araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: The Final Diagnosis and Treatment Result of Metastatic Cervical Carcinoma of Unknown Primary

Summary: Investigate the final diagnosis and treatment result of metastatic cervical carcinoma of unknown primary

Detailed description: Carcinoma of unknown primary (CUP) is defined as biopsy-proven metastasis of an epithelial malignancy in the absence of an identifiable primary site after complete history and physical examination, basic laboratory studies, chest X-ray and additional directed studies indicated by positive findings during the initial work-up. It is characterized by its slow local development and its high metastatic potential.1,2 Patients with CUP represent 4–10% of all new cancer patients.3,4 The presenting sites of metastasis identified pathologically, radiographically or by physical examination were found most frequently in the lymph nodes (37.1%), followed by the liver, bone, lung, pleura/pleural space, brain, peritoneum, adrenal and skin. Of the lymph nodes of metastasis, the supraclavicular cervical area is the leading site (31.3%), followed by the mediastinum, axilla, retroperitonium, and inguina.5 The incidence of metastatic cervical CUP (MCCUP) varies between 2% and 9% of all head and neck cancers.6-8 The level of cervical metastatic involvement may give some clue as to the likely primary site. A submandibular mass (level I) would most commonly be related to a primary in the oral cavity or skin. Level II nodes, including the jugulodigastric node, may point to a primary in the oral cavity, oropharynx, or supraglottic larynx. Tumours of the nasopharynx generally spread to level II or the posterior triangle, as well as retropharyngeal nodes. Middle and lower jugular nodes (levels III and IV) are more likely related to a laryngeal or hypopharyngeal cancer. Metastatic disease restricted to the supraclavicular region is often due to an infraclavicular primary site.9 The prognosis is different according to the involved lymph node level and possible primary site. Modern cancer management relies heavily on recognition of the primary tumor; thus the absence of a primary site poses major diagnostic and therapeutic problems. The patient benefits from identification of the initial tumor site because postoperative irradiation ports may be reduced and because surveillance for recurrence may be improved.10 In order to identify the likely primary site of MCCUP and compare the prognoses of known and unknown primary groups, we report the results according to the different levels of metastatic cervical lymph nodes.

Eligibility: Inclusion Criteria:
  -  cases of metastatic cervical carcinoma of unknown primary
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Effect of Food Upon Pharmacokinetics of Single Oral Dose of Cediranib (AZD2171, Recentin™)

Summary: The purpose of this study is to determine whether food has any effect on a single dose of Cediranib (AZD2171, Recentin™)followed by an assessment of the safety and tolerability of fixed daily dosing in comparison to varying dose levels on a patient-by-patient basis.


Eligibility: Inclusion Criteria:
  -  Clinical diagnosis of advanced solid tumour.
  -  Ability to eat a high fat breakfast
  Exclusion Criteria:
  -  Poorly controlled high blood pressure.
  -  History of significant gastrointestinal problems

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Post-Operative Drainage Following Lymph Node Dissection

Summary: The purpose of this study is to determine whether the use of fibrin sealant reduces post-operative drainage following groin and axillary lymph node dissection.

Detailed description: Background: Fibrin sealant has been used for many years in clinical practice and has a wide range of applications including the control of lymphatic leaks and haemostasis. The physiological mechanism of action of fibrin was first described by Morawitz in 1905; fibrin sealant was first marketed in 1983.
  Lymph node dissection is undertaken for the control of malignant disease - frequently malignant melanoma or squamous cell carcinoma. Following groin or axillary dissection, excessive post operative drainage may necessitate the presence of wound drains for 10 days or more. This may prolong hospital stay in some patients, and may be associated with an increased complication rate (such as wound infection).
  Hypothesis: the use of fibrin sealant prior to wound closure following either groin or axillary dissection may reduce post-operative wound drainage.
  Comparison: patients who require an elective groin or axillary dissection who either undergo standard wound closure or those who have fibrin sealant instilled into the surgical wound prior to wound closure.

Eligibility: Inclusion Criteria:
  -  Patients over 18 years of age
  -  Requiring groin or axillary lymph node dissection for malignant disease.
  Exclusion Criteria:
  -  Patients under age 18 years.
  -  Patients unable to speak English.
  -  Patients with learning difficulties.
  -  Patients with mental illness.
  -  Prisoners.
  -  Other vulnerable groups.

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Genetic Analysis of Familial Melanoma

Summary: In collaboration with members of The International Melanoma Consortium, we propose to study melanoma in families lacking mutations in the cyclin-dependent kinase inhibitor 2 (CDKN2 or p16) gene, or the cyclin-dependant kinase 4 (CDK4). CDKN2 and CDK4 are both genes that encode presumed tumor suppressor genes, mutant forms of which are known to cause increased susceptibility to melanoma. The purpose of the present study then is to confirm the existence of and to identify additional gene(s) involved in heritable melanoma (cutaneous and ocular) and their precursor lesions (atypical nevi) by linkage analysis and gene mapping strategies. It is clear that the risk to develop atypical nevi and/or melanoma is strongly influenced by genetic and environmental factors (e.g. sun exposure). Characterization of such genes could provide important insights into the inheritance, pathogenesis, and treatment of this increasingly important disease.

Detailed description: In collaboration with members of The International Melanoma Genetics Consortium, we propose to study melanoma in families lacking mutations in the cyclin-dependent kinase inhibitor 2 (CDKN2A), or the cyclin-dependant kinase 4 (CDK4) genes. CDKN2 and CDK4 are both genes that encode presumed tumor suppressor genes, mutant forms of which are known to cause increased susceptibility to melanoma. The purpose of the present study then is to confirm the existence of and to identify additional gene(s) involved in heritable melanoma (cutaneous and ocular) and their precursor lesions (atypical nevi) by linkage analysis and gene mapping strategies. It is clear that the risk to develop atypical nevi and/or melanoma is strongly influenced by genetic and environmental factors (e.g. sun exposure). Characterization of such genes could provide important insights into the inheritance, pathogenesis, and treatment of this increasingly important disease.

Eligibility: -  INCLUSION CRITERIA:
  Inclusion into this study was restricted to families containing at least three CMM cases with DNA available for genotyping, and CDKN2A and CDK4 involvement and had been excluded.
  All families must be mutation negative for both CDKN2A and CDK4.
  This study will also include families with at least one case of ocular and two cases of other cutaneous melanomas, or at least 2 ocular melanomas (except where they occur in parent and child).
  EXCLUSION CRITERIA:
  Any family showing evidence of haplotype sharing in the 9p21-p22 region, where CDKN2A is located, was also excluded.

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Cytogenetic Study of Ocular Melanoma

Summary: Patients who are diagnosed with choroidal melanoma and undergo I-125 plaque or enucleation surgery consent to participate in the study. A tumor sample taken during surgery is studied in the lab for genetic features. These features and features of subjects' clinical course are recorded. Analysis of the data may identify genetic features that are indicative of prognostic factors including risk of metastasis.

Detailed description: The Jules Stein Eye Institute Ocular Melanoma Research Group is conducting cytogenetic studies of choroidal melanoma to improve the screening of biopsy samples of choroidal melanoma through cytogenetic analysis. Our goal is to identify molecular probes that specifically target regions of chromosomes that undergo changes characteristic of metastatic choroidal melanoma.

Eligibility: Inclusion Criteria:
  1. Patient with diagnosis of ocular melanoma
  2. Patient with local treatment plan for ocular melanoma- plaque brachytherapy or enucleation
  3. Patient 18 years of age or older
  4. Archival enucleation specimens with diagnosis of ocular melanoma
  Exclusion Criteria:
  1. Patient who refuses local melanoma treatment
  2. Patient who refuses to participate in this study

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Melanoma Biomarker Study

Summary: The purpose of this study is to measure the level of a specific protein, CXCL1, in the blood of patients with untreated, metastatic (Stage IV) melanoma. These levels will be compared to blood levels in normal controls. If the levels are elevated in metastatic melanoma, further studies to determine if this correlates with presence and extent of disease will be pursued.

Detailed description: Malignant Melanoma has rapidly increased in incidence over the past thirty years, at a rate of roughly 3% per year. In 2005, approximately 59,000 new cases of melanoma were diagnosed with 8000 deaths. While the majority of early melanomas can be surgically cured, advanced melanoma has an extremely poor prognosis. Current chemotherapy and immunotherapy options for advanced melanoma still offer response rates of only 10-20%. Thus, the elucidation of biomarkers in melanoma, both diagnostic and prognostic, is an important area for investigation.
  CXCL1 is a chemokine whose expression is upregulated in melanoma. We postulate that CXCL1 plays an important role in the progression of melanoma to invasive disease. Our hypothesis states that serum CXCL1 levels correlate with the presence of melanoma.
  Aims:
  1. To measure serum levels of CXCL1 in untreated, metastatic melanoma patients and to compare to serum CXCL1 levels in normal controls.
  2. To measure and compare centrally and peripherally collected serum CXCL1 levels in untreated, metastatic melanoma.
  Blood will be collected from metastatic melanoma patients on one occasion, both peripherally and centrally. Control will have blood collected peripherally on one occasion. The blood will be processed and then tested in a blinded, batched fashion.

Eligibility: Inclusion Criteria:
  1. Histologic diagnosis of melanoma; primary may be cutaneous, mucosal or ocular.
  2. Evidence of metastatic disease based on standard AJCC staging.
  3. Willing to give written informed consent.
  4. Willing and able to comply with protocol procedures.
  5. At least 18 years of age.
  6. No prior chemotherapy, immunotherapy, or radiotherapy.
  7. Are able to safely donate 50 mL of blood.
  8. Have a central venous catheter in place (this will not be placed for participation in this trial)
  Exclusion Criteria:
  1. Known diagnosis of a chronic inflammatory disease, ie: Rheumatoid Arthritis, Systemic Sclerosis, Inflammatory bowel disease
  2. Known diagnosis of NYHA class 3 or 4 Congestive Heart Failure
  3. Are unable to safely donate 50 mL blood
  4. Known HIV, Hepatitis B, or Hepatitis C infection.
  5. Any malignancy within 5 years, other than melanoma (for patients); Have any malignancy within the past 5 years including melanoma (for normal controls). Basal cell and squamous cell skin cancers are permitted in all participants.

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Bioelectric Field Imaging in Diagnosing Melanoma and Other Skin Cancers in Patients With Skin Lesions

Summary: RATIONALE: New diagnostic procedures, such as bioelectric field imaging, may help find and diagnose melanoma and other skin cancers. It may also be a less invasive way to check for skin cancer.
  PURPOSE: This phase I trial is studying bioelectric field imaging in diagnosing melanoma and other skin cancers in patients with skin lesions.

Detailed description: OBJECTIVES:
  -  To determine if the hand-held Bioelectric Field Imager can be used to measure the electric field in skin of various body surfaces, including face, neck, shoulders, arms, hands, chest, back, legs, and feet, during the course of examination and treatment of patients with suspected malignant skin lesions.
  -  To determine if there is a significant difference between the lateral electric field strength near benign and malignant skin lesions in the same individual.
  OUTLINE: Patients undergo scanning of their skin lesions and nearby healthy skin using the Bioelectric Field Imager (BFI). The lesions are then biopsied for histological diagnosis. Histological data from the biopsy is correlated with the electric field data from the BFI.

Eligibility: DISEASE CHARACTERISTICS:
  -  Suspected malignant skin lesion
  -  Seeking treatment for skin lesion at the VA Medical Center
  PATIENT CHARACTERISTICS:
  -  Not pregnant
  -  No acute illness, including upper respiratory tract infection or flu that could result in fever
  -  No trauma to the skin lesion area
  -  No prisoners
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Efficacy of Albumin Interferon Alfa-2b With Ribavirin Compared With Peg-IFN Alfa-2a With Ribavirin in IFN Naive Patients

Summary: This is a phase 3, randomized, multi-center study to evaluate the efficacy and safety of albumin interferon alfa 2b (alb-IFN)in combination with ribavirin compared with peginterferon alfa-2a (PEGASYS or PEG-IFNa2a) in combination with ribavirin in subjects with chronic hepatitis C, genotype 1 who are IFNa treatment naive.


Eligibility: Key Inclusion Criteria:
  -  Diagnosis of chronic hepatitis C.
  -  Liver biopsy performed within 2 years of Day 0 or during screening.
  -  Infected with hepatitis C virus genotype 1.
  -  Interferon alfa treatment naïve (ie, have never been treated with an interferon product).
  -  Subjects are eligible to enter the study if they (or their partners) are not pregnant or nursing, are sterile, or of non childbearing potential, or are willing to practice abstinence or use appropriate birth control methods during the study and for 7 months after the last dose of ribavirin.
  -  Have compensated liver disease.
  Key Exclusion Criteria:
  -  Decompensated liver disease including those subjects with a past history or presence of ascites, bleeding varices or hepatic encephalopathy.
  -  History of moderate, severe or uncontrolled psychiatric disease, especially depression, including a history of hospitalization or prior suicidal attempt.
  -  Positive for human immunodeficiency virus (HIV-1) or hepatitis B surface antigen (HBsAG).
  -  Clinical diagnosis of other causes of chronic liver disease including but not limited to hepatitis B, autoimmune hepatitis, primary biliary cirrhosis, alcoholic liver disease, hemochromatosis, Wilson's Disease, or alpha 1-antitrypsin deficiency.
  -  A history of immunologically mediated disease (eg, rheumatoid arthritis, inflammatory bowel disease, moderate/severe psoriasis, sarcoidosis, systemic lupus erythematosus).
  -  Active seizure disorder within the last 2 years.
  -  Organ transplant other than cornea and hair transplant.
  -  Clinically significant hemoglobinopathy (eg, thalassemia, sickle cell anemia).
  -  Cancer within the last 5 years(with the exception of adequately treated basal cell carcinoma of the skin or in situ carcinoma of the uterine cervix).
  -  Drug or alcohol addiction within the last 6 months. Subjects in a supervised methadone treatment program may be enrolled in the study.
  -  Received any experimental agent within 28 days prior to Day 0.

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Safety Study of PLX4032 in Patients With Solid Tumors

Summary: The primary objective of this FIH study is to assess the safety and pharmacokinetics of PLX4032 in patients with solid tumors. The secondary objective is to assess the pharmacodynamic activity in paired biopsy specimens obtained from patients with malignant melanoma who have the V600E BRAF oncogenic mutation.

Detailed description: Activating mutations of the BRAF gene have been observed in a variety of cancers, including 55-68% of malignant melanomas. In general, oncogenic mutations of BRAF correlate with a poor outcome. PLX4032 is a compound that selectively inhibits oncogenic B-Raf kinase.
  Two extension cohorts of patients with confirmed V600E mutations will be recruited, consisting of advanced melanoma and metastatic colorectal carcinoma.

Eligibility: Inclusion Criteria:
  -  Solid tumors confirmed histologically whose tumors are refractory to standard therapy, or for whom standard or curative therapy does not exist
  -  Patients from whom paired melanoma biopsies are planned must have a V600E+ BRAF mutation confirmed prior to the administration of PLX4032
  -  Previous chemotherapy, immunotherapy, or radiation therapy must have been completed at least 2 weeks prior to starting PLX4032 therapy, and all associated toxicity must be resolved prior to administration of PLX4032
  -  Patients in the Extension cohorts (melanoma or adenocarcinoma of the colon or rectum) must have both a V600E+ BRAF mutation and measurable disease (by RECIST V 1.0 criteria) prior to the administration of PLX4032. All patients enrolled must provide archival or fresh melanoma tumor biopsy for confirmation of V600E+ BRAF mutation status by TaqMan assay
  -  ECOG performance status 0 or 1
  -  Life expectancy ≥ 3 months
  -  Adequate hematologic, hepatic, and renal function
  Exclusion Criteria:
  -  Brain metastases that are progressing or have been documented to be stable for less than 3 months, or for which systemic corticosteroids are required
  -  Investigational drug use within 28 days of the first dose of PLX4032
  -  Uncontrolled intercurrent illness
  -  Refractory nausea and vomiting, malabsorption, or significant bowel resection that would preclude adequate absorption

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Validation of a Molecular Prognostic Test for Eye Melanoma

Summary: Up to half of patients with ocular melanoma (also called iris, choroidal or uveal melanoma) develop metastasis. We have found that certain molecular features of the eye tumor can be detected by gene expression profiling and accurately predict which patients will develop metastasis. This molecular test could eventually allow high risk patients to receive preventative therapy to delay or prevent the development of metastasis. The goal of this study is to prospectively validate the predictive accuracy of the gene expression-based molecular test and compare it to monosomy 3, the most common but potentially less accurate molecular marker for metastasis in ocular melanoma.

Detailed description: We have discovered a gene expression profile derived from primary uveal melanomas that accurately predicts which patients will develop metastasis. Tumors with a class 1 gene expression signature have a very low risk, and those with a class 2 signature have a high risk of metastasis. The molecular test was initially performed on tissue obtained from enucleated eyes using commercial microarray platforms. We are now able to perform the molecular test on fine needle biopsy specimens, and we have developed a customized test that has greater dynamic range and sensitivity than commercial microarray platforms. The goal of this study is to validate the prognostic accuracy of the customized platform by performing the molecular test on primary uveal melanomas obtained from enucleation, local tumor resection or fine needle biopsy. Each sample will be diagnosed as either class 1, class 2 or indeterminate. Outcomes will be collected and the ability of the molecular diagnosis to predict metastasis will be evaluated at regular intervals.

Eligibility: Inclusion Criteria:
  -  clinical diagnosis of melanoma of the iris, ciliary body and/or choroid
  -  treatment to include enucleation, radiotherapy or local tumor resection
  Exclusion Criteria:
  -  evidence of marked tumor necrosis

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: A Study of ADH-1 in Combination With Normothermic Isolated Limb Infusion of Melphalan

Summary: N-cadherin, a protein involved in blood vessel cell binding and on the surface of many tumor cells, is increased as cancer progresses. ADH-1 blocks N-cadherin. This study will test the safety and effects of the combination ADH-1 with Normothermic Isolated Limb Infusion of Melphalan in subjects with locally advanced malignant melanoma.


Eligibility: Inclusion Criteria:
  -  Signed written informed consent
  -  Male and female patients > or = 18 years of age with diagnosis of melanoma for which treatment with Normothermic Isolated Limb Infusion (ILI) of melphalan would be appropriate
  -  Measurable disease
  -  Disease site(s) must be distal to the planned site of tourniquet placement
  -  Available for immunohistochemical testing of N-cadherin expression tumor tissue
  -  Adequate performance status and organ function, as evidenced by hematological and biochemical blood testing and ECG
  Exclusion Criteria:
  -  Receipt of ADH-1 prior to this clinical study (prior melphalan via ILI, is okay)
  -  Stage IV melanoma
  -  Chemotherapy, radiotherapy, or any other investigational drug within 4 weeks before study entry
  -  History of tumors that have shown clinically significant evidence of active bleeding within 12 weeks before study entry
  -  Stroke, major surgery, or other major tissue injury within 4 weeks before study entry
  -  Uncontrolled congestive heart failure, coronary artery disease, or life threatening arrhythmias; myocardial infarction within 12 months; significant electrocardiogram (ECG) abnormalities
  -  Allergic reaction to any therapeutic peptide or to melphalan

Relevance to patient case: not relevant