araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Analysis of Dendritic Phenotype and Function of Patients Receiving VEGF-Trap on VGFT-ST-0202

Summary: RATIONALE: Studying the dendritic cells in samples of blood from patients with cancer receiving aflibercept may help doctors learn about the effect of aflibercept on dendritic cells.
  PURPOSE: This laboratory study is evaluating dendritic cells in patients with advanced solid tumors or non-Hodgkin lymphoma receiving aflibercept on clinical trial VGFT-ST-0202.

Detailed description: OBJECTIVES:
  -  Evaluate the effect of in vivo aflibercept on the presence of different populations of dendritic cells (DC) and immature cells (ImC) in the peripheral blood of cancer patients by characterizing the time course (kinetics) of the improvement in antigen presenting cell (APC) phenotype (decline in DC/ImC ratio) occurring early and late after aflibercept administration.
  -  Evaluate the effect of aflibercept administration on DC function based on ability to stimulate antigen specific proliferative (allogeneic and tetanus toxoid) and cytolytic T cell responses (influenza) by characterizing the time course (kinetics) of the improvement in APC function occurring early and late after aflibercept administration.
  -  Explore the relationship of baseline aflibercept level and host APC phenotype.
  OUTLINE: This is a multicenter study.
  Patients undergo phlebotomy and blood collection at baseline and on days 15, 29, and 57. Samples are analyzed for dendritic cell phenotype, subpopulations, maturation status, and function in terms of ability to activate autologous T cells.

Eligibility: Inclusion Criteria:
  -  Diagnosis of advanced solid tumor or non-Hodgkin lymphoma and enrolled on clinical trial VGFT-ST-0202
  -  Hemoglobin ≥ 10 g/dL
  -  Willing to undergo phlebotomy
  Exclusion Criteria:
  -  none listed
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Studying Tumor Tissue Samples From Patients With Melanoma Who Have Undergone Sentinel Lymph Node Biopsy

Summary: RATIONALE: Studying samples of tumor tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer. It may also help the study of cancer in the future.
  PURPOSE: This laboratory study is looking at tumor tissue samples from patients with melanoma who have undergone sentinel lymph node biopsy.

Detailed description: OBJECTIVES:
  -  Develop a predictive model for sentinel lymph node biopsy positivity in patients with melanoma who have undergone sentinel lymph node biopsy.
  -  Develop a survival model for relapse based on sentinel lymph node biopsy positivity.
  -  Assess the genetic determinants in primary melanomas that predict a metastatic phenotype and thereby improve understanding of the biology of the metastases in melanoma.
  OUTLINE: This is a retrospective, case-controlled, multicenter study. Patients are stratified according to Breslow thickness of the tumor (0.75-1.50 mm vs 1.51- 4 mm vs > 4 mm) and gender.
  Archived tumor tissue is analyzed by immunohistochemistry (IHC) for AP2, vascular endothelial growth factor, MMP 2, MCM4, and others, if feasible. Sentinel node biopsies are analyzed by IHC for CD31, LYVE-1, and D2-40 expression. RNA and DNA are also extracted for genetic expression studies and mutation analysis (e.g., BRAF, NRAS, PTEN, CDKN2A).
  Patient data related to relapse and recurrence is collected, if available.
  Peer reviewed and funded or endorsed by Cancer Research UK
  PROJECTED ACCRUAL: A total of 1,000 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Confirmed diagnosis of cutaneous melanoma
  -  Breslow thickness > 0.75 mm
  -  Has undergone sentinel lymph node biopsy
  -  No primary melanoma that has not originated in the skin
  -  No multiple primary melanomas
  -  Currently under clinical followup OR discharged from follow up within the past 3 months
  PATIENT CHARACTERISTICS:
  -  No other malignancy except for nonmelanoma skin cancer or cervical carcinoma in situ
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Studying T Cells in Blood and Bone Marrow Samples From Patients With Multiple Myeloma

Summary: RATIONALE: Studying samples of blood and bone marrow from patients with cancer in the laboratory may help doctors learn more about T cells and plan better treatment for multiple myeloma.
  PURPOSE: This research study is looking at T cells in blood and bone marrow samples from patients with multiple myeloma.

Detailed description: OBJECTIVES:
  Primary
  -  To evaluate the feasibility of expanding myeloma-specific T cells using autologous ex vivo expanded B cells loaded with myeloma antigens as antigen-presenting cells (B-APCs) in peripheral blood and bone marrow samples from patients with multiple myeloma.
  Secondary
  -  To examine the feasibility of selecting and expanding myeloma-specific T cells ex vivo using interferon γ release and CD3/CD28 stimulation.
  OUTLINE: Peripheral blood and bone marrow samples are collected periodically for laboratory studies. Samples are analyzed to assess the feasibility of expanding autologous B cells ex vivo using CD40L and IL-4; the antigen-presenting phenotype of autologous B-cell antigen-presenting cells (B-APCs) using flow cytometry; and the antigen-presenting function of B-APCs using ELISPOT and chromium-release assay. Myeloma-specific interferon γ secreting T cells are isolated and selected using Miltenyi beads. The selected myeloma-specific T cells are expanded ex vivo using anti CD3/CD28 beads.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of multiple myeloma
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Messenger Ribonucleic Acid (mRNA) Transfected Dendritic Cell Vaccination in High Risk Uveal Melanoma Patients

Summary: 1. Rationale
  Immunotherapy applying ex vivo generated and tumor antigen-loaded dendritic cells (DC) has now successfully been introduced in the clinic. A limited, but consistent, number of objective immunological and clinical responses have been observed. Most of the successful results have been observed in patients with minimal residual disease, rather than patients with advanced metastatic disease. Moreover, the investigators' preliminary results show that presence of tumor epitope specific T cells in biopsies taken from delayed type hypersensitivity (DTH) reaction sites highly correlates with prolonged progression free survival (PFS).
  Within uveal melanoma patients, a group with high risk of metastatic disease can be identified on basis of tumor specific genetic changes in loss of chromosome 3.
  At present no standard adjuvant or systemic treatment is available. Applying DC-based immunotherapy in this group of high risk patients might reduce the risk of recurrence without interference in the current treatment guidelines.
  2. Objectives
  In this joint clinical study of Radboud University Nijmegen Medical Centre (RUNMC) and Rotterdam Eye Hospital, the investigators aim to determine the in vivo immunological response induced in high risk uveal melanoma patients vaccinated with mRNA-transfected DC.
  3. Study design
  This study is an open label non-randomized phase II intervention study.
  4. Study population
  The investigators' study population consists of HLA-A2 positive patients with a high risk uveal melanoma with proven expression of melanoma associated antigens tyrosinase and/or gp100.
  5. Main study endpoints
  This is an exploratory study aiming to demonstrate proof of principle. The first study endpoints are in vivo immunological response induced in high risk uveal melanoma patients vaccinated with mRNA-transfected DC, administered i.v./i.d. and toxicity. Secondary study endpoints are progression free survival, overall survival, and toxicity.


Eligibility: Inclusion Criteria:
  -  histological documented uveal melanoma
  -  HLA-A2.1 phenotype (intervention arm)
  -  non-HLA-A2.1 phenotype (control arm)
  -  melanoma expressing gp100 and/or tyrosinase
  -  high risk genetic profile (loss of chromosome 3) determined by FISH
  -  interval since local treatment of uveal melanoma < 12 months
  -  no signs of liver metastasis determined by diagnostic CT-abdomen
  -  normal serum LDH
  -  no signs of cerebral metastases
  -  bilirubin < 25 micromol/l
  -  WHO performance scale 0-1
  -  age 18-75 years
  -  written informed consent
  -  expected adequacy of followup
  -  no pregnant or lactating women
  Exclusion Criteria:
  -  history of second malignancy, except adequately treated basal cell carcinoma
  -  serious active infections
  -  autoimmune disease or organ allografts
  -  concomitant use of immunosuppressive drugs
  -  known allergy to shell-fish

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: (Hyoscine Butylbromide) for Abdominal Pain Associated With Cramping on Demand Basis

Summary: The primary objective of this pilot study is to assess effects of Hyoscine Butylbromide (HBB) 20 mg in comparison to placebo, when used as needed, as measured by the subject's assessment of intensity of abdominal pain associated with cramping (APC) in the treatment of two episodes.


Eligibility: Inclusion Criteria:
  History of recurrent abdominal pain with cramping (APC) for at least three months.
  Recorded at least two episodes of APC of at least "moderate" intensity (i.e., 5 or above on a 0-10 point scale) lasting one hour in the eDiary during the run-in period.
  Exclusion Criteria:
  Experiencing daily episode of APC during Run-in period Active gastrointestinal disease during the past 12 months including malignancy, inflammatory bowel disease, celiac disease or complete or partial bowel obstruction and who have undergone major gastrointestinal surgery with the past 12 months (patients with history of appendectomy, cholecystectomy, bilateral tubal ligation and c-section within past 12 months are allowed in the study).

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Study of Tumor Tissue From Patients With Melanoma Treated on Clinical Trial EST-1690

Summary: RATIONALE: Studying samples of tumor tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer. It may also help doctors predict how patients will respond to treatment.
  PURPOSE: This research study is looking at tumor tissue samples from patients with melanoma treated on clinical trial EST-1690.

Detailed description: OBJECTIVES:
  -  To validate the prognostic role of several biomarkers suggested by gene expression profiling and tissue microarray (TMA) studies (e.g., NCOA3, SPP1, and RGS1) on the outcome associated with melanoma in the EST-1690 cohort using IHC analysis.
  -  To examine the potential predictive role of such biomarkers in patients undergoing adjuvant interferon alfa therapy.
  -  To analyze the correlation between the intensity of biomarker expression and survival of this cohort both in the observation and in the interferon-treated groups.
  -  To examine the prognostic role of these biomarkers on the outcome associated with melanoma in the EST-1690 cohort using quantitative-PCR.
  -  To isolate RNA from the primary specimens from patients enrolled in the EST-1690 cohort to assess the expression of genes suggested by cDNA microarray and IHC analyses (e.g., NCOA3, SPP1, and RGS1) as prognostic or predictive markers.
  OUTLINE: Samples from the EST-1690 cohort are obtained and analyzed for several biomarkers (i.e., NCOA3, SPP1, and RGS1) via immunohistochemistry and quantitative PCR. RNA is isolated from the specimens to assess gene expression via quantitative PCR.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of melanoma
  -  No metastatic disease at diagnosis
  -  Treated on protocol EST-1690
  -  Primary tumor tissue specimens available
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Effect of Intrapulmonary Recombinant Human Activated Protein C (APC) on Coagulation and Inflammation After Lipopolysaccharide (LPS)

Summary: Recombinant human Activated Protein C (rhAPC) has been shown to reduce the mortality of patients with severe sepsis. The biological effects of APC are pleiotropic, and can be roughly divided in anticoagulant and cytoprotective effects. Lung infection and inflammation are associated with reduced bronchoalveolar levels of endogenous APC. Recent evidence derived from animal studies indicates that local administration of rAPC into the lungs exerts local anti-inflammatory and anticoagulant effects. In this study we propose to study the potential of locally administered APC, within a lung subsegment, to inhibit lipopolysaccharide (LPS) induced lung inflammation and coagulation in humans.


Eligibility: Inclusion Criteria:
  -  Male, 18-35 years of age
  -  No clinically significant findings during physical examination and hematological and biochemical screening
  -  Normal spirometry and ECG
  -  Able to communicate well with the investigator and to comply with the requirements of the study
  -  No medication
  -  Written informed consent
  -  No smoking
  Exclusion criteria:
  -  Known diseases
  -  A history of smoking within the last six months, or regular consumption of greater than three units of alcohol per day
  -  Administration of any investigational drug within 30 days of study initiation
  -  Donation of blood within 60 days, or loss of greater than 400 ml of blood within 12 weeks of study initiation
  -  History of enhanced bleeding tendency
  -  History of heparin-induced thrombocytopenia
  -  History of serious drug-related reactions, including hypersensitivity

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Activated Protein C in Severe Acute Pancreatitis

Summary: Activated protein C (APC)has been shown to reduce mortality in severe sepsis(Bernard et al. 2001b). The clinical picture of severe acute pancreatitis (AP) is similar to that of sepsis. The investigators conducted a randomised double-blinded placebo-controlled pilot study in AP patients (16+16) with the same dose of APC that has been proven to be efficacious and safe in septic patients.
  The aim of the study is to investigate whether the APC replacement therapy diminishes the occurrence and severity of organ dysfunction in patients with severe AP. The effect of APC on inflammatory and hemostatic parameters is also assessed.

Detailed description: The study started in 2003 and was finished in 2007. The study was registered in The Helsinki University Central Hospital study register in 2003.

Eligibility: Inclusion Criteria:
  -  Admitted to hospital within 72 h of the onset of pain.
  -  Plasma amylase concentration more than three times the upper limit of the normal range and/or CT findings compatible with AP.
  -  Organ failure and <48h of the onset of the first organ failure
  Exclusion Criteria:
  -  HIV / B- or C hepatitis infection
  -  Pregnancy or breast feeding
  -  Active bleeding
  -  Increased risk of bleeding (thrombocytes <30x10E9/L or INR>3.0
  -  Gastrointestinal bleeding within 6 weeks or intracranial stroke within 3 months before the study
  -  Intravenous contrast extravasation or other signs (fresh hematoma) suggesting active hemorrhage within the pancreas or in the peripancreatic area on admission CT scan
  -  Use of antithrombin III within 12 h
  -  Use of acetylsalicylic acid or glycoprotein IIB/IA antagonist within 7 days / Thrombolytic therapy within 3 days
  -  Surgery requiring general or spinal anaesthesia within 12 h
  -  Previous pancreatic surgery
  -  Application of an epidural catheter within 48 h

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Study of BMS-650032 With Peginterferon Alfa-2a Plus Ribavirin

Summary: The purpose of this study is to identify one or more doses of BMS-650032 that, when used in combination with pegylated-interferon alpha and ribavirin are safe and demonstrate sufficient activity against hepatitis C virus (Genotypes 1 and 4).


Eligibility: Inclusion Criteria:
  -  Subjects chronically infected with HCV genotype 1 (Phase 2a and Phase 2b)
  -  Subjects chronically infected with HCV genotype 4 (Phase 2b only)
  -  HCV RNA viral load of ≥ 10*5* IU/mL at screening
  -  BMI of 18 - 35 kg/m² at screening
  Exclusion Criteria:
  -  Cirrhosis (Phase 2a only)
  -  Decompensated cirrhosis (Phase 2b)
  -  Co-infection with HBV or HIV
  -  Hepatocellular carcinoma
  -  Prior treatment with anti-HCV drugs

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Rosuvastatin in Visceral Adiposity

Summary: The purpose of this study is to investigate whether 6 months treatment with the cholesterol-lowering drug rosuvastatin may reduce visceral fat tissue in obese middle aged men.

Detailed description: The accumulation of intra-abdominal fat has been suggested to be of primary importance in the development of the metabolic syndrome and associated metabolic disturbances and it has been hypothesized that a selective reduction of visceral fat tissue would improve the symptoms of the metabolic syndrome. Treatment with statins decrease levels of LDL-cholesterol and reduce coronary artery disease (CAD) events. Although it is widely accepted that the majority of benefit obtained with statins is a direct result of their lipid-lowering properties, they also demonstrate additional cholesterol-independent or pleiotropic effects. The results of experimental studies have now shown that statins decrease fat mass in the visceral region in an animal model. In the present study, we will investigate whether statins can decrease visceral obesity in humans.

Eligibility: Inclusion Criteria:
  -  Male patients between 40 and 65 years of age.
  -  Abdominal obesity
  -  Dyslipidemia
  -  Written informed consent.
  Exclusion Criteria:
  -  Uncontrolled hypertension
  -  Diabetes mellitus
  -  Severe liver disease
  -  Severely reduced renal function
  -  Uncontrolled endocrine disorders
  -  History of or ongoing malignant disease
  -  Patients with known myopathic disease
  -  Recent alcohol or drug abuse
  -  Weight loss or weight gain during the three months prior to screening.
  -  Ongoing treatment with statins
  -  Ongoing treatment with calcineurin-inhibitors
  -  Ongoing treatment with anti-inflammatory drugs
  -  Received an investigational drug within 30 days prior to screening.
  -  Strong clinical indication for statin treatment
  -  In the Principal Investigator's opinion, the patient has other clinically significant cardiac, oncologic, neurologic or psychiatric disease that could be adversely affected by Study participation.
  -  For any reason the patient is considered by the Principal Investigator to be an unsuitable candidate to participate in the Study.

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: A Study of Avastin (Bevacizumab) in Combination With Fotemustine in Patients With Metastatic Melanoma

Summary: This study will investigate the efficacy and safety of bevacizumab + fotemustine in patients with stage IV melanoma, previously untreated with chemo- or immunotherapy for metastatic disease. Patients will receive Avastin (15mg/kg intravenously[IV]) on Day 1 of every 3 week cycle, in combination with fotemustine (100mg/m² IV) on Days 1, 8 and 15, followed by 4 weeks rest, followed by 100mg/m² IV every 3 weeks for 4-6 cycles. The anticipated time on study treatment is until disease progression, and the target sample size is <100 individuals.


Eligibility: Inclusion Criteria:
  -  cutaneous malignant melanoma;
  -  advanced, inoperable stage IV melanoma;
  -  measurable and/or evaluable sites of metastases.
  Exclusion Criteria:
  -  prior chemotherapy and/or IFN/IL2 based immunotherapy for metastatic disease;
  -  prior malignancies within past 5 years, with the exception of cured non-melanoma skin cancer, or in situ cancer of cervix;
  -  clinically significant cardiovascular disease;
  -  ongoing treatment with aspirin (>325mg/day) or other medications known to predispose to gastrointestinal ulceration.

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Melanoma Vaccine in Treating Patients With Stage III Melanoma After Surgery to Remove Lymph Nodes

Summary: RATIONALE: Vaccines made from dendritic cells and tumor antigen peptides or a person's tumor cells may help the body build an effective immune response to kill tumor cells.
  PURPOSE: This phase I/II trial is studying the side effects and best way to give melanoma vaccine in treating patients with stage III melanoma after surgery to remove the lymph nodes.

Detailed description: OBJECTIVES:
  -  Determine the feasibility of adjuvant melanoma vaccine comprising autologous dendritic cells pulsed with tumor antigen peptides in patients with stage III melanoma following lymphadenectomy.
  -  Determine the immune response (skin test of delayed-type hypersensitivity and flow cytometric enumeration of peripheral blood CD8+ lymphocytes producing IFN-γ) to this regimen in these patients.
  -  Determine clinical outcome (disease-free survival, overall survival, and adverse events) in patients treated with this regimen.
  OUTLINE: Patients undergo leukapheresis for collection of peripheral blood mononuclear cells (PBMCs) and bone marrow mononuclear cells. Autologous dendritic cells (DCs) prepared from PBMCs and bone marrow mononuclear cells are exposed to various antigens and peptides, and autologous tumor cell lysate, if available. Patients receive autologous DCs pulsed with melanoma-associated antigen peptides, and autologous DCs pulsed with tumor lysates (if available), subcutaneously in weeks 0, 2, 5, 8, 12, 16, 20, 26, 31, 50, and 102. Patients with no evidence of disease may receive another booster injection 5 years after the start of vaccination.
  Blood samples are examined via flow cytometry and skin testing is performed to evaluate immune response.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of stage III melanoma
  -  Has undergone therapeutic lymphadenectomy
  -  More than 1 lymph node involvement or extracapsular extension of metastatic melanoma cells (stage N1b-N3 disease according to AJCC 2002)
  -  HLA type A1 and/or A2 or A3 (if autologous tumor lysate is available)
  -  No presence of distant metastases
  PATIENT CHARACTERISTICS:
  -  No other malignancy
  -  No evidence of lung, heart, liver, or renal failure or severe neurologic disorder
  -  No autoimmune disease or atopic allergy
  -  No HIV infection or presence of anti-HIV antibodies
  -  No presence of hepatitis B surface antigen or antibodies against hepatitis C virus
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant