araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Clinical and Histopathologic Characteristics of BAP1 Mutations

Summary: The goal of this protocol is to determine the prevalence of somatic and germline mutations in BAP1 (BRCA associated protein-1) among patients with mesothelioma , choroidal nevus, primary uveal melanoma (UM), or metastatic UM seen at our institution.


Eligibility: Inclusion Criteria:
  All consents:
  -  > or = to 18 years of age
  -  Ability to provide informed consent
  Consent 1:
  Mesothelioma
  -  Histologically proven diagnosis of Mesothelioma OR Choroidal nevus
  -  Diagnosis of choroidal nevus by direct examination and/or ultrasound/optical coherence tomography and possibly fluorescein angiography OR Primary uveal melanoma
  -  Diagnosis of uveal melanoma by direct examination and/or ultrasound/optical coherence tomography and possibly fluorescein angiography
  Consent 2:
  Mesothelioma
  -  Histologically proven diagnosis of Mesothelioma AND
  -  BAP1 mutation or loss of expression identified in tumor sample
  OR one of the following:
  -  Age<50 at diagnosis
  -  No history of asbestos exposure
  -  Personal history of choroidal nevus, uveal melanoma, melanoma, renal cell carcinoma, or cholangiocarcinoma
  -  Family history of choroidal nevus, uveal melanoma, mesothelioma, renal cell carcinoma, or cholangiocarcinoma
  -  History of malignancy in more than two first-degree relatives OR Choroidal nevus
  -  Diagnosis of choroidal nevus by direct examination and/or ultrasound/optical coherence tomography and possibly fluorescein angiography AND one of the following:
  -  More than one clinical risk factor, which may include: orange pigment, thickness > 1 < 2.5mm
  -  Personal history of uveal melanoma, skin melanoma, mesothelioma renal cell carcinoma, or cholangiocarcinoma
  -  Family history of choroidal nevus, uveal melanoma, mesothelioma renal cell carcinoma, or cholangiocarcinoma OR Primary uveal melanoma
  -  Diagnosis of uveal melanoma by direct examination and/or ultrasound/optical coherence tomography and possibly fluorescein angiography
  AND one of the following:
  -  Personal history of uveal melanoma, skin melanoma, mesothelioma, renal cell carcinoma, or cholangiocarcinoma
  -  Family history of choroidal nevus, uveal melanoma, mesothelioma, renal cell carcinoma, or cholangiocarcinoma
  -  History of malignancy in more than two first-degree relatives OR Metastatic uveal melanoma
  -  Histologically proven diagnosis of metastatic uveal melanoma AND
  -  BAP1 mutation or loss of expression identified in tumor sample
  OR one of the following:
  -  Personal history of uveal melanoma, skin melanoma, mesothelioma renal cell carcinoma, or cholangiocarcinoma
  -  Family history of choroidal nevus, uveal melanoma, mesothelioma renal cell carcinoma, or cholangiocarcinoma
  -  History of malignancy in more than two first-degree relatives
  Consent 3:
  -  Relative of patient with germline BAP1 mutation identified through identified testing
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: A Phase II Study of Imatinib Versus Interferon as Adjuvant Therapy in KIT-mutated Melanoma

Summary: The purpose of this study is to compare the relapse free survival and overall survival of Imatinib (Gleevec) or high dose Interferon (Intron) in treating melanoma which has primary tumor and regional lymphonode (if have) removed in patients whose disease carries a c-kit mutation. It is assumed that Gleevec may be more effective on relapse free survival as the adjuvant treatment compared with Interferon.

Detailed description: If mutation tests show that the patient is eligible and they choose to participate in the study, they will be randomized and receive imatinib/Interferon. Each imatinib pill will be 100mg and the participants will take 4 pills once daily (400mg).Participants randomized to the interferon arm will receive Interferon 1500wiu/m2 d1-5 for 4 weeks followed by 900wiu IH TIW for 11 months. The following study procedures will also be performed at routine intervals throughout the course of treatment including blood tests, medical history updates, physical exams and Chest/Abdomen/Pelvic CT examinations.Participants will be on this study for one year and then be followed up to relapse or distal metastasis.

Eligibility: Inclusion Criteria:
  -  Melanoma patients whose primary tumor and regional lymphonodes (if have)have been resected
  -  Histologically documented AJCC stage IIB to IIIC
  -  C-kit mutation documented from either primary or metastatic lymphnode site
  -  ECOG performance status 0 or 1
  -  Age 18 years or older
  -  Creatinine < 1.5 x ULN
  -  ANC > 1500 ul
  -  Platelets > 100,000 ul
  -  Total bilirubin, AST, and ALT < 2 x ULN
  -  Amylase and lipase < 1.5 x ULN
  -  no prior chemotherapy or investigational drug
  Exclusion Criteria:
  -  Severe and/or uncontrolled medical disease
  -  Pregnant or nursing mothers
  -  Any other significant medical, surgical, or psychiatric condition that may interfere with compliance
  -  Patient is < 5 years free of another primary malignancy except: basal cell skin cancer or a cervical carcinoma in situ
  -  Concurrent treatment with Warfarin
  -  Prior treatment with c-kit inhibitor
  -  Patient with Grade III/IV cardiac problems as defined by NYHA criteria
  -  No H2 blockers or proton pump inhibitors
  -  Known chronic liver disease
  -  Known diagnosis of HIV infection
  -  Major surgery within 2 weeks prior to study entry
  -  Patient has received any other investigational agent within 28 days of first study drug dosing
  -  Chemotherapy within 4 weeks prior to study entry

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: A Phase 2 Study of Panitumumab in Patients With Cetuximab-refractory Metastatic Colorectal Cancer

Summary: The purpose of this study is to assess if panitumumab is active enough to warrant comparative studies in patients with metastatic colorectal cancer that has progressed after treatment with cetuximab.

Detailed description: The study was amended with modification of inclusion criteria (from wild-type tumor KRAS gene to wild-type RAS gene, including KRAS and NRAS exons 2, 3 and 4)
  RAS mutational status of tumors of patients enrolled before amendment 1 approval will be centrally revised. Patients whose tumors will result RAS mutated at the biomarkers central revision, will be replaced. Therefore, the overall sample size at both the stages may be higher than the one initially planned.

Eligibility: Inclusion Criteria:
  -  Pathologic diagnosis of metastatic colorectal adenocarcinoma
  -  a wild-type RAS tumor (mutational status has to be determined by an experienced laboratory using validated test methods for detection of KRAS exons 2, 3, and 4, and NRAS exons 2, 3, and 4
  -  Failure from previous treatment with fluoropyrimidine, oxaliplatin and irinotecan. Patients may or may not have been treated with bevacizumab.
  -  Documented disease progression following a treatment with cetuximab in patients who showed either an objective response after 8 weeks or stable disease after 16 weeks of cetuximab treatment.
  -  Age at least 18 years
  -  ECOG Performance Status 0-2
  -  Neutrophils at least 1,500 mm3, platelets at least 100,000 mm3, and hemoglobin at least 9 g/dL
  -  Bilirubin level less than 1.5 times ULN
  -  AST (SGOT) and ALT (SGPT) not greater than 2.5 times ULN (or 5 times ULN in presence of liver metastasis)
  -  Serum creatinine less than 1.5 times ULN
  -  Effective contraception, if the risk of conception exists
  -  Life expectancy at least 3 months
  -  Written informed consent
  Exclusion Criteria:
  -  Symptomatic brain metastasis
  -  Interstitial pneumonitis or pulmonary fibrosis
  -  Any other malignancies within 5 years (except for adequately treated carcinoma in situ of the cervix or non melanoma skin cancer)
  -  Chemotherapy, radiotherapy or immunotherapy within the past 4 weeks
  -  Any unstable systemic disease (including active infections, any significant hepatic, renal or metabolic disease), metabolic dysfunction, physical examination finding, or clinical laboratory finding that contraindicates the use of study drugs or render the patient at high risk from treatment complications
  -  Subject pregnant or breast feeding, or planning to become pregnant within 6 months after the end of treatment

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Pilot Study Evaluating the Efficacy and Safety of Metformin in Melanoma

Summary: In western countries, melanoma represents a major mistake of public health by its frequency, lethality and the increasing of incidence. Surgery can cure melanoma diagnosed very early. In other cases, it exists a risk of recurrence of lymph node and visceral. At the stage of visceral metastases, the prognosis of melanoma is catastrophic, with a median survival of 6 months. Indeed, the reference chemotherapy by dacarbazine induces a very limited response rate of 10-20%, the ipilimumab which has been authorized in the second intention, has a response rate of 10%, and other available treatments don't have a superior efficiency. Metformin is an oral antidiabetic of biguanides family which acts by inducing the activation of AMPK, a molecule which is inactivated in many cancers including the melanoma. In agreement with these data, several preclinical studies suggested that metformin has antineoplastic activity. In the case of melanoma, a study published recently has showed that metformin inhibits proliferation of melanoma cells in vitro and we confirmed for our part these results in our laboratory (INSERM U895).


Eligibility: Inclusion Criteria:
  -  Major patients with metastatic melanoma (stage IIIC non-résécable or no surgically curable or stage IV with classification AJCC) in progression after a first-line of treatment by vemurafenib or chemotherapy, and non-eligible or non-responders to ipilimumab.
  Metastases measurable by RECIST criteria. Hematologic, renal and hepatic appropriate functions. Negative pregnancy test.
  Exclusion Criteria:
  -  Patients with symptomatic brain metastases and Performans Status (PS)>2. Patients with carcinomatous meningitis. Pregnant or breathfeeding women. Patients with a contraindication to the metformine. HIV infection, active infection with HBV or HCV. Patients already treated with metformin in the context of diabetes.

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

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: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Biomarker Development for Response Prediction by DNA Mutational Analysis

Summary: The purpose of this study is to determine whether it is possible to predict response to chemotherapy in patients with metastatic cancer who are treated with irinotecan by determining the mutational profile of the tumor.


Eligibility: Inclusion Criteria:
  1. Patients with a metastatic solid tumor who have failed at least one line of palliative chemotherapy and are irinotecan naïve.
  2. Patients who are, as per local protocol, eligible for palliative treatment with (standard of care) irinotecan.
  3. Measurable metastatic lesion(s), according to RECIST 1.1 criteria.
  4. Radiological measurable metastatic lesion(s) of which a histological biopsy can safely be obtained:
  1. Patients with safely accessible metastases.
  2. Patients not known with bleeding disorders (such as hemophilia) or bleeding complications from biopsies, dental procedures or surgeries.
  3. Patients not using any anti-coagulant medication at the time of biopsy: all aspirin derivatives, NSAID's, coumarines, platelet function inhibitors, heparins (including LMWHs) and oral factor Xa inhibitors are not allowed, unless medication can either be safely stopped or counteracted.
  4. Adequate coagulation status on the day of biopsy as measured by:
  -  PTT < 1.5 x ULN
  -  APTT < 1.5 x ULN
  -  Platelet count 100 x 10*9 / L or higher
  -  PT-INR < 1.6
  -  HB > 6
  5. Biopsies should be performed at least four weeks after last bevacizumab administration.
  5. Patients age 18 years or up, willing and able to comply with the protocol as judged by the investigator with a signed informed consent.
  Exclusion Criteria:
  Patients not meeting all of the above inclusion criteria.

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

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

Summary: This study is based on the hypothesis that stimulation of the immune response against the tumor can help destroy residual tumor in melanoma patients with very high risk for disease recurrence and in patients with relatively low tumor burden who already got first line treatment for their disease.
  Ongoing clinical trials in the Hadassah Hospital have shown that vaccination of patients with a cell line of tumor cells from the patient himself, or with a combination of three cell lines that partially match the patient's cell characteristics, could improve the immune response against the tumor, was associated with improved disease-free and overall survival.
  In this study, the investigators will evaluate the efficacy of a modified tumor cell vaccine, in terms of immune response,improved disease-free and overall survival. The vaccine consists of a cell line that has a high expression level of melanoma molecules, and has been genetically modified to induce a strong immune response.


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 (over 4 mm) or IIc (ulcerated melanoma over 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 cutaneous malignant melanoma of respective stages including uveal and mucosal melanoma.
  6. Melanoma can be of either mutant or wild-type B-RAF.
  7. Karnofsky performance status over 80 (Normal activity with effort).
  8. No active cardio-respiratory disease.
  9. Hematocrit over 25% and WBC over 3000.
  10. 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 cortico-steroids.
  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 wish to withdraw from the study at any stage.

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

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: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: BAP1 Testing in Instance Choroidal Nevi or Uveal Melanoma

Summary: The BAP1 trial will examine the blood of patients diagnosed with choroidal nevi or uveal melanoma for a germline BAP1 mutation and other genetic markers associated with developing malignancy as well as additional sequencing of the uveal melanoma genome.

Detailed description: A germline BAP1 mutation predisposes a person to developing uveal melanoma and other cancers. If a mutation is discovered, it changes the potential approach to managing the nevus. In the presence of a known genomic change associated with aggressive disease, closer follow up and more aggressive treatment could preserve the patient's vision and prevent micrometastatic spread. This new screening technique will be able to extend the length and quality of life of patients with more frequent targeted cancer screens.

Eligibility: Inclusion Criteria:
  any person with choroidal nevi
  -  Willingness to provide signed informed consent
  -  Age > 18 years
  -  Diagnosis of choroidal nevi or uveal melanoma
  Threre are no exclusionary criteria for this study.

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Study of Nivolumab (BMS-936558) Plus Ipilimumab Compared With Ipilimumab Alone in the Treatment of Previously Untreated, Unresectable, or Metastatic Melanoma

Summary: The primary purpose of this study is to compare the objective response rate, as determined by investigators, of Nivolumab combined with Ipilimumab versus Ipilimumab monotherapy in patients with untreated, unresectable, or metastatic melanoma


Eligibility: For more information regarding BMS clinical trial participation, please visit www.BMSStudyConnect.com
  Key Inclusion Criteria:
  -  Eastern Cooperative Oncology Group performance status of 0 or 1
  -  Histologically confirmed unresectable Stage III or Stage IV melanoma
  -  No prior systemic anticancer therapy for unresectable or metastatic melanoma. Note that prior adjuvant or neoadjuvant melanoma therapy is permitted if it was completed at least 6 weeks prior to date of first dose, and all related adverse events have either returned to baseline or stabilized
  -  Tumor tissue obtained in the metastatic setting or from an unresectable site must be provided for biomarker analyses and sent to the central laboratory. Biopsy should be excisional, incisional punch, or core needle. Fine needle aspirates or other cytology samples are insufficient
  -  Known BRAF V600 mutation status as determined by an FDA-approved test. Patients with either V600 wild-type or V600 mutation-positive melanoma are eligible.
  Key Exclusion Criteria:
  -  Active brain metastases or leptomeningeal metastases. Patients with treated brain metastases are eligible if there is no evidence of progression on magnetic resonance imaging scan for at least 8 weeks after completion of treatment and within 28 days prior to first dose of study drug administration. There must also be no requirement for high doses of systemic corticosteroids that could result in immunosuppression (>10 mg/day prednisone equivalents) for at least 2 weeks prior to study drug administration
  -  Ocular melanoma
  -  Patients with active, known, or suspected autoimmune disease. Those with vitiligo, type I diabetes mellitus, residual hypothyroidism due to autoimmune condition only requiring hormone replacement, psoriasis not requiring systemic treatment, or conditions not expected to recur in the absence of an external trigger are permitted to enroll.

Relevance to patient case: not relevant