araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Genetic Risk Factors and Acquired Oncogenic Mutations of Melanoma

Summary: Though it is generally accepted that exposure to sunlight is a major causative factor for skin cancer, the risk for developing melanoma is not directly linked to sun exposure such as in non-melanoma skin cancer. Therefore, a dual pathway has been proposed, distinguishing melanoma that develops on skin that is chronically exposed to sunlight from those that occur on skin that is normally protected. The risk for each type of melanoma is believed to be determined in part by genetic factors. To define these markers reproducibly, the investigators plan to establish a large cohort with comprehensive information regarding sun sensitivity (skin type), history of experienced sun exposure, skin pigmentation phenotypes, total number of nevi, and other types of skin tumors in a central European population. The investigators will obtain blood from all participants for DNA as well as serum analyses. Based on the finding that genetic variants of the melanocortin-1 receptor (MC1R) gene, associated with red hair and fair skin, have been shown to be associated with increased risk for melanoma, particularly those harboring BRAF mutations, the investigators will now focus on the study of recently discovered genetic variants associated with pigmentation. Furthermore, the investigators will study the relation of these variants with oncogenic mutations of melanoma in BRAF, RAS and c-Kit. The study of other genetic variants will follow, once a sufficiently large cohort has been established to reveal an independent genetic risk factor in a multivariate analysis including potential covariates as mentioned above. The identification of genetic risk factors for melanoma will not only help identify individuals with increased risk but also improve our understanding of the molecular background of the development of melanoma.


Eligibility: Inclusion Criteria:
  -  patients with or without melanoma
  Exclusion Criteria:
  -  HIV and Hepatitis C positive individuals.

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

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: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

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: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

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: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

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: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Study of Tumor Samples From Patients With Ewing Sarcoma

Summary: This laboratory study is looking at tumor samples from patients with Ewing sarcoma. 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

Detailed description: Study Subtype: Ancillary/Correlative Observational Study Model: Cohort Time Perspective: Prospective Biospecimen Retention: Samples With DNA Biospecimen Description: Tissue Study Population Description: Samples collected from AEWS0031 and patients registered on AEWS08B1 Sampling Method: Non-Probability Sample
  PRIMARY OBJECTIVES:
  I. Determine if mutation of p53, and/or deletion of the p16 locus, have prognostic value in patients with Ewing sarcoma.
  SECONDARY OBJECTIVES:
  I. Estimate the incidence of p53 mutation in Ewing sarcoma samples collected from COG studies.
  II. Estimate the incidence of p16 deletions in Ewing sarcoma samples collected from COG studies.
  III. Prepare and archive amplified genomic DNA from Ewing sarcoma samples collected from COG studies for future biologic analysis.
  OUTLINE: This is a multicenter study.
  Previously archived tumor samples are analyzed for p53 mutations and p16 deletion by immunohistochemistry, FISH, PCR, and DNA sequencing.

Eligibility: Inclusion Criteria:
  -  Diagnosis of Ewing sarcoma
  -  Banked specimens from patients enrolled on AEWS0031

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

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: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Comparison of AZD6244 in Combination With Dacarbazine Versus (vs) Dacarbazine Alone in BRAF Mutation Positive Melanoma Patients

Summary: To assess the efficacy in terms of overall survival of AZD6244 in combination with dacarbazine, compared with dacarbazine alone, in first line patients with BRAF mutation positive advanced cutaneous or unknown primary melanoma


Eligibility: Inclusion Criteria:
  -  Histological or cytological confirmation of advanced (inoperable stage III and stage IV) cutaneous or unknown primary melanoma
  -  Tumor sample confirmed as BRAF mutation positive
  Exclusion Criteria:
  -  Diagnosis of uveal or mucosal melanoma
  -  Any prior Investigational therapy comprising inhibitors of Ras, Raf or MEK
  -  Having received an investigational drug within 30 days of starting treatment, or have not recovered from side effects of an investigational drug

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

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: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Citrate Pharmacokinetics and Regional Citrate Anticoagulation in CRRT

Summary: 1. To compare the differences of citrate pharmacokinetics in healthy individuals and critically ill patients as well as the influential factors.
  2. To validate a pharmacokinetic model which has been established in a formal paper.
  3. To create a safe and effective RCA-CRRT protocol.


Eligibility: Inclusion Criteria:
  -  healthy individuals, none-pregnant
  -  diagnosed with acute renal failure according to RIFLE criteria
  -  ARF with hepatic insufficiency
  -  ARF with MODS or sepsis
  -  within informed consent
  Exclusion Criteria:
  -  used drugs with citrate within one week
  -  infused with blood,plasma or platelet or undergone plasma exchange therapy within 48 hours
  -  serious alkalosis with PH>7.55
  -  serious lactic acidosis
  -  not in resuscitation state

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: A Study of Vemurafenib in Previously Treated Patients With Metastatic Melanoma

Summary: This open-label single arm study will assess the efficacy, safety and tolerability of Vemurafenib in previously treated patients with metastatic melanoma. Patients will receive oral Vemurafenib [RG7204; PLEXXIKON: PLX4032] at a dose of 960 mg b.i.d. continuously until disease progression or withdrawal from study and will be assessed at regular intervals for tumour response and tolerability. Target sample size is <100 patients.


Eligibility: Inclusion Criteria:
  -  adult patients >/=18 years of age
  -  histologically confirmed metastatic melanoma (Stage IV, AJCC)
  -  patients must have completed and failed at least one prior standard of care regimen (e.g. DTIC, temozolomide, etc.)
  -  BRAF V600E positive mutation (by Roche CoDx BRAF mutation assay)
  -  measurable disease by RECIST criteria
  -  negative pregnancy test and, for fertile men and women, effective contraception during treatment and for 6 months after completion
  Exclusion Criteria:
  -  active CNS metastases on CT/MRI within 28 days prior to enrollment
  -  history of or known carcinomatous meningitis
  -  previous treatment with BRAF (sorafenib allowed) or MEK inhibitor
  -  cardiac dysrhythmias >2 NCI CTCAE or treatment with drugs with dysrhythmic potential
  -  uncontrolled hypertension(>150/100mmHg) despite optimal medical therapy
  -  infectious disease including HIV, HBV and HCV

Relevance to patient case: not relevant
Patient case: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

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