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: Early Diagnosis of Oral Cancer by Detecting p16 Methylation

Summary: The purpose of this study is to verify the function of p16 methylation diagnostic reagents in early diagnosis of oral cancer.

Detailed description: Background:Oral epithelial dysplasia (OED) is one of the common precancerous lesions among Chinese adults. To investigate the clinical predictive value of p16 methylation diagnostic reagents in the early diagnosis of oral cancer, the investigators carried out the prospective multi-center double-blind cohort study.
  Methods:180 patients with histologically confirmed mild or moderate OED were included in the present study. The investigators using p16 methylation diagnostic reagents to analysis of the p16 methylation status in these patients. Building two follow-up queue by p16-methylated and p16-unmethylated. The Statistical analysis used SAS6.12 software. All P-values were two-sided. P<0.05 was considered to test for statistical significance difference.

Eligibility: Inclusion Criteria:
  -  Histopathological diagnosis of oral lesions meet the epithelial diagnostic criteria for mild to moderate grade OED
  -  No local area stimulate by residual root and crown, sharp cusp, poor restoration and biting cheek or lips
  -  Without the OCE treatment history by laser , radiation or chemical
  -  Be able to Sign the informed consent
  Exclusion Criteria:
  -  Histopathological diagnosis of oral lesions do not meet the epithelium of mild to moderate dysplasia diagnostic criteria; histological diagnosis of severe grade OED or malignant disease
  -  Pregnancy or breast-feeding women
  -  Serious heart, lung, liver , kidney and other systemic diseases
  -  local area stimulate by residual root and crown, sharp cusp, poor restoration and biting cheek or lips
  -  OED treatment history by LASER, radiotherapy, or chemotherapy
  -  Tumor and psychiatric patients
  -  Patients are unable to cooperate

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: Impact of BRAFV600E Intratumor Heterogeneity in Thyroid Cancer Treated With Tyrosine Kinase Inhibitors

Summary: -  Background: BRAFV600E is the most frequent oncogene in differentiated thyroid cancer (DTC) occurring in about 50% of cases. Clinical trials with tyrosine kinase inhibitors (TKI) with specific activity against BRAF in metastatic radioiodine-resistant DTC (MRR-DTC) are ongoing. Very recently it has been demonstrated that DTC often consists of a mixture of tumor cells with wild-type and mutant BRAF. The subclonal occurrence of BRAFV600E in MRR-DTC could disable the therapy with BRAF targeted TKI and be responsible of the frequent defeats of this treatment. A therapeutic strategy based upon BRAF inhibitors in tumors bearing subclonal BRAFV600E could be initially successful hitting the tumor cells expressing the oncogene, and after the initial tumor growth arrest and/or shrinkage, the oncogene negative cells insensitive or less sensitive to the treatment, could restart the growth of the tumor causing the progression of the disease and the escape from the clinical response.
  -  Aims: To determine the impact of subclonal BRAFV600E on the efficacy of BRAF inhibitors in the treatment of MRR-DTC.
  -  Study design: Primary tumor tissues will be analyzed for the presence of BRAFV600E by pyrosequencing or other quantitative assay. If available, synchronous metastases and post-therapy metachronous metastases will be analyzed as well. The clinical response will be determined according to RECIST, and the association with the percentage of BRAFV600E alleles will be evaluated. Attention will be paid to the possible difference of BRAFwild-type/BRAFV600E ratio between primary tumors and synchronous metastases, primary tumors and post-therapy metachronous metastases, and between responsive and resistant synchronous tumor lesions.


Eligibility: Inclusion Criteria:
  -  subjects any sex any age with metastatic or unresectable thyroid carcinoma treated with tyrosine kinase inhibitors
  -  evidence of measurable disease by Response Evaluation Criteria in Solid Tumors (RECIST)
  -  availability of study end points including best response, duration of response, and time to disease progression (based on RECIST), clinical progression, or death
  -  availability of tumor tissue samples, frozen or formaldehyde fixed-paraffin embedded from block, genomic DNA already extracted from tumor tissue
  Exclusion Criteria:
  -  concurrent Hashimoto's thyroiditis

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: Assessment of the V600E Mutation in the B-RAF Gene in Chronic Lymphoproliferative Disease

Summary: The presence of a specific mutation in the gene known as B-RAF has been found in patients who have Hairy Cell Leukemia. In this study this specific mutation known as V600E will be ascertained in peripheral blood samples of patients who have this disease and in a group of patients who have a similar chronic lymphoproliferative conditions such as splenic marginal lymphoma. The finding of this specific mutation will help to verify or exclude the diagnosis of Hairy Cell Leukemia and determine whether patients are in remission.


Eligibility: Inclusion Criteria:
  Patients over the age of 18 years -
  Exclusion Criteria:
  Patients less than 18 years in age or mentally defectives.

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: Comparison of In-House Methods and Cobas BRAF V600 Mutation Assay in Melanoma Tumor Samples

Summary: This non-interventional study will compare the Cobas BRAF V600 mutation assay with in-house methods used in molecular laboratories for the assessment of the BRAF mutation status in melanoma tumor samples. No patients will be enrolled in this study. Data will be collected for approximately 6 months.


Eligibility: Inclusion Criteria:
  No patients are enrolled. Use of tumor samples only.
  -  Histologically proven melanoma tumor sample
  -  Any type of tumor sample: biopsy or surgical specimen of primary tumor or metastasis
  -  Tumor samples must be fixed and paraffin-embedded.
  Exclusion Criteria:
  No patients are enrolled. Use of tumor samples only.
  -  Fixative unknown

Relevance to patient case: definitely relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Vitamin D Supplementation in Cutaneous Malignant Melanoma Outcome

Summary: To assess whether vitamin D supplementation after surgery of a first cutaneous malignant melanoma protects against relapse of the disease.

Detailed description: To assess whether vitamin D supplementation, in the follow up period after diagnosis and surgery of a first cutaneous malignant melanoma, has a protective effect on relapse of cutaneous malignant melanoma and whether this protective effect correlates with vitamin D levels in serum and vitamin D receptor (VDR) immunoreactivity in the primary tumor.

Eligibility: Inclusion Criteria:
  1. Older than 18 years and younger than 80 years of age.
  2. Histologically proven malignant melanoma, stage one B (IB) to three (III) Not participating in other clinical trial.
  3. The only treatment for melanoma is surgical treatment.
  4. Complete resection of melanoma.
  5. Single primary invasive cutaneous melanoma
  6. Signed ethical committee approved informed consent
  7. Serum phosphate, serum calcium at the entry of the study within normal limits of laboratory reference
  Exclusion criteria
  1. Pregnant/lactating women or planning on becoming pregnant during the study
  2. Known hypersensitivity to vitamin D or its components.
  3. Pre-existing renal stone disease, chronic renal disease with glomerular filtration rate (eGFR) < 30 mL/min/1.73 m2 or renal dialysis.
  4. Liver failure or chronic liver disease with liver enzymes > 2 fold upper limit of normal (ULN).
  5. History of parathyroid disease or granulomatous disease (TBC and sarcoidosis)
  6. History of malabsorption syndrome or any medical condition that might interfere with vitamin D absorption.
  7. History of small intestine resection.
  8. History of other malignancy within the last 5 years except for carcinoma in situ of the cervix or basal cell carcinoma or squamous cell carcinoma of the skin or in situ malignant melanoma.
  9. Chronic alcohol abuse.
  10. Medical or logistic problems likely to preclude completion of the study.
  11. Taking medication that predisposes to hypercalcemia (digoxin, lithium, thiazide diuretics) or taking medication that would affect metabolism of vitamin D (anticonvulsants, corticosteroids, H2-receptor antagonists)
  12. Intake of vitamin D supplements within 6 months prior to entry of the 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 and Efficacy of LEE011 and LGX818 in Patients With BRAF Mutant Melanoma.

Summary: To evaluate the safety, tolerability and efficacy of LEE011 and LGX818 when administered orally to patients with BRAF mutant melanoma.

Detailed description: In response to developments in the treatment of melanoma, the sponsor reviewed the data from the ongoing study and decided to halt further enrollment of patients in the Phase Ib part of the study. Consequently, the Phase II part of the study was not performed. Early termination of the study was not due to any safety concerns.

Eligibility: Inclusion Criteria:
  -  Age ≥18 years.
  -  Diagnosis of locally advanced or metastatic melanoma along with written documentation of BRAF V600 mutation.
  -  ECOG performance status of 0 - 2.
  -  Patients enrolled into Phase Ib must have evidence of evaluable and/or measurable disease as determined by RECIST v1.1.
  -  Patients enrolled into Phase II (BRAFi naïve and resistant) must have evidence of measurable disease as determined by RECIST v1.1.
  -  Archival tumor tissue must be obtained for patients enrolled in Phase Ib and Phase II arm 1a/b- BRAFi naïve patients. If an archival tumor tissue is not available, a fresh tumor sample is acceptable.
  -  For patients enrolled in the phase II arm 2, patients must agree to undergo a fresh tumor biopsy unless one was collected prior to study entry but at the time of disease relapse from the most recent BRAFi treatment.
  Exclusion Criteria:
  -  Symptomatic brain metastases.
  -  Symptomatic or untreated leptomeningeal disease.
  -  Patients with inadequate laboratory values during screening.
  -  In the phase II BRAFi naïve arms (1a/b), prior exposure to CDK4/6 inhibitor (e.g., PD 0332991)
  -  Impaired cardiac function or clinically significant cardiac diseases.
  -  Impairment of gastro-intestinal (GI) function or GI disease that may significantly alter the absorption of LEE011 or LGX818.
  -  Patients with concurrent severe and/or uncontrolled concurrent medical conditions.
  -  Previous or concurrent malignancy.
  -  Major surgery < 2 weeks before starting study treatment
  -  Known diagnosis of human immunodeficiency virus (HIV) or hepatitis C.
  Other protocol-defined inclusion/exclusion criteria may apply.

Relevance to patient case: definitely relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: A Screening Study to Detect BRAF V600 Mutation-Positive Patients For Enrollment Into Clinical Research Studies of Zelboraf (Vemurafenib)

Summary: This is a screening study to detect BRAF V600 mutation-positive patients for enrollment into clinical research studies of Zelboraf (vemurafenib). Tumor samples will be collected and analyzed from eligible patients with solid tumors (other than metastatic melanoma or papillary thyroid cancer) or multiple myeloma. All institutions with identified patients as defined by this screening protocol will have potential access to the separate vemurafenib protocol MO28072.


Eligibility: Inclusion Criteria:
  -  Histologically confirmed solid tumors (excluding melanoma and papillary thyroid cancer) or multiple myeloma refractory to standard therapy or for which standard or curative therapy does not exist or is not considered appropriate by the investigator
  -  Patients with multiple myeloma must have received at least one line of prior systemic therapy for the treatment of multiple myeloma
  Exclusion Criteria:
  -  Eastern Cooperative Oncology Group (ECOG) performance status > 2
  -  Uncontrolled concurrent malignancy
  -  Active or untreated CNS metastases
  -  History of known carcinomatous meningitis
  -  Prior treatment with a BRAF or MEK inhibitor (prior sorafenib is allowed)
  -  Uncontrolled, severe medical illness or condition as defined in protocol MO28072

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 1b Open Label, Dose Escalation Study of PLX3397 in Combination With Vemurafenib in V600-mutated BRAF Melanoma

Summary: The purpose of this research study is to test the safety of an investigational new drug called PLX3397 when used in combination with Vemurafenib (Zelboraf™) at different dose levels. Vemurafenib has been approved by the United States Food and Drug Administration (FDA)/European Medicines Agency (EMA) for the treatment of a specific category of unresectable or metastatic melanoma.


Eligibility: Inclusion Criteria:
  -  Male or female ≥18 years old.
  -  Patients with histologically confirmed unresectable Stage III or Stage IV metastatic melanoma who have not been previously treated with a selective BRAF inhibitor.
  -  Presence of a BRAF V600 mutation in the tumor tissue using the cobas BRAF mutation assay or comparable standard of care methodology.
  -  Measurable disease per RECIST v. 1.1 criteria.
  -  ECOG performance status 0 or 1.
  Exclusion Criteria:
  -  Radiation therapy within 14 days of C1D1.
  -  Investigational drug use within 28 days of C1D1.
  -  Patients with active CNS lesions are excluded (i.e., those with radiographically unstable, symptomatic lesions). However, patients treated with stereotactic therapy or surgery are eligible if they remain without evidence of disease progression in the brain for ≥3 weeks.

Relevance to patient case: definitely relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Utility of Novel BRAF Test for Melanoma

Summary: This primary purpose of this study is to obtain blood samples from participants with both early and later stages of melanoma (Stage II/III and Stage IV). The researchers hope to better understand an abnormal protein found in many melanoma tumors called the BRAFV600 mutation.
  There will be two separate cohorts (groups) of participants on this study. You will be placed in one of the Groups.
  Group 1-For participants with advanced melanoma: Your existing tumor tissue sample will be compared to the blood samples given in order to further analyze and to understand the BRAFV600E gene mutation.
  Group 2-For participants with stage II/III melanoma: Following surgery, blood samples will be collected and analyzed.
  Understanding the BRAFV600E gene mutation in melanoma will help the researchers better understand the disease, and help plan treatment options for people with melanoma of all stages in the future.

Detailed description: There will be no extra clinic visits for this study. These research blood samples will be drawn at the same time as your regularly scheduled blood draws that are part of standard care for melanoma.
  About 2 to 4 teaspoons of blood will be drawn for each research sample.
  Depending on which group you are in, you will have either a one time blood draw or ongoing blood work for 1-2 years.

Eligibility: Inclusion Criteria:
  -  Biopsy proven advanced (unresectable stage IIIC or stage IV)or high risk (stage II or stage III) malignant melanoma
  Exclusion Criteria:
  -  History of a different malignancy except for the following circumstances: disease-free for at least 2 years and deemed by the investigator to be at low risk for recurrence; or non-metastatic prostate cancer, cervical cancer in situ and basal cell or squamous cell carcinoma
  -  Known history of a different BRAF mutant malignancy

Relevance to patient case: definitely relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Circulating Melanoma Cells in Metastatic Patients Treated With Selective BRAF Inhibitors

Summary: The purpose of this study, is to evaluate Circulating Melanoma Cell (CMC) changes in Metastatic Melanoma (MM) patients, undergoing treatment with selective inhibitors of mutated BRAF.

Detailed description: This is an observational prospective pilot study aimed to investigate the association between changes of total and apoptotic CMC count and disease progression in MM patients undergoing treatment with selective inhibitors of mutated B-RAF.

Eligibility: Inclusion Criteria:
  -  Fourth stage Melanoma patients with both measurable and not measurable lesions undergoing treatment with selective B-RAF inhibitors will be included. To determine the prevalence of CMC-positive patients in IV stage Melanoma, patients without mutated B-RAF undergoing chemotherapy and/or vaccines will be also enrolled at baseline, as part of study protocols approved and activated in the participating centers.
  -  Informed written consent.
  Exclusion Criteria:
  -  Inadequate compliance to multiple blood draws (baseline, 15 days, 1th month, 4th month, and/or at progression) as scheduled in this adjunctive biologic study for patients carrying B-FAF mutation; inadequate compliance to adjunctive blood draws, as scheduled at baseline for BRAF wild-type
  -  Previously exposure to immunological treatment.

Relevance to patient case: definitely relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Modified Melanoma Vaccine for High Risk or Low Residual Disease Patients

Summary: This study is designed for patients who had malignant melanoma and, following tumor removal, are now free of disease, or have only very minor residual disease, and are at a very high risk of disease recurrence. These patients will be treated with the A2/4-1BBL melanoma vaccine, a compatible melanoma cell line that has been engineered to express a molecule termed 4-1BBL, which enhances the chances of the cell line to be recognized by the patient's immune system, and to induce its stimulation. The hypothesis that drives the study states that the immune response against the cell line will also be effective against the residual tumor that may still be present in the body.


Eligibility: Inclusion Criteria:
  1. Patients included in this protocol must carry one or more of the following tissue typing alleles: HLA-A2, -A24, -A33, -B35, -B49, -CW04/12(04/08). We estimate that 50% of melanoma patients will be eligible.
  2. Cutaneous malignant melanoma AJCC stage IIb (>4 mm) or IIc (ulcerated melanoma >4mm).
  3. Metastatic melanoma AJCC stage III (nodal involvement, N1-3a,b) post-surgical removal of lymph nodes.
  4. Metastatic melanoma AJCC stage IV, completely resected.
  5. Non-resectable metastatic melanoma of low burden disease and normal LDH who have undergone at least two treatment lines, including chemotherapy (DTIC, temodal, taxanes, platinum compounds), anti-CTLA-4 (ipilimumab) and B-RAF inhibitor if harboring the V600E BRAF mutation in their tumor.
  6. Non cutaneous malignant melanoma of respective stages including uveal and mucosal melanoma.
  7. Melanoma can be of either mutant or wild-type B-RAF.
  8. Karnofsky performance status > 80 (Normal activity with effort).
  9. No active cardio-respiratory disease.
  10. Not pregnant or nursing. Women must take contraceptives during the treatment period.Hematocrit >25% and WBC >3000.
  11. Informed consent of the patient.
  Exclusion Criteria:
  1. Administration of cytotoxic drugs or extensive radiotherapy less than 28 days prior to protocol administration.
  2. Active brain metastases requiring corticosteroids.
  3. Concurrent malignancy (other than skin cancer, carcinoma in situ of cervix and early stage prostate cancer).
  4. Active serious infection.
  5. Allergy to penicillin.
  6. Patient's will to withdraw from the study at any stage.
  7. HIV and chronic hepatitis B and C carrier

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: An Open-Label Study of Zelboraf (Vemurafenib) in Patients With Braf V600 Mutation Positive Metastatic Melanoma

Summary: This open-label, single-arm, multicenter study will assess the safety and efficacy of Zelboraf (vemurafenib) in patients with Braf V600 mutation positive metastatic melanoma. Patients will receive Zelboraf 960 mg twice a day until progressive disease, unacceptable toxicity, consent withdrawal, death, reasons deemed by the treating physician or study termination.


Eligibility: Inclusion Criteria:
  -  Adults patients >= 18 years of age
  -  Patients with histologically confirmed metastatic melanoma (surgically incurable and unresectable stage IIIC or stage IV; AJCC) with documented BRAF V600 mutation determined by the cobas® BRAF V600 Mutation Test prior to administration of vemurafenib. Unresectable stage IIIC disease must have confirmation from a surgical oncologist
  -  Patients with either measurable or non-measurable disease (RECIST Version 1.1)
  -  Patients may or may not have received prior systemic therapy for metastatic melanoma
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0, 1 or 2
  -  Patients must have recovered from all side effects of their most recent systemic or local treatment for metastatic melanoma
  -  Adequate hematological, renal, and liver function
  -  Negative serum pregnancy test at screening
  -  Fertile men and women must use an effective form of contraception during the study and for at least 6 months after completion of the study
  Exclusion Criteria:
  -  Evidence of symptomatic CNS lesions as determined by the investigator, use of steroid or anti-seizure medication for treatment of brain metastases prior to the first administration of vemurafenib
  -  Patients with previous malignancies (other than melanoma) within the past 2 years except patients with treated and controlled basal or squamous cell carcinoma (SCC) of the skin or carcinoma in-situ of the cervix.
  -  Concurrent administration of any anti-cancer therapies (e.g. chemotherapy, other targeted therapy, experimental drug, etc.) other than those administered in this study
  -  Known hypersensitivity to vemurafenib or another BRAF inhibitor
  -  Pregnant or lactating women
  -  Refractory nausea and vomiting, malabsorption, external biliary shunt, or significant bowel resection that would preclude adequate absorption.
  -  Any of the following within the 6 months prior to the first vemurafenib administration: myocardial infarction, severe/unstable angina, symptomatic congestive heart failure, cerebrovascular accident or transient ischaemic attack, pulmonary embolism, hypertension not adequately controlled by current medications.

Relevance to patient case: definitely relevant