araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

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: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

Clinical trial: Phase II Safety and Efficacy Study of Crizotinib in East Asian Patients With ROS1 Positive, ALK Negative Advanced NSCLC

Summary: To assess treatment effectiveness and safety of oral crizotinib administered to East Asian patients with Advanced Non-Small Cell Lung Cancer (NSCLC) that is confirmed to be positive for a ROS1 positive gene mutation (translocation or inversion) and confirmed negative for an ALK mutation


Eligibility: Inclusion Criteria:
  -  Histologically or cytologically proven diagnosis of NSCLC that is locally advanced or metastatic
  -  treatment-naïve or have received no more than 3 systemic treatment regimen(s)
  -  Positive for translocation or inversion events involving the ROS1 gene
  -  Negative for translocation or inversion events involving the ALK gene
  -  Patients with brain metastases are eligible if asymptomatic, or if treated, must be neurologically stable for at least 2 weeks and are not taking any contraindicated medications
  -  Any prior treatment (chemotherapy, radiation [except for palliative], or surgery) must have been completed at least 2 weeks prior to initiation of study medication
  -  At least 1 measurable tumor lesion as per RECIST v1.1
  -  Female or male, 18 years of age or older
  -  ECOG performance status 0 to 1
  -  Adequate organ function
  -  Signed and dated informed consent
  -  Willingness and ability to comply with scheduled visits, treatment plans, laboratory tests, and other study procedures, including completion of the PRO measures
  -  Agree to use effective contraception during the study period and for at least 90 days after completion of the study treatment
  Exclusion Criteria:
  -  Current treatment on another therapeutic clinical trial
  -  Prior therapy specifically directed against ALK or ROS1 fusion genes
  -  Spinal cord compression unless treated with the patient attaining good pain control and stable or recovered neurologic function, carcinomatous meningitis, or leptomeningeal disease
  -  known interstitial fibrosis or interstitial lung disease
  -  myocardial infarction, severe/unstable angina, coronary/peripheral artery bypass graft, congestive heart failure, or cerebrovascular accident including transient ischemic attack within 3 months prior to start of study treatment
  -  Ongoing cardiac dysrhythmias of NCI CTCAE v4.03 Grade >/=2, uncontrolled atrial fibrillation of any grade, or QTc >470 msec
  -  Pregnant or breast feeding
  -  Use of drugs or foods that are known potent CYP3A4 inhibitors or inducers
  -  Use of other anti-cancer drugs including traditional Chinese medicine on the SFDA list
  -  Evidence of active malignancy within last 3 years

Relevance to patient case: not relevant
Patient case: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

Clinical trial: Translational Study for BRAFV600 Serum and Plasma Determination in Patients With BRAFV600 Metastatic Melanoma

Summary: This is a multi-centric translational study with biological samples collection. The aim of this study is to validate a method to detect BRAFV600 in blood samples.
  Samples: Blood from patients with BRAFV600 metastatic melanoma collected following standard medical practice.
  The treatment is not the aim of the study. Patients can be treated either with specific or no-specific drug.


Eligibility: Inclusion Criteria:
  -  Confirmed diagnosis of melanoma and BRAFV600
  -  Signed Informed Consent Form
  -  Unresectable phase III or phase IV melanoma
  -  The patients should be starting a treatment for melanoma (either first line or subsequent lines)

Relevance to patient case: not relevant
Patient case: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

Clinical trial: Bevacizumab Combined With Carboplatin Plus Paclitaxel Chemotherapy to Treat Metastatic Mucosal Melanoma

Summary: Mucosal melanoma is rare and associated with extremely poor prognosis.No effective treatment for advanced mucosal melanoma patients.Investigators conducted a randomized phase II study in patients with previously untreated metastatic mucosal melanoma to characterize the efficacy and safety of bevacizumab when combined with carboplatin plus paclitaxel.

Detailed description: Mucosal melanoma is rare and associated with extremely poor prognosis.It is the second most common subtype in Asians.No effective treatment for advanced mucosal melanoma patients.Malignant melanoma is a highly vascular tumor in which vascular endothelial growth factor(VEGF) is strongly expressed and seems to play an important role in disease progression.A randomized phase II study evaluated the activity of Bevacizumab in combination with carboplatin plus paclitaxel(CPB arm) in patients with previously untreated advanced melanoma.Overall response rates was 25.5%,median overall survival time(OS) was 12.3 months in the CPB arm. Investigators conducted a randomized phase II study in patients with previously untreated metastatic mucosal melanoma to characterize the efficacy and safety of bevacizumab when combined with carboplatin plus paclitaxel.

Eligibility: Inclusion Criteria:
  1. Histologically confirmed mucosal melanoma with metastases and has no received any systemic treatment.
  2. ECOG performance status 0, 1
  3. Estimated life expectancy of 12 weeks or greater
  4. Age 18 years or older, male or female
  5. At least one measurable site (diameter≥1cm) of disease (RECIST 1.1).
  6. Adequate organ function
  7. Without symptoms of brain metastases and stable in neuro-functions.
  8. Willingness and ability to comply with scheduled visits, treatment plans, laboratory tests, and other study procedures
  Exclusion Criteria:
  1. Mutations in C-KIT or BRAF-V600E, asked for other target treatments
  2. Pregnant or lactation women
  3. Acute infections without control.
  4. Heart disease history, cardiac function class≥NYHA II.
  5. HIV positive or chronic HBV/HCV in active stage.
  6. Brain metastases or primary tumor with positive symptoms
  7. Need anti-epileptic treatments
  8. Organ transplantation history
  9. Hemorrhagic tendency or related history
  10. Renal dialysis patients
  11. Diagnosis of any second malignancy within the last 3 years, except for adequately treated.
  12. Current treatment on another clinical trial
  13. The other improper situations which investigator judged.

Relevance to patient case: not relevant
Patient case: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

Clinical trial: Aggressive Squamous Cell Carcinoma in Organ Transplant Recipients

Summary: To identify risk factors for aggressiveness in Squamous Cell Carcinoma of the skin in organ transplant recipients.

Detailed description: Squamous Cell Carcinomas (SCC) are one of the most common skin cancers. They belong to the epithelial neoplasm of the skin, which manifest a local aggressive growth and have potential for metastasis. Organ transplant recipients have a hundredfold higher incidence of SCC.
  Unfortunately the primary tumor, regional nodes, metastasis (TNM)-Classification for the prognosis of SCC in this group of patient has not yet been established. Therefore there are no standardised criteria for evaluation of local recurrence or prognosis.
  The aim of this study is to identify criteria, which permit a risk assessment relating to aggressiveness of SCC.

Eligibility: Inclusion Criteria:
  Organ transplant recipients with:
  -  > 9 SCC in total or
  -  > 2 SCC per year (in any one year) or
  -  any single "index" SCC that has a very poorly differentiated cell morphology or that behaved aggressively in Terms of local recurrence or local/systemic metastasis
  Exclusion Criteria:
  -  Non organ transplant recipients

Relevance to patient case: not relevant
Patient case: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

Clinical trial: Study of Oral RXDX-101 in Adult Patients With Locally Advanced or Metastatic Cancer Targeting NTRK1, NTRK2, NTRK3, ROS1, or ALK Molecular Alterations.

Summary: Entrectinib (RXDX-101) is an orally available inhibitor of the tyrosine kinases TrkA (coded by the gene NTRK1), TrkB (coded by the gene NTRK2), TrkC (coded by the gene NTRK3), ROS1 (coded by the gene ROS1), and ALK (coded by the gene ALK). Molecular alterations to one or more of these targets are present in several different tumor types, including non-small cell lung cancer (NSCLC), colorectal cancer (CRC), prostate cancer, papillary thyroid cancer, pancreatic cancer, and neuroblastoma. Patients with locally advanced or metastatic cancer with a detectable molecular alteration in targets of interest may be eligible for enrollment.
  Phase 1 will assess safety and tolerability of entrectinib via standard dose escalation scheme and determine the recommended Phase 2 dose. Safety and efficacy will be assessed in the dose expansion portion of the study.


Eligibility: Key Inclusion Criteria:
  -  Histologically or cytologically confirmed diagnosis of locally advanced or metastatic solid tumors that have a NTRK1, NTRK2, NTRK3, ROS1, or ALK molecular alteration.
  -  Measurable disease according to RECIST version 1.1.
  -  Prior cancer therapy is allowed, including crizotinib, ceritinib, and investigational drugs.
  -  Prior radiotherapy is allowed
  -  Patients with controlled asymptomatic central nervous system involvement are allowed.
  -  Resolution of all acute toxic effects (excluding alopecia) of any prior anti-cancer therapy to National Cancer Institute Common Terminology Criteria for Adverse Events (NCI CTCAE) Version 4.03 Grade less than or equal to 1.
  -  Eastern Cooperative Oncology Group (ECOG) performance status (PS) ≤ 2.
  -  Adult patients age 18 years or older.
  -  Life expectancy of at least 3 months.
  Key Exclusion Criteria:
  -  Current participation in another therapeutic clinical trial.
  -  Prior treatment with entrectinib.
  -  History of prolonged QTc interval (e.g., repeated demonstration of a QTc interval > 450 milliseconds).
  -  History of additional risk factors for torsade de pointes (e.g., family history of long QT syndrome).
  -  Known active infections (bacterial, fungal, viral including HIV positivity).
  -  Gastrointestinal disease (e.g., Crohn's disease, ulcerative colitis, or short gut syndrome) or other malabsorption syndromes that would impact on drug absorption.
  -  Known interstitial lung disease, interstitial fibrosis, or history of tyrosine kinase inhibitor-induced pneumonitis.
  -  Peripheral neuropathy ≥ Grade 2.

Relevance to patient case: not relevant
Patient case: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

Clinical trial: Oral TRK Inhibitor LOXO-101 for Treatment of Advanced Adult Solid Tumors

Summary: This is a multicenter, open-label, Phase 1 study of orally administered larotrectinib in adult subjects with advanced solid tumors that have progressed or are non responsive to available therapies and for which no standard or available curative therapy exists.

Detailed description: The trial will be conducted in 2 parts: an initial dose escalation phase of larotrectinib in subjects with advanced solid tumors. This will be followed by an expansion phase in solid tumor subjects with an NTRK fusion, documented alteration of the TRK gene or investigator documentation of perceived benefit from a TRK targeted agent. During the escalation phase, larotrectinib will be taken once daily (QD) or twice daily (BID). During the expansion phase, the larotrectinib dose selected from the escalation phase will be explored in approximately 40 additional subjects.
  The objectives of the dose escalation phase are to determine the safety, tolerability, pharmacokinetic profile, and recommended dose of orally administered larotrectinib. The objectives of the expansion phase are to better characterize the safety and efficacy of larotrectinib in patients with specific NTRK genes or proteins, or patients who, in the opinion of the Investigator, may derive benefit from a highly selective TRK inhibitor such as larotrectinib.

Eligibility: Escalation Phase [Inclusion]
  -  Locally advanced or metastatic adult solid tumor that has progressed or was nonresponsive to available therapies, are unfit for standard chemotherapy or for which no standard or available curative therapy exists;
  -  ECOG score of 0, 1 or 2;
  -  Adequate hematologic, hepatic, and renal function;
  Expansion Phase [Inclusion]
  -  Escalation Phase inclusion criteria
  -  Evidence of the NTRK or TRK molecular characteristic as specified for that cohort, such as an NTRK translocation, amplifications, mutations or other alterations that may interfere with TRK signaling as previously determined with prior testing from a Clinical Laboratory Improvement Amendments (CLIA)-certified or equivalent certified laboratory. Additionally, patients who, in the opinion and clinical judgement of the local Investigator, may derive benefit from a targeted TRK inhibitor like larotrectinib, may also enroll.
  Exclusion (for both Escalation and Expansion)
  • Current treatment with a strong cytochrome P450 (CYP) 3A4 inhibitor or inducer (EIAEDs and dexamethasone for CNS tumors or metastases, on a stable dose, are allowed)

Relevance to patient case: not relevant
Patient case: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

Clinical trial: A Single-Arm, Open-Label, Multicenter Clinical Trial With Nivolumab (BMS-936558) for Subjects With Histologically Confirmed Stage III (Unresectable) or Stage IV Melanoma Progressing Post Prior Treatment Containing an Anti-CTLA4 Monoclonal Antibody (CheckMate 172)

Summary: The purpose of this study is to determine the rate and frequency of high-grade (CTCAE v4.0 Grade 3 or higher), treatment-related, select adverse events in subjects with histologically confirmed stage III (unresectable) or stage IV melanoma and progression post prior treatment containing an anti-Cytotoxic T Lymphocyte Antigen (CTLA-4) monoclonal antibody, treated with Nivolumab (BMS-936558) at a dose of 3 mg/kg every two weeks.


Eligibility: For more information regarding BMS clinical trial participation, please visit www.BMSStudyConnect.com
  Inclusion Criteria:
  -  Subjects with histologically confirmed malignant melanoma
  -  Eastern Cooperative Oncology Group (ECOG) Performance Status (PS):
  -  PS 0 to 1
  -  PS 2
  -  Previously treated unresectable stage III or stage IV melanoma as per the American Joint Committee on Cancer 2010 Guidelines regardless of BRAF mutation status
  -  Subjects must have experienced evaluable Response Evaluation Criteria In Solid Tumors (RECIST 1.1)-defined disease progression
  -  Prior treatment with chemotherapy, interferon (adjuvant setting), Interleukin (IL-2), BRAF/MEK inhibitors for subjects with known BRAF mutations, Mitogen-activated or extracellular signal- regulated protein kinase (MEK) inhibitors for Neuroblastoma Ras Viral (v-ras) oncogene homolog (NRAS) mutations, and cKIT inhibitor subjects with known cKIT mutations are allowed
  -  Patients with CNS metastases are eligible:
  -  if CNS metastases are treated, patients are asymptomatic or neurologically returned to baseline
  -  if they have previously untreated CNS metastases and are asymptomatic
  -  if they have leptomeningeal metastases, are treated and asymptomatic or neurologically returned to baseline with life expectancy > 3 months
  -  Patients with a known history of Grades 3-4 immune-related adverse reactions during/after anti-CTLA-4 therapy if all toxicities have resolved at least to Grade 1
  Exclusion Criteria:
  -  Subjects with untreated, active Central Nervous System (CNS) metastases are excluded

Relevance to patient case: not relevant
Patient case: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

Clinical trial: Study to Determine the Feasibility of Sentinel Node Biopsy in Patients With Anal Cancer

Summary: The purpose of this study is assess the technical and operational feasibility of a specialised biopsy technique, sentinel lymph node biopsy (SLNB), in patients with anal cancer.

Detailed description: SLNB is based on the premise that lymphatic dissemination from a tumour occurs in a stepwise fashion, with initial involvement of a primary node, called the sentinel node, before dissemination to the remainder of the lymphatic chain. If the sentinel node is histologically negative, then the remainder of the nodes in the same anatomic region will be at a lower (assumed to be minimal) risk of containing metastases. SLNB is part of standard care for patients with malignant melanoma and with breast cancer but has yet to be prospectively evaluated in patients with anal cancer.
  Currently, the standard way to treat patients with anal cancer is to deliver a combination of chemotherapy and radiation to the tumour at the anus together with 'preventative' (prophylactic) radiotherapy to the lymph glands of the groin and pelvis. There is a growing perception for the need to reduce the morbidity of radiotherapy i.e. current regimens over-treat the patient and one approach is to reduce radiotherapy volume and/or dose where there is an absence or very low risk of nodal metastases.
  This feasibility study is a vital first step in informing the design of a larger study examining the role of SLNB in clinical decision-making and outcomes for patients with anal cancer. In this trial eligible patients will attend for lymphoscintigraphy, to locate the lymph node, before sentinel lymph node removal by surgery. Detection rate of the sentinel node(s) will be the key outcome for the study.

Eligibility: Inclusion Criteria:
  -  Patients with squamous cell carcinoma (SCC) of the anus (any T size and/or those with recurrent disease)
  -  Equivocal lymph node involvement on standard CT staging or magnetic resonance (MR) staging or PET-CT scan, as determined by the anal cancer multidisciplinary team (MDT)
  -  Age >= 18 years
  -  Written informed consent provided by the patient
  Exclusion Criteria:
  -  Patients with unequivocal lymph node involvement on standard CT staging or MR staging, as determined by the anal cancer MDT.
  -  Unfit for surgical biopsy
  -  Patients undergoing palliative treatment
  -  Previous pelvic or inguinal area radiotherapy
  -  Other coincident cancers
  -  Previous inguinal surgery (e.g. hernia repair) with mesh insertion

Relevance to patient case: not relevant
Patient case: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

Clinical trial: Pancreatic Cancer Early Detection Program

Summary: Early detection testing is recommended for individuals at elevated risk for the development of Pancreatic Cancer. This Protocol will define sufficiently elevated risk as either equal to or greater than five times the general population risk, or five times the average risk (1.5%) of developing pancreatic cancer by age 70; that is a 7.5% lifetime risk. Our inclusion criteria has a strong focus on the risk for pancreatic cancer imparted by the presence of hereditary cancer genes, as well as by family history. Enrolled subjects will undergo Endoscopic Ultrasound (EUS) alternating with Magnetic Resonance Imaging (MRI), every six to 12 months, for up to 5 years.

Detailed description: Interested individuals can be referred by physicians, or by family or friends.
  Individuals are informed that the purpose of this study is to collect outcome data following early detection testing based upon our criteria for elevated risk.
  Consent is obtained by any of the co-investigators. Consent is obtained for the primary PCEDP, and also obtained to allow for data to be used by our Cancer Program.
  We have a weekly review of all calls made and of all enrollments.
  We have a monthly meeting to review all proceeding regarding the study.
  Our IRB routinely reviews the proceedings of the study
  Our institution has a monthly Clinical research Committee meeting.

Eligibility: Inclusion Criteria: Any of the following:
  1. Known carrier of either the BRCA2 or CDKN2A mutation;
  2. Known carrier of any of the following mutations (BRCA1, MLH1, MSH2, PMS2, MSH6, EPCAM , P53, PALB2, APC, or ATM) PLUS first or second degree relative affected with pancreatic cancer;
  3. Individual with Peutz-Jeghers Syndrome;
  4. Familial Pancreatic Cancer, defined as at least two affected relatives with Pancreatic Cancer, who are first degree relatives with each other, and at least one of those affected must be first degree relative to the study subject;
  5. Both parents affected, any age:
  6. Any first degree relative diagnosed with pancreatic cancer under age 50;
  7. Chronic Pancreatitis Syndrome, defined by either PRSS1 or SPINK1 mutations AND appropriate clinical and family history
  Exclusion Criteria:
  1. Any medical condition that contraindicates endoscopy or biopsy
  2. Any medical condition that contraindicates MRI
  3. Status post partial or complete resection of the pancreas
  4. History of pancreatic cancer, either endocrine or exocrine
  5. Clinical suspicion of pancreatic cancer, or any previous radiographic or histologic diagnosis of a pre-malignant finding, including IPMN (Intraductal papillary mucinous neoplasm) and PanIN (Pancreatic intraepithelial Neoplasm).
  6. diagnosis of dementia
  7. Uncontrolled, current illness
  8. Renal insufficiency with serum creatinine greater than 2.0 mg/dl

Relevance to patient case: not relevant