skin, or carcinoma in-situ of the cervix
  -  Concurrent administration of any anticancer therapies other than those administered in the study
  -  Treatment with any cytotoxic, investigational drug or targeted therapy 4 weeks prior to first dose of study drug. Radiation therapy ≤1 week prior to first administration of vemurafenib; and stereotactic radiotherapy ≤1 day prior to prior to first administration of vemurafenib
  -  Prior treatment with BRAF or MEK inhibitors
  -  Clinically significant cardiovascular disease or event within the 6 months prior to first dose of study drug

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Ph I Ipilimumab Vemurafenib Combo in Patients With v-Raf Murine Sarcoma Viral Oncogene Homolog B1 (BRAF)

Summary: Treatment of subjects who have metastatic melanoma that expresses an activated mutant form of the BRAF oncogene (V600E) with a combination of the specific BRAF inhibitor, Vemurafenib, and the Cytotoxic T Lymphocyte Antigen 4 (CTLA-4) inhibitor mAb Ipilimumab will be safe and feasible and will show preliminary evidence of anti-tumor efficacy and survival in comparison to historical results following treatment with either agent alone.


Eligibility: For more information regarding BMS clinical trial participation, please visit www.BMSStudyConnect.com.
  Inclusion Criteria:
  -  Metastatic melanoma with activating V600 BRAF mutation
  -  Measurable Tumor
  -  Eastern Cooperative Oncology Group (ECOG) Performance Status (PS) 0-1
  Exclusion Criteria:
  -  Autoimmune disease
  -  Active Brain Metastasis (must be stable after radiation for at least one month)
  -  Prior therapy with immune stimulating agents

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Tissue Procurement for Gastric Cancer, Gastrointestinal Stromal Tumors (GIST), Esophageal Cancer, Pancreas Cancer, Hepatocellular Cancer, Biliary Cancer, Neuroendocrine, Peritoneal Mesothelioma, Anal Cancer and Colorectal Cancer in Patients Undergoing Surgery or Biopsy

Summary: The purpose of this study is to collect and store normal and malignant tissue from patients with gastric cancer, GIST, esophageal cancer, pancreas cancer, hepatocellular cancer, biliary cancer, neuroendocrine, peritoneal mesothelioma, anal cancer and colorectal cancer, an estimated 50 to 100 of each tumor type. To collect and store blood samples from patients with gastric cancer, GIST, esophageal cancer, pancreas cancer, hepatocellular cancer, biliary cancer, neuroendocrine, peritoneal mesothelioma, anal cancer and colorectal cancer. To create a database for the collected tissue and allow access to relevant clinical information for current and future protocols. To create tissue microarrays for each gastrointestinal cancer subtype, namely, gastric cancer, GIST, esophageal cancer, pancreas cancer, hepatocellular cancer, biliary cancer, neuroendocrine, peritoneal mesothelioma, anal cancer and colorectal cancer, to facilitate future molecular studies. To grant access to Dr Kindler, Dr. Salgia, and Dr. Catenacci to this database (as it is being acquired) of the coupled patient tissue samples (normal and malignant) and relevant clinical information for the investigation of tyrosine kinases, such as Met and Ron, receptor tyrosine kinase family members, STATs, paxillin, focal adhesion proteins, cell motility/migration proteins, tyrosine/serine/threonine kinase family members, related molecules, and downstream targets implicated in the pathogenesis of GI cancers. Examples of molecular testing include evaluation of DNA mutation, alternative splice variants, protein expression and phosphorylation, and immunohistochemistry on samples. These studies will be correlated with clinical information as stated above.


Eligibility: Inclusion Criteria:
  -  any patient diagnosed with Gastric (stomach) Cancer, Esophageal (foodpipe) Cancer, Pancreas Cancer, Liver Cancer, Biliary (gallbladder) Cancer, Gastrointestinal Stromal Tumor, Peritoneal Mesothelioma (cancer in the lining of the abdomen), Neuroendocrine (of or relating to the cells that release a hormone into the blood in response to a neural stimulus) Tumor, Anal Cancer or Colorectal Cancer cancer that requires you to undergo a surgical or diagnostic procedure.

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: BRAF V600E Mutations In Papillary Thyroid Carcinoma

Summary: The purpose of this study is to determine whether BRAF V600E mutation in our patients with papillary thyroid cancer has an association with poor prognosis.

Detailed description: Papillary thyroid carcinoma (PTC) is the most common type of thyroid malignancy and BRAF V600E mutation is the most common genetic alteration identified in PTC, ranging from 25 to 80%, with the average rate about 45%. Various studies demonstrated a relationship between BRAF V600E mutation and aggressive characteristics of the cancer, including the worse patient prognosis. But,there are no studies from Turkey regarding this topic. So the investigators will examine BRAF V600E mutation in our patients with PTC and try to assess the role of this mutation in prognosis and further management of the patients.

Eligibility: Inclusion Criteria:
  -  Patients with papillary thyroid cancer
  Exclusion Criteria:
  -  Patients who do not want to be a part of this study

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Safety Study of a Melanoma Vaccine (GVAX) With or Without Cyclophosphamide in Patients With Surgically Resected Melanoma

Summary: The primary objective of this study is to evaluate the safety and feasibility of administering an allogeneic GM-CSF-secreting lethally irradiated whole melanoma cell vaccine ("melanoma GVAX"), alone or in combination with low dose cyclophosphamide (CPM), for the adjuvant treatment of patients with surgically resected stage IIB-IV melanoma. Secondarily, the investigators will assess in vitro correlates of anti-melanoma immunization by melanoma GVAX, including serological and cellular immune responses in patients treated with either the vaccine alone or the vaccine given with low dose CPM.


Eligibility: Inclusion Criteria:
  -  Any patient age ≥18 years with melanoma of cutaneous or mucosal origin, and with clinicopathologic stage IIB, IIC, III or IV that has been completely resected
  -  Patients must be able to provide informed consent.
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1.
  -  Life expectancy of at least 6 months.
  -  Adequate hematologic function.
  -  Adequate renal function
  -  Adequate hepatic function
  -  Patients of both genders must agree to practice effective birth control during the study period and for at least 4 weeks after the last treatment.
  Exclusion Criteria:
  -  Patients whose primary site of melanoma is ocular.
  -  Are undergoing or have undergone in the past 4 weeks any systemic treatment for melanoma.
  -  Are undergoing or have undergone in the past 2 weeks any surgery or focal radiation therapy.
  -  Have active systemic infections, coagulation disorders (including therapeutic anticoagulation), or other major medical or psychiatric illnesses.
  -  Are known to be positive for hepatitis B surface antigen, anti-Hepatitis C Virus or anti-Human Immunodeficiency Virus (HIV) antibody (because of possible immune effects of these conditions).
  -  Documented history of autoimmune disease, for example, systemic lupus erythematosus, sarcoidosis, rheumatoid arthritis, glomerulonephritis, or vasculitis.
  -  Any form of primary or secondary immunodeficiency. This would include hereditary disorders such as ataxia-telangiectasia or Wiskott-Aldrich syndrome, or acquired immune deficiencies such as following bone marrow transplantation.
  -  Requirement for systemic steroid therapy or immunosuppressive therapy.
  -  Have received any type of cancer immunotherapy, including but not limited to interleukin-2, interferon alfa or melanoma vaccines.
  -  Have been diagnosed with another invasive cancer within the past 3 years.
  -  Radiographic evidence of melanoma recurrence.
  -  Pregnant or lactating women.
  -  Known or suspected hypersensitivity to GM-CSF, pentastarch, hetastarch, corn, Dimethyl sulfoxide, fetal bovine serum or trypsin (porcine origin).

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: A Phase I Study of Oral LGX818 in Adult Patients With Advanced or Metastatic BRAF Mutant Melanoma

Summary: CLGX818X2101 is a first-time in-human, phase I study to establish the maximum tolerated dose (MTD) and/or recommended phase 2 dose (RP2D) of daily administered LGX818 (daily, twice daily and/or every-other-day), a RAF kinase inhibitor. Patients with locally advanced or metastatic melanoma harboring the BRAF V600 mutation (during dose escalation phase and expansion phase) and patients with metastatic colorectal cancer harboring the BRAF V600 mutation (during the expansion phase) will be enrolled. The study consists of a dose escalation part were cohorts of patients will receive escalating oral doses of LGX818, followed by a safety dose expansion part were patients will be treated with oral dose of LGX818 given at the MTD or RP2D.


Eligibility: Inclusion Criteria:
  For the dose escalation phase:
  1. Histologically confirmed diagnosis of locally advanced or metastatic melanoma (stage IIIB to IV per American Joint Committee on Cancer [AJCC]). For the dose expansion phase: (i) Histologically confirmed diagnosis of locally advanced or metastatic melanoma (stage IIIB to IV per American Joint Committee on Cancer [AJCC]), or (ii) confirmed diagnosis and non-resectable advanced metastatic colorectal cancer (mCRC) for which no further effective standard therapy exists.
  2. Written documentation of BRAF V600E mutation, or any other BRAF V600 mutation.
  3. Evidence of measurable disease
  Exclusion Criteria:
  1. Previous therapy with a MEK inhibitor.
  2. Symptomatic or untreated leptomeningeal disease.
  3. Symptomatic or untreated brain metastasis.Patients previously treated for these conditions that are asymptomatic in the absence of corticosteroid therapy are allowed to enroll. Brain metastasis must be stable with verification by imaging.
  4. Known acute or chronic pancreatitis.
  5. Clinically significant cardiac disease
  6. Impairment of gastrointestinal (GI) function or GI disease that may significantly alter the absorption of oral LGX818
  7. Previous or concurrent malignancy. Exceptions to this exclusion criteria include: adequately treated basal cell or squamous cell skin cancer; in situ carcinoma of the cervix, treated curatively and without evidence of recurrence for at least 3 years prior to study entry; or other solid tumor treated curatively, and without evidence of recurrence for at least 3 years prior to study entry.
  8. Pregnant or nursing (lactating) women, where pregnancy is defined as the state of a female after conception and until the termination of gestation, confirmed by a positive hCG laboratory test (> 5 mIU/mL).
  9. History of thromboembolic or cerebrovascular events within the last 6 months
  Other protocol-defined inclusion/exclusion criteria may apply

Relevance to patient case: definitely relevant