araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 55-year-old male with Melanoma. Genetic variant: NRAS (Q61K). Other conditions: Hypertension.

Clinical trial: Immunohistochemical Expression Patterns of microRNA Processing Enzyme Dicer in Cutaneous Malignant Melanoma, Benign and Dysplastic Melanocytic Naevi

Summary: MicroRNAs (miRNAs) are very small endogenous RNA molecules about 22-25 nucleotides in length, capable of post-transcriptional gene regulation. miRNAs bind to their target messenger RNAs (mRNAs), leading to cleavage or suppression of target mRNA translation based on the degree of complementarity. miRNAs have recently been shown to play pivotal roles in diverse developmental and cellular processes and linked to a variety of skin diseases and cancers. In the present study the researchers investigate the immunohistochemical distribution of Dicer in benign and dysplastic melanocytic naevi as well as in cutaneous malignant melanoma compared to intraindividual healthy control.


Eligibility: Inclusion Criteria:
  -  Patients with benign melanocytic naevi, dysplastic melanocytic naevi and cutaneous malignant melanoma.
  Exclusion Criteria:
  -  Patients under 18 years of age
  -  Patients with other forms of cancer in previous medical history
  -  Pregnancy

Relevance to patient case: not relevant
Patient case: 55-year-old male with Melanoma. Genetic variant: NRAS (Q61K). Other conditions: Hypertension.

Clinical trial: Effect of Biological Therapy on Biomarkers in Patients With Untreated Hepatitis C, Metastatic Melanoma, or Crohn Disease

Summary: RATIONALE: Studying samples of blood from patients with cancer, hepatitis C, or Crohn disease in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer and other diseases.
  PURPOSE: This laboratory study is looking at the effect of biological therapy on biomarkers in patients with untreated hepatitis C, metastatic melanoma, or Crohn disease.

Detailed description: OBJECTIVES:
  -  To determine how a variety of immune-modulating therapies (i.e., interferon alfa [IFN-α] in patients with untreated acute or chronic hepatitis C, anti-tumor necrosis factor in patients with active inflammatory bowel disease (i.e., Crohn disease), and anticytotoxic T-lymphocyte antigen immunoglobulin in patients with metastatic melanoma) affect the tissue expression of indoleamine 2, 3 dioxygenase (IDO), a major immune-regulatory mechanism.
  -  To determine whether administration of pegylated INF-α in patients with untreated acute and chronic hepatitis C causes systemic changes in the IDO pathway, as indicated by lowered serum tryptophan (TRP) and elevated serum kynurenine (KYN).
  -  To determine whether administration of ticilimumab (i.e., anti-CTLA4 human monoclonal antibody CP-675,206) in patients with metastatic melanoma inhibits activation of the IDO pathway as indicated by normal serum TRP and normal serum KYN.
  -  To determine whether administration of infliximab in patients with Crohn disease inhibits activation of the IDO pathway, as indicated by normal serum TRP and normal serum KYN.
  OUTLINE: Serum samples are collected from patients with hepatitis C and metastatic melanoma at baseline and at 3 to 4 weeks after treatment is initiated. Previously collected samples from patients with Crohn disease are also assessed at these time points. Samples are analyzed for tryptophan and kynurenine levels via high-performance liquid chromatography.
  PROJECTED ACCRUAL: A total of 15 patients with untreated acute or chronic Hepatitis C, 15 patients with metastatic melanoma, and 20 patients with Crohn disease will be accrued for this study.

Eligibility: Inclusion Criteria:
  DISEASE CHARACTERISTICS:
  -  Diagnosis of 1 of the following:
  -  Acute or chronic hepatitis C
  -  Receiving pegylated interferon alfa and ribavirin
  -  Metastatic melanoma
  -  Receiving ticilimumab
  -  Crohn disease
  -  Received prior infliximab
  Exclusion Criteria:
  -  Not specified
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 55-year-old male with Melanoma. Genetic variant: NRAS (Q61K). Other conditions: Hypertension.

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: 55-year-old male with Melanoma. Genetic variant: NRAS (Q61K). Other conditions: Hypertension.

Clinical trial: Biomarkers in Patients With High-Risk Melanoma Receiving High-Dose Interferon Therapy

Summary: RATIONALE: Studying samples of blood from patients with cancer in the laboratory may help doctors identify biomarkers related to cancer and predict how patients will respond to treatment.
  PURPOSE: This research study is looking at biomarkers in patients with high-risk melanoma receiving high-dose interferon therapy.

Detailed description: OBJECTIVES:
  -  To screen serum specimens using a high throughput protein profiling platform that tests for the highest number of known biomarkers (detectable by antibodies) that could be predictors of response to interferon treatment, autoimmunity, and disease outcome in patients with high-risk melanoma undergoing high-dose interferon (IFNa2b) therapy .
  -  To compare soluble factors across all patients at each time point (baseline and during therapy).
  -  To compare pre-therapy vs post-therapy serum samples from these patients.
  -  To assess the kinetics of soluble factors' appearance, persistence, and disappearance during the 12 months of therapy.
  -  To assess whether the amount of specific soluble factors in the pre-therapy sample is predictive of response independent of therapy.
  -  To correlate statistically significant factors with S100 and autoimmunity in these patients.
  -  To confirm the data obtained with the Luminex technology.
  OUTLINE: Patients are stratified according to survival (< 2 years vs > 5 years).
  Blood samples collected from patients enrolled in E-1694 are analyzed using high throughput protein profiling by ELISA to compare changes in levels of putative biomarkers of interferon alfa-2b, including cytokines and paired receptors, chemokines, cell adhesion molecules, metalloproteinases, angiogenic markers, growth factors, soluble receptors, signal transduction molecules, hormones, and other biomarkers of disease and dysregulated immune processes, at baseline and during therapy.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of high-risk melanoma
  -  Receiving interferon alfa-2b therapy in arm II of clinical trial E-1694
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 55-year-old male with Melanoma. Genetic variant: NRAS (Q61K). Other conditions: Hypertension.

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: 55-year-old male with Melanoma. Genetic variant: NRAS (Q61K). Other conditions: Hypertension.

Clinical trial: Axillary Lymph Node Preservation Surgery in Reducing Lymphedema in Patients With Breast Cancer

Summary: This pilot phase I and randomized phase II trial studies the best way to perform axillary lymph node preservation surgery and to see how well it works in preventing lymphedema in patients with breast cancer. Lymph node mapping may help in planning surgery to remove breast cancer and affected lymph nodes. It is not yet known whether reverse mapping guided axillary lymph node dissection is more effective than standard axillary lymph node dissection in preventing lymphedema.

Detailed description: PRIMARY OBJECTIVES: I. To produce a map of the lymphatic drainage of the upper extremity as it relates to breast drainage, to determine the proportion of women undergoing axillary lymphadenectomy at risk for lymphedema. II. To determine if blue lymphatics contain lymph node metastases. III. To evaluate the incidence of lymphedema and associated other surgical related quality of life in those undergoing this procedure as compared to the current standard of care.
  OUTLINE: This is a phase I study followed by a randomized phase II study.
  PILOT PORTION: Patients receive isosulfan blue dye subcutaneously (SC) and then undergo reverse mapping-guided axillary lymph node dissection.
  RANDOMIZED PORTION: Patients are randomized to 1 of 2 treatment arms. ARM I: Patients receive isosulfan blue dye subcutaneously (SC) and then undergo reverse mapping-guided axillary lymph node dissection. ARM II: Patients undergo standard axillary lymph node dissection and then receive isosulfan blue dye SC.
  After completion of study treatment, patients are followed up periodically.

Eligibility: Inclusion Criteria:
  - Patients diagnosed with breast cancer with a planned axillary lymph node dissection planned for breast cancer
  Exclusion Criteria:
  -  Prior lymphedema in either arm
  -  Prior history of axillary surgery (except for sentinel node biopsies)
  -  Prior history of chest/axillary radiation
  -  Need for bilateral axillary node dissection surgery
  -  Prior neurologic deficits (either motor or sensory) in ipsilateral arm
  -  Known allergy to vital blue dyes
  -  No prior diagnosis of inflammatory breast cancer
  -  Cannot be pregnant or planning to continue breast-feeding immediately after surgery

Relevance to patient case: not relevant
Patient case: 55-year-old male with Melanoma. Genetic variant: NRAS (Q61K). Other conditions: Hypertension.

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: 55-year-old male with Melanoma. Genetic variant: NRAS (Q61K). Other conditions: Hypertension.

Clinical trial: Genetic Identification (ID) of Segmental Dysplastic Nevi

Summary: The investigators' goal is to identify the mutation in the gene that is responsible for the development of segmental dysplastic nevi. To identify the gene the investigators may use a candidate gene approach (i.e. sequence specific genes that are thought to be involved: NRAS, BRAF, etc) or a genome-wide approach trying to implicate regions in the genome (Loss-of-heterozygosity or copy number changes on comparative genomic hybridization).

Detailed description: Dysplastic (atypical) melanocytic (DMN) nevi have been identified as being potential precursors of melanoma and markers for patients at risk of developing primary melanoma1. In addition, having an increased number of nevi is associated with increased risk1. DMN are present in 2-5% of white adults in the U.S. population and international studies have documented up to 18% prevalence2. These lesions may be present in at least 17% of white adults with melanoma and 20-50% of melanomas may arise in nevi and atypical nevi2. The exact gene(s) involved in the development of nevi have yet to be elucidated.
  Segmental dysplastic nevi are nevi that are restricted to one area of the body3. This condition is much rarer than the occurrence of dysplastic nevi, but nonetheless, may involve the same genetic mutation. The pattern of distribution in SDN is thought to result from mosaicism, i.e. the part of the body that expresses the dysplastic nevi has a mutation in a gene, however, the rest of the body does not contain this same mutation. Other mosaic disorders that have been studied in greater detail than SDN have been shown to be caused by a single gene mutation4. It appears that SDN is no different and that it too is caused by a mutation in a single gene, however, this gene is not yet known.
  In this study we will perform a genetic analysis of tissue from a patient known to have SDN. With the information we gather from this analysis, we may be able to find the gene responsible for the development of dysplastic nevi.
  Primary Research Objective:
  To investigate the genetic mutation involved in the development of dysplastic nevi by examining a patient with SDN.

Eligibility: Inclusion Criteria:
  -  Patient with a positive history of segmental dysplastic nevi
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 55-year-old male with Melanoma. Genetic variant: NRAS (Q61K). Other conditions: Hypertension.

Clinical trial: Study of Tumor Tissue Samples From Patients With Stage I, Stage II, or Stage III Malignant Melanoma

Summary: RATIONALE: Studying the genes expressed in samples of tumor tissue from patients with cancer may help doctors identify biomarkers related to cancer.
  PURPOSE: This research study is looking at tumor tissue samples from patients with stage I, stage II, or stage III malignant melanoma.

Detailed description: OBJECTIVES:
  -  Determine the genetic profile of primary melanomas with and without synchronous regional nodal involvement by examining for 1) activating mutations B-Raf and N-Ras associated with melanoma development, and 2) allelic imbalances across the genome.
  -  Compare the genetic profile of primary melanomas from patients with and without lymph node involvement.
  -  Determine the combinations of genetic lesions that correlate with nodal metastasis by adopting a statistical machine learning approach to build a lesion-based classifier for nodal metastasis.
  OUTLINE: Laser capture microdissection is performed on the archived tissue samples to isolate melanoma cells. DNA is then purified from the samples and amplified using PCR. Matrix-assisted laser desorption/ionization (MALDI)-time of flight mass spectrometry technology is used to detect mutations of B-Raf and N-Ras. Single nucleotide polymorphism arrays are also performed.
  Information about the patient's demographics (e.g., TNM staging, sex, age, and tissue collection dates) will be gathered by chart review or from the Multidisciplinary Melanoma Conference at University Hospitals tumor conference report in order to match cases.

Eligibility: Inclusion Criteria:
  -  Node positive Group (experimental group)
  -  Primary melanoma > 2 mm in depth
  -  Metastasis must be > 0.1 mm and detectable by IHC or hematoxylin and eosin (H&E) to be considered node positive
  -  Slides and block for primary and node must be archived in UH dermatopathology
  -  Node Negative Group (control group)
  -  Primary melanoma > 2 mm in depth
  -  A negative sentinel lymph node must be negative by IHC and H&E
  -  No stage IV disease
  -  No acral and mucosal histology
  -  No history of prior invasive melanoma
  -  Underwent primary excision and sentinel lymph node biopsy within 3 months of each other
  -  Archived tissue available
  -  Slides and block for primary tumor and node biopsy must be archived in University Hospitals Case Medical Center (UH) dermatopathology
  Exclusion Criteria:
  -  Acral and mucosal histology
  -  Previous diagnosis of invasive melanoma
  -  previous chemotherapy or immunotherapy
  -  patients who are found to have stage IV disease during workup

Relevance to patient case: not relevant
Patient case: 55-year-old male with Melanoma. Genetic variant: NRAS (Q61K). Other conditions: Hypertension.

Clinical trial: A Study of Cetuximab Combined With Cisplatin or Carboplatin/Pemetrexed as First Line Treatment in Patients With Malignant Pleural Mesothelioma.

Summary: Multicenter, open phase 2 study on patients with malignant mesothelioma. Standardly, 4 to 6 cycles of palliative chemotherapy, platinum in combination with pemetrexed, are given. Despite of this treatment, median survival is poor (9-12 months). By combining conventional cytotoxic agents with a novel agent, hopefully treatment and survival can be approved. Cetuximab or Erbitux is a monoclonal antibody against the EGFR (Epidermal Growth Factor Receptor). By blocking the receptor, it interferes with cel growth and division. Most mesothelioma show a strong expression of the EGFR protein. Apart from that, Cetuximab also has antibody-dependent cell-mediated cytotoxicity (ADCC).
  In this trial, patients will be treated with standard chemotherapy, combined with Cetuximab weekly. After a maximum of 6 cycles of chemotherapy, administration of Cetuximab will be continued until disease progression. Every 6 weeks, a CT scan will be done to evaluate therapy. Most common side effect of Cetuximab is acneiform rash.
  The translation research program consists of the determination of EGFR- and K-Ras mutations on the tumor tissue and the correlation with outcome.
  In the first part of the trial, 18 patients will be included. After a positive interim analysis, a total of 43 patients will be included.


Eligibility: Inclusion Criteria:
  -  Histologically proven malignant pleural mesothelioma, epitheloid subtype
  -  Recurrent after radical surgery or disease not considered suitable for radical treatment
  -  EGFR IHC + as assessed by DAKO kit with at least 1% of cells showing staining
  -  Performance status WHO 0 or 1
  -  Life expectancy > 12 weeks
  -  Weight loss < 10% in last 3 months
  -  Adequate bone marrow reserve, renal and hepatic function
  -  Measurable disease (modified RECIST)
  -  No prior chemotherapy
  -  No prior or other malignancies, except if longer than 5 yrs ago and adequately treated or basocellular skin or in situ cervical cancer
  -  No uncontrolled infection
  -  Written informed consent.
  -  Male/Female
  -  > 18 years
  Exclusion Criteria:
  -  Evidence of brain or leptomeningeal metastases
  -  Patients who are unable to interrupt aspirin, other nonsteroidal anti-inflammatory drugs for a 5-day period starting 2 days before administration of pemetrexed (8-day period for long acting agents such as piroxicam)
  -  Patients that cannot be treated with folic acid and vitamin B 12
  -  Patients that cannot be treated with dexamethasone.
  -  Presence of clinically detectable (by physical examination) third-space fluid collections, for example ascites of pleural effusions that cannot be controlled by drainage or other procedures prior to the study entry.
  -  Use of investigational drugs

Relevance to patient case: not relevant