araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Efficacy of Chemotherapy Combined With Regional Hypothermia in Advanced Malignant Melanoma Patients With Progressive Soft Tissue Metastases

Summary: The incidence of malignant melanoma continues to rise throughout the world. Approximately 12 in 100,000 Germans are diagnosed with malignant melanoma per year. Malignant melanoma is often very aggressive since it may spread both through the lymphatic system and the bloodstream at an early stage of disease.
  While treatment of localized disease is mostly surgical, in patients with extensive disease, prognosis remains poor; the primary standard therapy of metastastic disease comprises dacarbazine (DTIC) eventually combined with other chemotherapeutic agents e.g., cisplatin or BCNU. The duration of response to systemic chemotherapy is generally short and so far, no standard second-line treatment has been established.
  To study the potential additional therapeutic effects of regional hyperthermia in advanced malignant melanoma patients with progressive chemotherapy refractory soft tissue metastases, in the present trial, we sought to compine local hyperthermia with concomitant systemic second-line chemotherapy.


Eligibility: Inclusion Criteria:
  -  age between 18 and 70
  -  histologically proven malignant melanoma with advanced inoperable soft tissue metastases
  -  progressive disease upon systemic first-line chemotherapy
  -  2 or more bidimensionally measurable soft tisue lesions
  -  WHO performance status (ECOG) of 2 or more
  -  life expectancy of 8 weeks and more
  -  prior informed consent
  Exclusion Criteria:
  -  participation in other therapy studies
  -  pregnancy or breast feeding
  -  concomitant clinically significant infection
  -  cardiac pacemaker or other medical implants, or implants within the hyperthermia treated region (including a safe distance of 5 cm)
  -  lack of physiological heat sensitivity within the hyperthermia treated region (including a safe distance of 5 cm)

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Immediate Radiotherapy or Observation After Surgery for Melanoma Involving Lymph Nodes

Summary: This trial seeks to establish the role of post-operative radiotherapy in patients who have had surgery for melanoma involving lymph nodes and who are at high risk of recurrence.

Detailed description: This is a randomised phase III trial which is being performed on patients at high risk of local recurrence after having a lymphadenectomy for stage 3 melanoma. The control arm is surgery alone with radiotherapy reserved for those who recur. The study arm is surgery plus post-operative radiotherapy. All 3 major node sites are eligible. The radiation dose administered is 48Gy in 20 fractions. It is likely to be the only study of its kind ever performed. The target is 230 patients.

Eligibility: Inclusion Criteria:
  -  Regional macroscopic nodal metastatic melanoma in one nodal basin region only which has been completely resected.
  -  melanoma involving lymph nodes at high risk of local recurrence (details in protocol)
  -  No evidence of metastases
  -  No active major cancer within 5 years
  -  Normal blood tests
  -  WHO performance status of 0 or 1
  -  Radiotherapy must be able to be commenced within 12 weeks of lymphadenectomy
  -  Patient must not be pregnant and if fertile must use a medically acceptable contraceptive throughout treatment
  -  No major concurrent illnesses likely to cause death within 2 years
  -  Written informed consent has been given
  Exclusion Criteria:
  -  Evidence of active or previous local recurrence or in transit disease
  -  Evidence of distant metastases on clinical or radiological investigation
  -  Patients with prior cancers

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

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: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Development of Tuberculosis Diagnostic Kit

Summary: Pulmonary tuberculosis is one of the most important infectious diseases in human with high mortality.
  Early diagnosis followed by antibiotic treatment is the only way for control of the disease. However, most of commercial tuberculosis diagnostic kits are of moderate sensitivity. Oncoprobe Inc. recently developed a tuberculosis diagnostic kit (HR-103) based on detection of antibody against Mycobacterium tuberculosis in serum. The main purpose of this project is to evaluate the sensitivity and specificity of the kit in detection of pulmonary tuberculosis from saliva, urine, pleura and serum samples.Capilia TB assay and another Immunochromatographic assay such as ESAT-6 and CFP-10 based or other PCR based immunochromatographic assay will be tried to detection tuberculous disease.

Detailed description: Sputum samples from 200 patients with chest or respiratory problems will be collected. Presence of M.
  tuberculosis in the samples will be checked by acid-fast stain and bacterial culture and identification methods.
  At the same time, saliva, urine, and serum samples from these 200 patients and 50 healthy volunteers will be collected. The tuberculosis diagnostic kit (HR-103) from Oncoprobe Inc. or capilia TB assay or another Immunochromatographic assay such as ESAT-6 and CFP-10 based or other PCR based immunochromatographic assay will be used to detect tuberculosis disease from these samples. By comparing the results with the stain and identification results of sputum samples from the 200 patients, the sensitivity and specificity of the kit in detection of pulmonary tuberculosis from saliva, urine,pleura and serum samples, as well as from combination of these samples, will be obtained. In addition to pulmonary tuberculosis, M. tuberculosis causes pleural tuberculosis. Diagnosis of pleural tuberculosis involves determination of activities of adenosine deaminase and interferon-gamma in pleural effusion, which is tedious. We also plan to collect pleural effusion samples from 100 patients, and examined by the tuberculosis diagnostic kit (HR-103) from Oncoprobe Inc. By comparing the results with the adenosine deaminase and interferon-gamma activities of the same samples, the sensitivity and specificity of the kit in detection of pleural tuberculosis from pleural effusion samples will be obtained.

Eligibility: Inclusion Criteria: clinical suspicious of tuberculosis
  Exclusion Criteria:
  -  HIV

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

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: 66-year-old female with melanoma; genetic feature: KIT amplification

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: 66-year-old female with melanoma; genetic feature: KIT amplification

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: 66-year-old female with melanoma; genetic feature: KIT amplification

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: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Imatinib in Patients With Mucosal or Acral/Lentiginous Melanoma

Summary: The purpose of this study is to evaluate how effective imatinib (Gleevec) is in treating acral/lentiginous and mucosal melanoma which has spread to other parts of the body in patients who's disease carries a c-kit mutation. Imatinib is a protein-kinase inhibitor. It is believed that imatinib may be effective in blocking signals on certain cancer cells which allow the malignant cells to multiply and spread.

Detailed description: OBJECTIVES:
  Primary
  -  To determine the response rate of patients with metastatic mucosal, acral/lentiginous, or chronically sun damaged melanomas to treatment with of imatinib.
  -  To determine the time to progression.
  Secondary
  -  To correlate c-kit mutational status with response to therapy.
  -  To evaluate the use of FDG-PET scanning in determining early biologic response to therapy.
  -  Tolerability of imatinib.
  -  To assess amplification of c-kit status through quantitative PCR and/or FISH and other related molecular pathway targets.
  -  To correlate c-kit amplification status with response to therapy.

Eligibility: Inclusion Criteria:
  -  Melanomas that arise on chronically sun damaged skin and have pathologic evidence of solar elastosis
  -  History of primary mucosal or acral/lentiginous melanoma
  -  Histologically documented stage IV metastatic melanoma
  -  ECOG performance status 0,1, or 2
  -  Estimated life expectancy of 6 months or greater
  -  Age 18 years or older
  -  Creatinine < 1.5 x ULN
  -  ANC > 1500 ul
  -  Platelets > 100,000 ul
  -  Total bilirubin, AST, and ALT < 2 x ULN
  -  Amylase and lipase < 1.5 x ULN
  -  C-kit mutation documented from either primary or metastatic tumor site
  -  > 4 weeks from prior chemotherapy or investigational drug
  -  At least one measurable site of disease as defined by at least 1 cm in greatest dimension
  Exclusion Criteria:
  -  Severe and/or uncontrolled medical disease
  -  Pregnant or nursing mothers
  -  Any other significant medical, surgical, or psychiatric condition that my interfere with compliance
  -  Patient is < 5 years free of another primary malignancy except: basal cell skin cancer or a cervical carcinoma in situ
  -  Concurrent treatment with Warfarin
  -  Prior treatment with c-kit inhibitor
  -  Patient with Grade III/IV cardiac problems as defined by NYHA criteria
  -  No H2 blockers or proton pump inhibitors
  -  Known brain metastasis
  -  Known chronic liver disease
  -  Known diagnosis of HIV infection
  -  Previous radiotherapy to > 25% of the bone marrow
  -  Major surgery within 2 weeks prior to study entry
  -  Patient has received any other investigational agent within 28 days of first study drug dosing
  -  Chemotherapy within 4 weeks prior to study entry

Relevance to patient case: possibly relevant