araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 72-year-old male with melanoma; genetic feature: TP53 loss of function

Clinical trial: Biomarkers to Predict Response to Interferon Therapy in Patients With Melanoma

Summary: RATIONALE: Collecting and storing samples of blood from patients with cancer to study in the laboratory may help doctors learn more about changes that may occur in DNA and identify biomarkers related to cancer, and may help doctors learn how well patients will respond to treatment.
  PURPOSE: This laboratory study is looking at biomarkers to predict the response to interferon therapy in patients with melanoma.

Detailed description: OBJECTIVES:
  -  Generate a comprehensive multiplexed array of melanoma-associated serological markers and validate it using serum samples from patients with melanoma and healthy control participants.
  -  Determine changes in the profile of serological markers induced by interferon-alfa 2b (IFN-α2b) therapy.
  -  Define panels of serological markers with prognostic and predictive power for IFN-α2b therapy responses in patients with melanoma.
  OUTLINE: This is a multicenter study.
  Serum samples are used for multiplex analyses. Biomarkers to be assessed include cytokines, chemokines, growth factors, angiogenic and antiangiogenic molecules, matrix metalloproteases (MMPs), tissue inhibitors of MMPs (TIMPs), melanoma-associated antigens, basic fibroblast growth factor, insulin-like growth factor I and II, thrombospondin, endostatin, angiostatin, vasostatin, and vascular endothelial growth factor inhibitor.
  PROJECTED ACCRUAL: A total of 1,716 samples will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of melanoma OR healthy volunteer (control)
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 72-year-old male with melanoma; genetic feature: TP53 loss of function

Clinical trial: Study of Tumor Samples From Patients With Lung Cancer

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.
  PURPOSE: This laboratory study is looking at tumor samples from patients with lung cancer.

Detailed description: OBJECTIVES:
  Primary
  -  To determine the correlation between c-Met expression, mutation and amplification, with stage and overall survival in patients with adenocarcinoma (AC) of the lung.
  Secondary
  -  To determine the correlation with epithelial mesenchymal transition (EMT), EGFR mutations and expression, Kras mutations, p53 mutations, c-CBL protein expression, mutation, loss of heterozygosity (LOH), DUB3 expression & regulation, and ALK translocation, with respect to survival.
  -  To determine the correlation with circulating c-Met and HGF in AC and evaluate prognostic implications of circulating markers in AC of lung.
  -  To determine (when available) levels of circulating Met and HGF in serum before and after surgery.
  OUTLINE: This is a multicenter study.
  Previously collected tissue samples from patients enrolled in CALGB 140202 are assessed for mutation analysis of c-Met, EGFR, and K-ras. DNA is examined by PCR, followed by agarose gel electrophoresis; gene amplification of c-Met is examined by real time quantitative PCR; met/HF protein in serum is examined by ELISA; and c-Met, EGFR, p53, c-CBL, DUB3 enzyme, and ALK, and epithelial mesenchymal transition examined by IHC.

Eligibility: Inclusion Criteria:
  -  Registration to Cancer and Leukemia Group B (CALGB) 140202
  -  Institutional Review Board (IRB) review and approval at the institution where the laboratory work will be performed is required
  -  Informed consent: the CALGB does not require that a separate consent form be signed for this study
  -  The subject population to be studied in this protocol includes patients selected from CALGB 140202; all such patients have signed a written informed consent document meeting all federal, state, and institutional guidelines as part of entry into that trial
  -  All samples to be studied were obtained and stored as part of CALGB 140202; the material and data obtained from the patient's protocol record will be used to obtain appropriate clinical information; in no instance will the patient be contacted directly
  -  There should be no physical, psychological, social, or legal risks associated with this study; no invasive procedures are recommended or requested
  -  All appropriate and necessary procedures will be utilized to maintain confidentiality; all patients who have had samples submitted for analysis will have their CALGB study number used to identify specimens
  -  This study does not require direct patient contact and no specific risk or benefits to individuals involved in the trial are anticipated; it is likely, however, that the information gained will substantially help similar patients in the future

Relevance to patient case: not relevant
Patient case: 72-year-old male with melanoma; genetic feature: TP53 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: 72-year-old male with melanoma; genetic feature: TP53 loss of function

Clinical trial: Pilot Study of Infrared Imaging of Cutaneous Melanoma

Summary: Design: this is a pilot study of infrared imaging of cutaneous lesions in patients and volunteers with and without clinically detectable melanoma, and with one or more palpable cutaneous lesions eligible for this imaging study. Participants will be evaluated with infrared camera imaging at cutaneous sites with known melanoma deposits, suspected melanoma deposits that are to be biopsied, or at cutaneous sites with other lesions, including other skin cancers, benign inflammatory lesions, benign neoplastic lesions (lipomas, epidermal cysts, dermatofibromas, scar, healing wound, etc.).


Eligibility: Inclusion Criteria:
  -  Patients or volunteers with or without a history of melanoma.
  -  One or more palpable skin or subcutaneous lesions for which at least one of the following is true:
  -  A tissue diagnosis has been made for the lesion(s) in question, by prior cytologic or histologic evaluation (Category A1).
  -  A tissue diagnosis will be obtained for the lesion(s) in question by cytologic or histologic evaluation (Category A2).
  -  A tissue diagnosis is not available, but a clinical diagnosis of melanoma or benign lesion is available with a high degree of confidence. Examples are hemangiomas, skin tags, seborrheic keratoses, dermatofibromas, lipomas, or growing pigmented skin lesions that are comparable to other cutaneous metastases of melanoma in the same patient (Category B).
  -  All patients must have the ability and willingness to give informed consent and must be age 18 years or older at the time of study entry.
  Exclusion Criteria:
  -  Known or suspected allergy to the adhesive skin markers or water-soluble ink used for the labeling of lesions.
  -  Very fragile skin that may be susceptible to injury from adhesive markers.
  -  Patients in whom there is a medical contraindication or potential problem in complying with the requirements of the protocol, in the opinion of the investigator.

Relevance to patient case: not relevant
Patient case: 72-year-old male with melanoma; genetic feature: TP53 loss of function

Clinical trial: Study of Tumor Samples in Patients Undergoing Radiation Therapy or Surgery For Primary Melanoma of the Eye

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.
  PURPOSE: This clinical trial is studying tumor samples in patients undergoing surgery or radiation therapy for primary melanoma of the eye.

Detailed description: OBJECTIVES:
  Primary
  -  To establish the feasibility of using fine needle aspiration (FNA) and FISH to determine tumor genotype in patients with primary uveal melanoma.
  Secondary
  -  To characterize ophthalmic complication rate of FNA for FISH analysis in patients undergoing plaque radiotherapy.
  -  To estimate disease-free survival in patients with and without tumor monosomy 3 and/or 8q amplification.
  -  To explore the relationship between tumor monosomy 3 and 8q amplification and plasma levels of tumor immune escape and invasion biomarkers (e.g., circulating granulysin, beta2-microglobulin, autotoxin, lysophosphatidic acid, matrix metalloproteinase-7, tissue inhibitor of matrix metalloproteinase, and soluble E- cadherin).
  -  To explore the psychological impact of prognostication in uveal melanoma.
  OUTLINE: Patients undergo plaque radiotherapy, enucleation, or tumor resection based upon standard of care guidelines.
  Trans-scleral fine needle aspiration (FNA) is performed at the time of plaque radiotherapy and ex vivo FNA is performed on enucleation and tumor resection specimens. Tissue samples are analyzed by fluorescence in situ hybridization (FISH). Blood samples are also collected for further analysis.
  After completion of study therapy, patients are followed up periodically.

Eligibility: Inclusion Criteria
  -  Patients must have a clinical diagnosis of melanoma of the iris, ciliary body and/or choroids
  -  Patients must have had a hepatic ultrasound and/or other suitable imaging studies to eliminate metastatic disease
  -  Patients must not have received any local or systemic therapy for uveal melanoma
  -  All patients must be informed of the investigational nature of this study and must provide written informed consent in accordance with institutional and federal guidelines. A copy of the informed consent document signed by the patient must be given to the patient
  -  Patients must have the following pretreatment laboratory findings:
  -  Bilirubin (total) </= 1.5 ml/dl
  -  AST </= 2 x normal
  -  ALT </= 2 x normal
  -  Alkaline phosphatase </= 2 x normal
  Exclusion Criteria
  -  Patients with metastasis
  -  Patients under the age of 18

Relevance to patient case: not relevant
Patient case: 72-year-old male with melanoma; genetic feature: TP53 loss of function

Clinical trial: International Melanoma Algorithm Training Study - IMATS

Summary: This is an international, multicenter, prospective, non controlled, non randomized, clinical study to collect electrical impedance data of potentially malignant pigmented nevi and histological diagnoses (International Melanoma Algorithm Training Study [IMATS]). The study objective is to collect data for training and optimization of an algorithm that can classify skin lesions using electrical impedance, i.e., to identify malignant melanomas.


Eligibility: Inclusion Criteria:
  -  Men and women of any ethnic group
  -  Lesion located on normal healthy skin
  -  Maximum number of eight lesions per patient
  -  etc.
  Exclusion Criteria:
  -  Lesion under finger and toe nails
  -  Lesion located on eczema, psoriasis areas or similar
  -  Lesion located on scars
  -  etc.

Relevance to patient case: not relevant
Patient case: 72-year-old male with melanoma; genetic feature: TP53 loss of function

Clinical trial: Transfected Dendritic Cell Based Therapy for Patients With Breast Cancer or Malignant Melanoma

Summary: The primary aim of this study is to evaluate the toxicity of the vaccine and the combination of the vaccine and Cyclophosphamide, and to evaluate the immune response induced by the vaccine. The secondary aim is to investigate the clinical tumour response and duration of tumour and immune response.

Detailed description: Phase I trial. Single center study; patients will be referred to the study center from other institutions in Denmark. 14 patients will be included in this phase I trial DC vaccination regime consists of primary 6 biweekly intradermal injections with transfected dendritic cells, followed by monthly injections until progression; Cyclophosphamide is used as vaccine adjuvant.
  Defined procedures are employed for generation of autologous dendritic cells for clinical application in a classified laboratory. Unmobilized leukapheresis will be used for isolation of large-scale mononuclear cells, and dendritic cells will be generated from monocytes by cytokine stimulation and transfected with mRNA encoding for hTERT, survivin and p53 if the tumour express p53. Frozen preparations of dendritic cells will be prepared using automated cryopreservation. Each patient will receive a minimum of 1x106 dendritic cells per treatment supplemented with Cyclophosphamide 50 mg twice a day every second week. Toxicity including autoimmunity will be evaluated using the Common Toxicity Criteria (CTC).

Eligibility: Inclusion Criteria:
  1. Histological verified metastatic breast cancer or malignant melanoma, in progression
  2. ≥ 18 years
  3. the patient must be habil
  4. Performance status ≤ 1 on Zubrod-ECOG-WHO-scale
  5. Leukocytes and platelets must be ≥normal. Hg ≥ 6.0
  6. creatinin must be normal
  7. Liverparametre <2.5 x normal. Bilirubin <30
  8. Expected survival > 3 months
  9. Informed consent
  11. At least one measurable lesion according to RECIST criteria.
  Exclusion Criteria:
  1. Indication for chemotherapy
  2. Other malignancies
  3. Brain metastases
  4. severe medical condition
  5. Acute/chronic infection with ex. HIV, hepatitis, tuberculose
  6. Severe allergy
  7. Autoimmune disease
  8. Other treatment with immune suppressing agents, other anticancer agents or experimental drugs
  9. Uncontrolled hypercalcemia.

Relevance to patient case: definitely relevant
Patient case: 72-year-old male with melanoma; genetic feature: TP53 loss of function

Clinical trial: Development of a Non-invasive Assessment of Skeletal Muscle Loss in Cancer Patients

Summary: The long-term objective of this research is to develop a non-invasive approach for early assessment of which patients are at high risk for future development of skeletal muscle atrophy. The investigators hypothesize that the rate constant for the terminal portion of the isotope decay curve following ingestion of a single oral dose of deuterated-3-methylhistidine (D-3MH) provides an accurate measure of this increased risk and that this rate constant can be measured non-invasively from timed spot urine samples. In addition, the investigators hypothesize that ingestion of a meat-containing meal will stimulate synthesis of skeletal muscle proteins to a greater extent than a non-meat-containing meal.


Eligibility: Inclusion Criteria:
  -  male
  -  30-85 years
  -  Body Mass Index (BMI) <30 kg/m2
  Exclusion Criteria:
  -  Uncontrolled hypertension
  -  Glomerular filtration rate less than 60 mL/min/1.73 m2
  -  History of recurrent gastrointestinal bleeding
  -  Unable or unwilling to provide informed consent
  -  Ongoing anti-coagulant therapy

Relevance to patient case: not relevant
Patient case: 72-year-old male with melanoma; genetic feature: TP53 loss of function

Clinical trial: Study of AntiCTLA4 in Patients With Unresectable or Metastatic Uveal Melanoma

Summary: This is a Phase 2, multi-center, open-label study in patients with surgically incurable stage III or IV uveal melanoma who have not received prior immunotherapy. CP-675,206 is thought to stimulate patients' immune systems to attack their tumors. CP-675,206 has been shown to induce durable tumor responses in patients with metastatic melanoma in phase 1 and phase 2 clinical studies.


Eligibility: Inclusion Criteria:
  -  Histologically confirmed uveal melanoma including choroidal melanoma, iris melanoma, and ciliary body melanoma
  -  Patients may either have measurable disease or non-measurable disease.
  -  Biopsies from a readily accessible site of disease on study enrollment are mandatory in principle. Waivers will be granted if there are no accessible lesions. The collection of a representative block of the diagnostic tumour tissue (if available) is mandatory.
  -  ECOG performance status of 0 or 1
  -  Age 18 years or older
  -  Adequate bone marrow, hepatic, and renal function determined within 14 days prior to registration, defined as:
  -  Serum lactic acid dehydrogenase (LDH) </= 1.5 x ULN.
  -  Alkaline phosphatase (ALP) </= 2 x ULN.
  -  No weight loss >/= 10% in the proceeding 4 weeks.
  -  CT scan of the brain with contrast or MRI of the brain within 28 days of registration showing no evidence of brain metastases.
  -  Females of childbearing potential must have a negative serum or urine pregnancy test within 14 days prior to registration. Females who have undergone surgical sterilization or who have been postmenopausal for at least 2 years are not considered to be of childbearing potential.
  -  Females of childbearing potential and males who have not undergone surgical sterilization must agree to practice a form of effective contraception prior to entry into the study and for 12 months following the last dose of study drug. The definition of effective contraception will be based on the judgment of the investigator.
  Exclusion Criteria:
  -  Melanoma of cutaneous, mucosal or conjunctival origin.
  -  History of brain or leptomeningeal metastases.
  -  Received any prior CTLA4 inhibiting agent (eg MDX-010, ipilimumab) or other immunotherapy.
  -  History of chronic inflammatory or autoimmune disease
  -  History of uveitis or melanoma-associated retinopathy.
  -  History of inflammatory bowel disease, celiac disease, or other chronic gastrointestinal conditions associated with diarrhea or bleeding, or current acute colitis of any origin.
  -  History of hepatitis due to Hepatitis B virus or Hepatitis C virus

Relevance to patient case: not relevant
Patient case: 72-year-old male with melanoma; genetic feature: TP53 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