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

Clinical trial: Pilot Study for Cell Based Therapies in Patients With Asthma

Summary: The aim of this study is to investigate the immunomodulatory potential of Isolated Plasmacytoide Dendritic Cells (pDCs) and Regulatory T-cells (TREGs) isolated with clinical grade magnetic bead isolations techniques (MACS®) on the antigen presenting cell-induced proliferation of lymphocytes after allergen uptake in an in vitro cell culture system.

Detailed description: pDCs as well as TREGs will be co-incubated with generated allergen presenting cells, lymphocytes, and allergen. For in vitro experimentation immune cells will be collected from blood of grass mix or house dust mite sensitized atopic/asthmatic patients.

Eligibility: Inclusion Criteria:
  -  Male subjects suffering from allergic rhinitis and/or allergic asthma against timothy grass pollen (phleum pratense) and/or house dust mite.
  -  age 18-60 years,
  -  Nonsmokers or smokers with a history of less than 1 pack years who have not smoked within the last 12 months.
  -  Positive skin prick test for timothy grass pollen (phleum pratense) and/or house dust mile within 12 months
  -  Able and willing to give written informed consent
  -  Hemoglobin ≥135 g/l
  -  Hematocrit ≥ 0,40
  -  Body weight ≥ 50 kg and Body Mass Index (BMI) within the range 19-32 kg/m²
  Exclusion Criteria:
  -  History of lower respiratory tract infection and /or exacerbation of asthma within four weeks prior to the informed consent visit
  -  Febrile illness within four week before the trial examination
  -  Administration of oral, injectable, or dermal corticosteroids within the last 8 weeks or intranasal and/or inhaled corticosteroids within the last 4 weeks.
  -  Intake of methylxanthines, antihistamines, antileukotrienes, oral cromolyn sodium, or oral nedocromil sodium
  -  Past or present disease, which as judged by the investigator, may affect the outcome of this trial. These diseases include, but are not limited to, cardiovascular disease, malignancy, hepatic disease, renal disease, hematological disease, neurological disease, endocrine disease, or pulmonary disease (including but not confined to chronic bronchitis, emphysema, tuberculosis, bronchiectasis or cystic fibrosis).
  -  Specific immunotherapy (SIT) within the last two years prior to screening
  -  Participation in another clinical trial 30 days prior to enrollment
  -  Donation of more than 500 ml of blood in the preceding 9 weeks before the trial-examination
  -  Hemoglobin below the normal lower limit
  -  History of drug and/or alcohol abuse or dependence within 12 months of the trial
  -  Risk of non-compliance with trial procedures
  -  Suspected inability to understand the protocol requirements, instructions and trial-related restrictions, the nature, scope, and possible consequences of the trial
  -  Patient is tested human immunodeficiency virus (HIV)-1/2Ab, hepatitis B surface antigen (HBsAg), or hepatitis C virus antibodies (HCV-Ab) positive

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

Clinical trial: Study to Evaluate Imatinib in Desmoid Tumors

Summary: The objective of the present study is to evaluate the activity and safety of imatinib in patients with aggressive fibromatosis who, after receiving the standard therapy, show an inoperable recurrent tumor or disease not readily controllable by surgery or radiotherapy.


Eligibility: Inclusion Criteria:
  -  Patients with histological confirmed aggressive fibromatosis (desmoid tumor)
  -  Measurable disease according to the RECIST criteria
  -  Evidence of relapse or disease progression within the last 6 months (based on RECIST criteria) in computed tomography or magnetic resonance imaging
  -  No possibility of complete surgical resection or cases in which surgical therapy leaving a large tissue defect, functional deficit or disfigurement would be required
  -  No possibility of curative radiotherapy with acceptable toxicity and/or late morbidity
  -  Previous treatment of the tumor region by surgical intervention and/or radiotherapy and/or antihormonal therapy possible
  -  Age > or = 18 years
  -  WHO PS < or = 1
  -  Effective contraception during study medication
  -  Signed informed consent form
  Exclusion Criteria:
  -  Surgical intervention < 4 weeks
  -  Prior therapy with imatinib
  -  Pregnancy or lactation
  -  Severe hepatic dysfunction
  -  Known allergic reaction to imatinib or one of its components
  -  The following laboratory values: Absolute neutrophil count < 1.5 x 103/mm3, Platelets < 100,000/mm3, Serum creatinine > or = 2.5 mg/dl, SGOT and/or SGPT > 2.5 x ULN (upper limit of normal), Total bilirubin > 1.5 x ULN
  -  Participation in another study (four weeks before and during the study)
  -  Prior malignancy apart from completely resected basal cell carcinoma of the skin or carcinoma in situ of the uterine cervix

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

Clinical trial: Biomarkers in Tissue and Blood Samples From Patients With Early-Stage Non-Small Cell Lung Cancer

Summary: RATIONALE: Studying samples of blood and 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.
  PURPOSE: This research study is studying biomarkers in tissue and blood samples from patients with early-stage non-small cell lung cancer.

Detailed description: OBJECTIVES:
  -  Evaluate aberrant methylation patterns in tissue and serum samples from patients with early-stage non-small cell lung cancer (NSCLC) to validate the Johns Hopkins single institutional study.
  -  Attempt to define subgroups of patients at greater risk for recurrent or metastatic disease who may benefit from more aggressive adjuvant therapeutic regimens.
  -  Develop prognostic indicators for disease-specific and overall survival.
  -  Define new potential molecular targets for therapy.
  OUTLINE: Archived tumor and intrathoracic lymph node tissue samples are analyzed for aberrant DNA methylation (p16/CDKN2A, DAP kinase, H-cadherin, APC, and RASSF1A) by methylation-specific PCR. Analyses are then compared with the preliminary data from the Johns Hopkins institutional study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of early-stage non-small cell lung cancer
  -  T1 or T2, N0 disease
  -  Had a lobectomy or greater resection with negative surgical margins (R0 resection)
  -  Available tumor and lymph node specimens from patients enrolled on ACOSOG-Z0040 and ACOSOG-Z0030 trials
  -  Node-negative with recurrent disease within 3 years (cases)
  -  Node-negative patients without recurrent disease (controls)
  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: Early Diagnosis of Malignant Transformation of Pigmentary Skin Lesions

Summary: Malignant Melanoma is a deadly skin cancer that can be cured if diagnosed early. To date atypical pigmented skin lesions are diagnosed by appearance alone and many moles and lesions are excised unnecessarily and on the other hand malignant lesions are missed and diagnosed too late. In this study a protein conjugated to a florescent dye is spread on a suspicious pigmented lesion, the hypothesis is that this protein binds to malignant cells only and thus with a special camera that picks up the dye we can find pigmented lesions with early malignant transformation.


Eligibility: Inclusion Criteria:
  -  pigmented lesion indicated for surgical excision
  -  over 18 years of age
  Exclusion Criteria:
  -  pregnancy

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

Clinical trial: Incidence of Bacteremia Following Argon Plasma Coagulation in Patients With Endobronchial Lesions

Summary: Incidence of Bacteremia Following Argon Plasma Coagulation in Patients with Endobronchial Lesions

Detailed description: Bacteremia is a well-recognized invasive medical condition. In most cases, it is a transient phenomenon without clinical consequences. In certain patients, such as those with structural cardiac abnormalities, it may lead to the development of infectious endocarditis. According to an American Heart Association statement, routine endocarditis prophylaxis is indicated prior to invasive procedures with relatively high bacteremia rates, such as dental care,certain types of catheterization and rigid bronchoscopy [1].Fibreoptic bronchoscopy, with or without biopsy is not included in this list due to a very low bacteremia rate [1].This even applies to particularly high risk patients with prosthetic valve or previous endocarditis. Yigla et al. assessed the incidence of bacteremia following bronchoscopy and found 6.5% of bacteremia rate. (2) Recently, Steinfort et al. assessed the bacteremia rate following endobronchial ultrasound and found 7% of bacteremia rate following the procedure. All bacterial isolates were typical oropharyngeal commensal organisms. The transbronchial needle aspiration washing culture was positive in 35% of the patients. However, none of the bacteremic patients had clinical features suggestive of infection and no complications were seen among the cohort. (3) No data are available, however about the bacteremic rate following interventional bronchoscopy for endobronchial obstruction and advance lung carcinoma. In these cases, palliative setting of alleviating central airway obstruction, laser resection, electrocautery, argon plasma coagulation and stenting are techniques that can provide immediate relief.
  Argon plasma coagulation (APC) is uses ionize argon gas jet flow to conduct electrons allowing a noncontact mode of treatment (lightning effect). (4, 5) APC has been popular in gastrointestinal endoscopy for superficial coagulation of large mucosal surfaces. The argon gas quite flexibly flows around bends and corners. Coagulated tissue has a higher resistance that automatically drives the argon gas flow away to nearby untreated tissue. An immediate effect really can be seen during electrocautery treatment, which corresponds well with the histological effect of coagulative necrosis.
  We therefore conduct a prospective study to assess the bacteremic rate following APC in patients with endobronchial involvement.

Eligibility: Inclusion Criteria:
  -  All patients that undergo bronchoscopy with the use of APC
  Exclusion Criteria:
  -  All patients under 18 years old All Patients with evidence of current respiratory infection or febrile illnesses and those that will receive antibiotic therapy within a week prior to the bronchoscopy

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

Clinical trial: IL15 Dendritic Cell Vaccine for Patients With Resected Stage III (A, B or C) or Stage IV Melanoma

Summary: The purpose of the study is to gather data on feasibility as well as immune and clinical efficacy of of a dendritic cell vaccine using IL15 in patients with resected stage III or stage IV melanoma

Detailed description: IL15 is a T cell growth factor that pre-clinical data overwhelmingly suggests could have a very important role in cancer immunotherapy. A desirable property for a dendritic cell vaccine directed against cancer is the ability to efficiently prime naïve, tumor associated antigen specific T cells into potent CTLs. Results of studies in healthy volunteers have shown that IL15 DCs are particularly efficient at priming functional melanoma specific CD8+ T cells. The use of IL15 in the manufacture of the DC vaccine could result in an improved immunotherapy product.

Eligibility: Inclusion Criteria:
  -  HLA A201 + phenotype
  -  Biopsy-proven melanoma, Stages III (A, B and C) or stage IV.- no evidence of disease at study entry
  -  Age: 21-75 years
  -  ECOG performance status 0-1
  -  Adequate marrow function
  -  Adequate hepatic function
  -  Adequate renal function
  -  Written informed consent
  Exclusion Criteria:
  -  Subjects with measureable non-resectable melanoma
  -  Subjects who have had chemotherapy less than 4 weeks before starting trial
  -  Subjects who received IFN-a or GM-CSF less than 4 weeks before starting trial
  -  Subjects who received IL2 less than 4 weeks before starting trial
  -  Subjects with a baseline LDH greater than 1.1 times the ULN
  -  Subjects who are HIV positive
  -  Female subjects who are pregnant
  -  Subjects who have received corticosteroids or other immunosuppressive agents less than 4 weeks before starting trial
  -  Subjects who have asthma and/or are on treatment for asthma
  -  Subjects with angina pectoris
  -  Subjects with congestive heart failure
  -  Subjects with history of autoimmune disease including lupus, rheumatoid arthritis or thyroiditis
  -  Subjects with active infections including viral hepatitis
  -  Subjects with a history of neoplastic disease othe than melanoma within the last 5 years
  -  History of neoplastic disease within the last 5 years except for carcinoma in situ of the cervix, superficial bladder cancer or basal/squamous cell carcinoma of the skin.
  -  Subjects who present with open wounds

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

Clinical trial: Differences in Evoked Intracellular Interferon Signaling Pathways Using Single Cell Phosphoprotein Profiling

Summary: Purpose:
  The purpose of this exploratory study is to evaluate phosphoprotein profiling to determine differences in the intracellular actions of interferon or interferon stimulated genes among people with different treatment outcomes to interferon based therapy for hepatitis C (HCV). Participants: Patients with genotype 1 HCV who have had interferon based therapy at the University of North Carolina (UNC). Procedures: Thirty patients with varied responses to treatment will be given a single subcutaneous injection of interferon alpha 2b. Prior to the injection and at 30 minutes, 1,2,4,6,12 and 20 hours after injection, blood will be drawn for analysis of phosphoprotein profiling and changes in serum cytokines.


Eligibility: Inclusion Criteria:
  To be eligible for this study, subjects must meet the following inclusion criteria:
  -  Willing and able to provide informed consent
  -  Males or females age 18 - 65 years
  -  For women of childbearing potential, negative blood pregnancy test documented within the 24-hour period prior to IFN-α administration
  -  History of genotype 1 HCV infection previously treated with peginterferon and ribavirin and with a virological response that can be determined from retrospective review of medical records
  -  A washout period of >12 weeks between the last dose of prescribed peginterferon and ribavirin and the screening visit
  Exclusion Criteria
  Subjects with any of the following will not be eligible for participation:
  -  Neutrophil count <1500 cells/mm3, Hgb <12 g/dL in women or 13 g/dL in men, or platelet count <75,000 cells/mm3 at screening
  -  Serum creatinine level >1.5 times the upper limit of normal at screening
  -  Poorly controlled psychiatric illness, as determined by the study physician, which can be exacerbated by interferon therapy
  -  Infection requiring antibiotics, symptomatic viral infection, inflammatory process requiring therapy, or allergic reactions in the week immediately preceding the inpatient study visit
  -  Use of medications that affect the immune system (e.g. glucocorticoids, chronic NSAIDs daily) in the week immediately preceding the inpatient study visit
  -  History of immunologically mediated disease (e.g., inflammatory bowel disease, idiopathic thrombocytopenic purpura, lupus erythematosus, autoimmune hemolytic anemia, psoriasis, rheumatoid arthritis)
  -  Women with ongoing pregnancy or breast-feeding
  -  History or other evidence of bleeding from esophageal varices or other conditions consistent with decompensated liver disease
  -  History of a seizure disorder or current anticonvulsant use
  -  History of major organ transplantation with an existing functional graft
  -  History of thyroid disease poorly controlled on prescribed medications
  -  History or other evidence of severe illness or any other conditions which would make the patient, in the opinion of the investigator, unsuitable for the study

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

Clinical trial: Micro-RNA Expression Profiles in High Risk Prostate Cancer

Summary: The purpose of this study is to determine whether specific Micro-RNA expression profiles are related to Prostate cancer outcome.


Eligibility: Inclusion Criteria:
  Patients with clinically localised high risk prostate cancer (cT>2, bx GS >7, PSA >20 ng/ml) scheduled for radical prostatectomy.
  Exclusion Criteria:
  Non high risk prostate cancer

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

Clinical trial: Trial of Vaccine Therapy With mRNA- Transfected Dendritic Cells in Patients With Advanced Malignant Melanoma

Summary: PRIMARY OBJECTIVES: Determination of safety and toxicity of vaccination with patients` tumour mRNA transfected DCs .
  SECONDARY OBJECTIVES:Determine immunological response to the vaccine (induction of specific T-cell response) and assessment of tumour response


Eligibility: Inclusion Criteria:
  -  Accessible tumour tissue for vaccine production (extraction of tumour mRNA) i.e.subcutaneous or lymph node metastases.
  -  Must be at least 18 years of age.
  -  Must have histologically confirmed advanced, metastatic cutaneous melanoma no longer amenable for surgery.
  -  Must have evidence of disease progression and measurable or evaluable metastases
  -  Must be ambulatory with a ECOG performance score of <2
  -  Must have lab.values as following :
  ANC > 1.5 x 109/L; platelets > 100 x 109/L, Hb > 9g/dL (> 5.6 mmol/L). Creatinine < 140 µmol/L (1.6 mg/dL); if borderline, the creatinine clearance > 40 mL/min, Bilirubin < 20% above the upper limit of normal, ASAT and ALAT < 2.5 the upper limit of normal. Albumin > 2.5 g/L.
  -  Prior radiotherapy: A minimum of 4 weeks (8 weeks in case of extensive radiotherapy) must have elapsed between the end of the prior radiotherapy and entry into the protocol.
  -  Prior chemotherapy: A minimum 4 weeks must have elapsed between the end of the prior chemotherapy and entry into the protocol.
  -  Signed informed consent of the patients for the treatment and follow up must be obtained and documented according to the ICH-GCP Guidelines.
  Exclusion Criteria:
  -  History of prior malignancy other than melanoma, with the exception of curatively treated basal cell or squamous cell carcinoma of the skin and ca. cervix stage 1B.
  -  Active infection requiring antibiotic therapy.
  -  Significant cardiac or other medical illness that would limit activity or survival, such as severe congestive heart failure, unstable angina, or serious cardiac arrhythmia.
  -  Autoimmune disease currently treated with steroids.
  -  Adverse reactions to vaccines such as anaphylaxis or other serious reactions.
  -  History of immunodeficiency or autoimmune disease such as rheumatoid arthritis, systemic lupus erythematosus, scleroderma, polymyositis-dermatomyositis, juvenile onset insulin dependent diabetes, or a vasculitic syndrome.
  -  Chemotherapy or other potentially immune-suppressive therapy that has been administered within 4 weeks prior to vaccination.
  -  Pregnancy or lactation.
  -  Any reason why, in the opinion of the investigator, the patient should not participate.

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

Clinical trial: Interferon Alfa Sensitivity in HIV/HCV Persons Before and After HIV Meds

Summary: The chief purpose of this research is to evaluate interferon alpha sensitivity and cell type specific levels of interferon receptor and interferon stimulated genes and proteins in HIV/ HCV (hepatitis C virus) coinfected persons before and after administration of HIV medications (antiretroviral therapy).

Detailed description: We plan to perform liver biopsy by microlaparoscopy on previously untreated HIV/HCV coinfected persons, then give them a dose of peginterferon alfa 2b. HCV and HIV kinetics will be studied. Afterward, HIV will be treated using antiretroviral therapy and the procedure will be repeated.

Eligibility: Inclusion Criteria:
  -  Adult Human
  -  Able to provide written informed consent
  -  HIV antibody positive
  -  HIV viral load positive
  -  HIV treatment naive
  -  Hepatitis C antibody positive
  -  Hepatitis C viral load positive
  -  Hepatitis C treatment naive
  -  Approved to take HIV medications for minimum 9 months
  -  Willing to use contraception, Life expectancy greater than 2 years
  Exclusion Criteria:
  -  Significant opportunistic infections within 12 month
  -  Hepatitis B positive
  -  Evidence of liver cirrhosis
  -  Decompensated liver disease
  -  Chronic alcohol abuse
  -  Allergy to raltegravir, tenofovir, and/or emtricitabine
  -  Active or suspected malignancy
  -  Sarcoidosis
  -  Active TB
  -  Coronary artery disease
  -  Uncontrolled seizures
  -  Untreated thyroid disease
  -  Untreated diabetes
  -  Weight greater than 125 kg
  -  Severe depression or severe psychiatric disorder
  -  Ongoing alcohol or illicit drug use
  -  Pregnant, nursing, pr planning to become pregnant
  -  Allergy to interferon

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

Clinical trial: A Cohort Study of Patients Treated With Brachytherapy for Selected Desmoid Patients in Gardner Syndrome

Summary: The purpose of this study is to assess the long-term outcome in a cohort of Gardner-Syndrome patients receiving prophylaxis and treatment for intestinal and non-intestinal tumors.

Detailed description: Since 1978, we have been following a family of 105 descendants with Gardner Syndrome (GS). Mutation carriers were screened by endoscopy, and colorectal resection was performed upon pending malignancy. Resectable desmoid tumors were excised, whereas large tumors of the abdominal wall were treated by a combination of brachytherapy (BT) and radiotherapy (RT). Outcome was analyzed with respect to length of tumor-free survival, and morbidity from surgery or radiotherapy. Results: 37 of 105 family members have GS. Preventive colorectal resections were performed in 16 patients (15%), with one death due to subsequent gastric cancer. In 4 patients who denied screening endoscopy, invasive tumors of the colon (3 patients) and stomach (one patient each) developed. Of 33 desmoid tumors, 10 (30%) were located in the mesentery, 17 (52%) in the abdominal wall, and 6 (18%) in extra-abdominal sites. Excision of 12 desmoids was performed in 8 patients (36%), and 4 were treated by a combination of BT and RT. Following BT/RT, all patients showed full or partial remission.

Eligibility: Inclusion Criteria:
  -  family with an identical adenomatous polyposis coli (APC-) germ line mutation
  Exclusion Criteria:
  -  negative testing for adenomatous polyposis coli (APC-) germ line mutation

Relevance to patient case: not relevant