araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Germline Alterations of Tumor Susceptibility Genes in New York Cancer Patients

Summary: The basic premise of this research proposal is to determine whether there is any significant association between germline polymorphisms and cancers of colon, bladder, breast, testicular, prostate, ovaries, kidney, lung, lymphoid organs, and head and neck. This is an exploratory study designed to generate hypotheses for further research.

Detailed description: To establish significant correlations between genetic polymorphisms and cancer, a largescale, systematic comparison of genetic alterations utilizing a case-control methodology is proposed. To date, such studies have been limited due to the large number of samples necessary for obtaining statistical significance, and the lack of rapid and accurate methods to screen for genetic polymorphisms. We propose to utilize an anonymized design to obtain DNA from residual material from routine diagnostic blood tests, to link these samples to a limited set of clinical variables, and to test for the frequency of candidate low-penetrance cancer susceptibility alleles. These data will be combined with similar data from a control group of age- and ethnically-matched volunteers for a related cohort study to be conducted separately. Polymorphisms to be screened for include those involving the genes PTEN, APC, TGF βR-I, BLM, CHK2, a p85 phosphoprotein, ATM, ER, PR, MCP-1, MPIF, CCR2/5, CCR3, and SULT1A1. Cancers to be included are breast, bladder, kidney,colon, testicular, lung, prostate, ovarian, lymphoid neoplasms, and head and neck carcinomas. Genes with SNPs known to be relevant for either the development or treatment of lymphoid malignancies will also be targeted. Specifically, candidate genes will be selected from 1) cytokine signaling, 2) DNA repair, and 3) apoptosis regulatory pathways.

Eligibility: Inclusion Criteria:
  -  Patients with a histologic diagnosis of cancer of the colon, breast, bladder, kidney, testicles, lungs, prostate, head and neck, or lymphoid organs, who have donated a diagnostic blood sample as either an inpatient or outpatient at MSKCC.
  -  All patients who have two or more histologic diagnoses of the same primary tumor type involving the above sites.
  -  Patients of Ashkenazi Jewish ancestry with a histologic diagnosis of cancer of any type.
  -  Samples ascertained as part of protocol 98-024A(1) are also eligible for ascertainment in this study.
  Exclusion Criteria:
  -  MSKCC patients without a histologic diagnosis of cancer of the breast, bladder, kidney, colon, testicles, lungs, prostate, or lymphoid malignancy (including all types of lymphoma) will not be eligible for the AMDeC sponsored component of the study.

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: A Pilot Study to Evaluate Optical Spectroscopy of Pigmented Skin Lesions

Summary: The incidence of malignant melanoma has increased dramatically in recent decades. In 1930, the lifetime risk of an individual in the United States developing melanoma was 1 in 1,500. This has been exponentially increasing over the years with the risk estimated to be 1 in 75 in 2000 . According to the American Cancer Society, approximately 59,580 new cases of melanoma will be diagnosed in the United States in 2005 and about 7,770 people are expected to die of the disease.

Detailed description: The researcher ucan use special imaging devices to obtain information about a typical mole and melanoma and use this information to determine the different between malignant and benign melanized lesions. The imaging devices are, Modified Two Layer Diffuse Optical Spectroscopy,multi-spectral imaging, and Spatially Modulated Quantitative Spectroscopy can use to measure atypical moles and melanoma and correlate the results of the biopsy tissue histology.
  The imaging devices can quantify melanin, oxy and deoxy hemoglobin concentration, water, lipid and reduced scattering coefficients and can compare results to histopathologic. Atypical moles and melanoma have a different optical profile based on physiological parameters compared to benign nevus.

Eligibility: Inclusion Criteria:
  -  18 years or older.
  -  Have atypical mole/s and melanoma
  Exclusion Criteria:
  -  Age less than 18 years old.
  -  have NO atypical mole/s and melanoma

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Halt Growth of Liver Tumors From Uveal Melanoma With Closure of Liver Artery Following Injection of GM-CSF

Summary: Patients with uveal melanoma metastatic to the liver will be treated with embolization of the hepatic artery every 4 weeks. GM-CSF (granulocyte-macrophage colony simulating factor) or normal saline will be injected into one of the liver arteries with an oily contrast dye, Ethiodol. This is followed by blockage of the artery with small pieces of gelatin sponge (embolization). It is hoped with this novel approach that:
  -  tumor cells will die due to a loss of their blood supply,
  -  local inflammatory reactions induced by GM-CSF will kill remaining tumor cells, and
  -  a systemic immune response against tumor cells may develop.

Detailed description: Patients with uveal melanoma metastatic to the liver will be treated with embolization of the hepatic artery every 4 weeks. GM-CSF (granulocyte-macrophage colony simulating factor) or normal saline will be injected into one of the liver arteries with an oily contrast dye, Ethiodol. This is followed by blockage of the artery with small pieces of gelatin sponge (embolization).

Eligibility: Inclusion Criteria:
  -  Metastatic uveal melanoma in the liver with histological confirmation
  -  Ability/willingness to give informed consent
  -  ECOG performance status of 0 or 1
  -  Adequate renal, liver and bone marrow function
  Exclusion Criteria:
  -  Solitary liver metastasis that is amenable to surgical removal
  -  Presence of symptomatic liver failure including ascites and hepatic encephalopathy
  -  Presence of extra-hepatic metastases
  -  Untreated brain metastases
  -  Uncontrolled hypertension or congestive heart failure or acute myocardial infarction within 6 months of entry
  -  Presence of any other medical complication that imply survival of less than six months
  -  Uncontrolled sever bleeding tendency or active GI bleeding
  -  Significant allergic reaction to contrast dye or GM-CSF
  -  Immunosuppressive treatments such as systemic steroids, radiation to pelvis or systemic chemotherapy within 4 weeks
  -  Previous embolization of the hepatic artery or intrahepatic arterial chemotherapy of liver metastasis
  -  Active hepatitis with serum glutamic oxaloacetic transaminase (SGOT) and serum glutamic pyruvic transaminase (SGPT) greater than 5 x normal
  -  HIV infection positive by ELISA
  -  Pregnancy or breast feeding women
  -  Biliary obstruction, biliary stent or prior biliary surgery except cholecystectomy
  -  Significant arteriovenous shunt identified on angiography of the hepatic artery
  -  Occlusion of main portal vein or inadequate collateral flow around an occluded portal vein

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Evaluation of Peginterferon Alfa-2b Monotherapy and Combination With Ribavirin in Participants With Acute Hepatitis C (P03552/MK-4031-137)

Summary: The objective of this study is to evaluate the efficacy of three regimens of pegylated interferon-alfa 2b (PEG-IFN) either as monotherapy or in combination with ribavirin in participants with acute hepatitis C. After 12 weeks of observation from disease onset, participants will receive one of the following regimens: (1) a 24-week course of PEG-IFN monotherapy (PEG-IFN 24); or (2) a 12-week course of PEG-IFN monotherapy (PEG-IFN-12); or (3) a 12-week course of PEG-IFN in combination with ribavirin (PEG-IFN + RVB 12). After the treatment period, participants will enter a 12-month follow-up.


Eligibility: Inclusion Criteria:
  -  Diagnosed with acute hepatitis C virus (HCV).
  -  Normal and Elevated serum alanine transferase (ALT) levels
  -  Positive serum HCV-RNA.
  -  Aged between 18 and 65 years.
  -  Negative urine or serum pregnancy test (for women of childbearing potential) documented within the 24-hour period prior to the first dose of the drug. Additionally, all fertile males with partners of childbearing age and females must be using reliable contraception during the study and additionally for participants treated with ribavirin, for 6 months (for woman) and 7 months (for man and his partner) after treatment completion
  Exclusion Criteria:
  -  Liver disease unrelated to HCV infection
  -  Hemoglobin (Hgb) <12g/dL in women and <13g/dL in men; white blood cells (WBC) <3,000/uL; platelets (PLTs) <100,000/ul
  -  Women with ongoing pregnancy or who are breast feeding
  -  History of severe psychiatric disease, especially depression
  -  History of neurologic disease, especially epilepsy
  -  History or evidence of symptoms of severe cardiac, gastrointestinal and kidney disease
  -  Positive anti-Human Immunodeficiency Virus (HIV) antibodies
  -  Positive anti-nuclear antibodies (ANA) and/or Anti-Smooth Muscle Antibody (ASMA) (>1/80)
  -  Positive Hepatitis B surface antigen (HBsAg)
  -  History of having received any systemic anti-neoplastic or immunomodulatory treatment in the previous 6 months
  -  History or other evidence of severe illness or any other conditions which would make the participants, in the opinion of investigator, unsuitable for the study (active drug addict except those under methadone treatment, thalassemic, dyalized included)

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Study of Genes and the Environment in Patients With Prostate Cancer Residing in the East Anglia, Trent, or West Midlands Regions of the United Kingdom

Summary: RATIONALE: Studying samples of blood 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 study is looking at genetic susceptibility and the interactions between genes and the environment in patients with prostate cancer.

Detailed description: OBJECTIVES:
  -  To obtain epidemiological information and biological material on a population-based series of prostate cancer cases.
  -  To identify novel cancer susceptibility genes by comparison of genotype frequencies in cases with the corresponding frequencies in large control series.
  -  To estimate the age and sex-specific risks associated with variants in predisposition genes.
  -  To evaluate interactions between polymorphisms in predisposition genes and potential lifestyle risk factors.
  OUTLINE: This is a multicenter study.
  Patients complete a detailed epidemiological questionnaire, including information on education, occupation, smoking habits, alcohol consumption, height, weight, family history of cancer, and past medical history.
  Blood samples are collected from patients. DNA is extracted from these blood samples and from samples collected from cancer-free control participants in MREC-SEARCH-CONTROL as well as from additional controls through the European Prospective Investigation of Cancer (EPIC) study (a population based study of diet and health based in Norfolk, East Anglia). DNA samples are analyzed for polymorphisms of low penetrance cancer susceptibility genes.
  In addition to the prostate cancer patients recruited for this study, patients with breast, ovarian, endometrial, colorectal, bladder, kidney, pancreatic, brain and esophageal cancer, malignant melanoma, and lymphoma cancer are recruited in the following related clinical trials: MREC-SEARCH-BREAST, MREC-SEARCH-OVARIAN, MREC-SEARCH-ENDOMETRIAL, MREC-SEARCH-COLORECTAL, and MREC-SEARCH-CANCER.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of prostate cancer within the past 5 years
  -  Identified through the cancer registry serving any of the following geographic regions of the United Kingdom:
  -  East Anglia
  -  Trent
  -  West Midlands
  PATIENT CHARACTERISTICS:
  -  Identified by the patient's general practitioner as fit to contact for this study
  -  No serious mental illness or retardation
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Ranibizumab in Combination With Proton Beam Irradiation for Choroidal Melanoma

Summary: The purpose of the study is to investigate the safety and tolerability of the anti-VEGF (vascular endothelial cell growth factor) treatment, ranibizumab, in combination with proton beam irradiation for the treatment of choroidal melanoma by determining the incidence and severity of ocular adverse events. Systemic adverse events will also be evaluated. A secondary objective is to assess the efficacy of ranibizumab in reducing ocular complications that can occur after irradiation.


Eligibility: Inclusion Criteria:
  -  Patients with newly diagnosed choroidal melanoma undergoing proton therapy
  -  Tumors >15 mm in largest diameter and/or >5 mm in height
  -  Tumors ≤ 15 mm in largest diameter and ≤ 5 mm in height located ≤ 3 mm from optic disc and/or macula, with best-corrected visual acuity 20/100 or better in study eye
  Exclusion Criteria:
  -  History of prior treatment for choroidal melanoma
  -  Pregnancy or lactation
  -  Presence of diabetic retinopathy
  -  History of retinal vascular occlusion or other retinal vascular disease
  -  Active ocular inflammation or history of uveitis in either eye
  -  History of uncontrolled glaucoma (defined as intraocular pressure >30mmHg despite treatment with anti-glaucoma medication) or filtering surgery in the study eye
  -  Previous intravitreal injections of Avastin® in the study eye or in the non-study eye within 30 days.
  -  Concurrent use of systemic anti-VEGF therapy

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Feasibility and Functionality of fPAM Imaging in Melanoma

Summary: Melanoma is a cutaneous malignancy that has the potential for local (skin) and regional (lymph node) recurrence. These recurrences may be difficult to detect in their earliest stages. We are attempting to use novel form of skin imaging that uses ultrasound combined with laser to identify these recurrences early, when they may be most amenable to treatment. This imaging will detect melanoma pigment below the surface of the skin and in the draining lymph nodes, as well as new blood vessel formation that occurs with these loco-regional metastases.

Detailed description: recruiting healthy individuals with pigmented lesions and individuals with melanoma and pigmented lesions

Eligibility: Inclusion Criteria:
  -  Adult patients (> 18 yrs of age) with recently diagnosed or a history of, Stage I - III melanoma who are able to give informed consent.
  Exclusion Criteria:
  -  Patients with melanomas < 1mm.
  -  Pregnant females.
  -  Children and young adults < 18 yrs of age and patients who are unable to give informed consent.

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN 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: possibly relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN 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: 68-year-old male with melanoma; genetic feature: PTEN 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