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: Study of Ipilimumab (MDX-010) Monotherapy in Patients With Previously Treated Unresectable Stage III or IV Melanoma

Summary: The purpose of this clinical research study is to compare the best overall response rate (BORR)(as per modified WHO criteria) in patients with previously treated, therapy-refractory, or -intolerant, Stage III (unresectable) or Stage IV melanoma receiving ipilimumab doses of 0.3, 3, and 10 mg/kg. The safety of this product will also be evaluated.


Eligibility: Inclusion Criteria:
  -  Patients with previously treated, therapy-refractory or -intolerant, Stage III (unresectable) or Stage IV melanoma

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: Phase III Randomized Trial of Adjuvant XP Chemotherapy and XP/RT for Resected Gastric Adenocarcinoma

Summary: The objective of the trial is to compare disease-free survival between adjuvant capecitabine/cisplatin alone vs capecitabine/cisplatin with radiotherapy (chemoradiation) in curatively resected gastric cancer patients.

Detailed description: Although gastrectomy is the only potentially curative treatment in gastric cancer patients, the overall survival results remain unsatisfactory. The main factor accounting for high mortality rate is the relapse after surgical resection. During the past few decades, the principle of combined modality treatment has been developed and applied in practice for various solid tumors and gastric cancer has not been an exception. In an attempt to prevent recurrence and increase the cure rate of gastric cancer patients after surgery, multiple studies using variable modalities have been undertaken. One of the landmark study in adjuvant trials was the Intergroup study INT-0116, which reported a significant improvement in survival with the use of chemoradiation therapy after gastric resection of stage Ib to IV gastric cancers. Thereafter, the chemoradiation therapy has gained popularity and has been increasingly recognized as a standard of care in U.S. Nevertheless, the result from INT-0116 study has been challenged by the fact that the surgical treatment applied in the trial was gastrectomy with limited lymph node dissection (D0 or D1) in 90% of cases. Therefore, it is debatable whether adjuvant chemoradiation therapy can confer survival benefit in patients with extensive lymph node dissection.
  It is still disputable if chemoradiotherapy after D2 can improve the results of D2 alone. Thus, the assessment of the effect of adjuvant chemoradiotherapy in D2 resected gastric cancer is essential.

Eligibility: Inclusion Criteria:
  1. Histologically proven gastric adenocarcinoma
  2. ≥ D2 resection
  3. Stage IB(T1N1,T2bN0), II, IIIA, IIIB, IV(T4,N3 포함, M1 lymph node 제외)
  4. 18 ≤ age ≤ 75
  5. ECOG 0-2
  6. No distant metastasis
  7. Adequate bone marrow functions (ANC ≥ 1,500/ul, blood platelet ≥ 100,000/ul, haemoglobin ≥ 10g/dl)
  8. Adequate renal functions(serum creatinine ≤ 1.5mg/dl)
  9. liver functions (serum bilirubin ≤ 1.5mg/dl, AST/ALT ≤ 3 times(normal value)
  10. Written informed consent
  Exclusion Criteria:
  1. Previous history of immunotherapy, chemotherapy, radiotherapy for gastric cancer
  2. Active infection requiring antibiotics
  3. Pregnant, lactating women
  4. Psychiatric illness, epileptic disorders
  5. Concurrent systemic illness not appropriate for chemotherapy
  6. Resection margin (+)
  7. Pathologic stage IA
  8. History of other malignancy within 5 years except for non-melanoma skin cancer, cervix in situ carcinoma
  9. M1 lymph node (+)
  10. D0, D1 resection

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: Safety and Efficacy Trial of Imexon Plus DTIC in Advanced Malignant Melanoma

Summary: AMP-005 is a Phase 1b/2 clinical trial designed to evaluate whether the new drug, imexon, can be administered in combination with the approved drug, dacarbazine (DTIC), for the treatment of patients with stage III or IV inoperable melanoma. The Phase 1b part of the study is designed to determine whether the two drugs can be safely combined together, and the Phase 2 part of the study is designed to provide additional safety data and to gain an understanding of whether adding imexon to DTIC can improve the outcome for melanoma patients versus the findings from prior clinical studies of DTIC alone.


Eligibility: Inclusion Criteria:
  -  Malignant melanoma; inoperable stage III or IV disease.
  -  Able to perform the activities of daily living.
  -  A projected life expectancy of at least 4 months.
  -  If female, neither pregnant nor nursing.
  -  Willing to use contraceptives to prevent pregnancy.
  -  Blood cell counts and blood chemistries in or near normal range.
  -  Prior radiation is permitted.
  -  No other serious illnesses.
  -  No other active malignancy.
  -  No serious infections.
  -  No other current drug therapy for the cancer or steroid therapy.
  Exclusion Criteria:
  -  No prior chemotherapy for the stage III or IV disease.
  -  Brain metastases

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

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

Clinical trial: Studying Genes to Identify Melanoma in Patients in Iceland and Their Family Members

Summary: RATIONALE: Studying the genes expressed in samples of blood from patients with cancer and their family members may help doctors identify biomarkers related to cancer.
  PURPOSE: This clinical trial is studying genes to identify melanoma in patients in Iceland and their family members.

Detailed description: OBJECTIVES:
  -  Assess the feasibility of Iceland Genomics Corporation (UVS) to identify melanoma in multiple-case families, individuals with multiple tumors, and selected additional family members in Iceland.
  -  Assess the feasibility of mutation detection using sequencing and HPLC.
  -  Determine UVS' ability to create datasets with demographic, epidemiologic and molecular data.
  OUTLINE: Participants and patients undergo blood collection and complete lifestyle questionnaires. All patients and population-based controls have DNA samples sequenced for MC1R. Demographic and epidemiologic data on all study participants is collected. Sequencing of the major melanoma susceptibility genes CFDKN2A, CDK4, and MC1R is also performed.

Eligibility: DISEASE CHARACTERISTICS:
  -  Patients diagnosed with melanoma and selected family members are eligible to participate
  -  Must live in Iceland
  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: 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: 45-year-old female with Melanoma. Genetic variant: BRAF (V600E), CDKN2A Deletion. Other conditions: None.

Clinical trial: Characterization of the Melanoma-Specific Immune Response

Summary: The aim of this study is to study T-cells. Blood will be collected and the samples will be used to generate T cell clones. Two separate blood draws will be required at the maximum.

Detailed description: The aim of the study is to in-vitro characterize and expand T cells specific for melanoma-derived antigens. Peripheral blood with be collected from 20 volunteers with biopsy proven melanoma and 10 age matched controls. Blood will be collected prior to the initiation of chemotherapy. There will be no more than two blood draws per patient. Most patients will receive a single blood draw; however, some participants may be asked to return for a single additional blood draw if investigators were unable to isolate melanoma-specific immune cells after the first blood draw. Two separate blood draws will be the maximum. The interval between these blood draws will be a minimum of 3 months apart. Blood samples will be used to determine the patient's HLA haplotype via PCR and DNA sequencing. After the patient's haplotype has been established melanoma-specific T cell clones will be generated from the peripheral blood samples and expanded in-vitro. These clones will then be assayed for specificity against commercially available melanoma cell lines. The T cell clones will also be assayed for reactivity to melanocyte differentiation antigens such as MART-1 and gp100. If the volunteer requires a palliative resection of a melanoma tumor then the patient's own tumor cells may also be used to test the specificity of the isolated T cell clones. All experiments will be conducted in-vitro.

Eligibility: Inclusion Criteria:
  -  Biopsy diagnosis of malignant melanoma
  -  Have had a biopsy diagnosis of malignant melanoma in the past
  Exclusion Criteria:
  -  Patients taking immunosuppressive medications

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: Sentinel Node With Ultrasound Contrast in Melanoma

Summary: The purpose is to evaluate,in 20 patients, if the sentinel node(s) in melanoma can be detected by lymph contrast ultrasound. In comparing the patients will also get lymph-scintigraphy and sentinel node detection wiht blue dye.
  The goal is to improve the method for detecting sentinel node(s) in melanoma.


Eligibility: Inclusion Criteria:
  -  Malignant melanoma on a extremity,
  -  No spread of the cancer,
  -  Patients over 18 years old,
  Exclusion Criteria:
  -  Pregnancy,
  -  Lactating,
  -  Severe hart disease,

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

Clinical trial: Study of Families With Melanoma

Summary: RATIONALE: A study that evaluates patients' lifestyle, skin, and blood and tissue samples may help doctors understand the risk factors for melanoma relapse.
  PURPOSE: This clinical trial is studying the risk factors for melanoma in families with melanoma.

Detailed description: OBJECTIVES:
  Primary
  -  Determine what lifestyle factors and which genes govern relapse from melanoma.
  Secondary
  -  Compare sun exposure and genes that cause melanoma in patients with melanoma vs healthy participants.
  -  Assess how unusual moles relate to sun exposure and genes that cause melanoma.
  OUTLINE: This is a multicenter, cohort study.
  Patients and healthy participants complete lifestyle questionnaires by mail and telephone. Some patients* and healthy participants undergo a skin examination to count moles and classify skin type (e.g., degree of freckling and wrinkling indicative of sun damage).
  NOTE: *Patients diagnosed with primary invasive melanoma after September 2005 do not need to consent to a skin examination.
  Patients and healthy participants also undergo blood collection for lymphocyte analysis, DNA extraction, and the measurement of minerals, vitamins, and beta carotene. Tissue samples from original diagnosis are examined by immunohistochemistry for gene expression and mutations, including CDKN2A and CDK4.
  Patients and healthy participants are followed annually.
  Peer reviewed and funded or endorsed by Cancer Research UK
  PROJECTED ACCRUAL: A total of 3,700 patients and healthy participants will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Meets 1 of the following criteria:
  -  Newly diagnosed primary invasive melanoma (patient group)
  -  Lentigo maligna malignant melanoma allowed
  -  Rare variants of melanoma allowed, including any of the following:
  -  Acral lentiginous
  -  Subungual
  -  Ear, nose, and throat
  -  Oropharyngeal
  -  Perineal
  -  Vaginal
  -  Vulval
  -  Rectal
  -  Nodal with no known primary
  -  Patients undergoing sentinel node biopsy are eligible
  -  No in situ melanoma, melanocytic intraepidermal neoplasia, or ocular melanoma
  -  Healthy participant meeting either of the following criteria (control group):
  -  Relative of a patient who was diagnosed with melanoma after September 2005
  -  Healthy volunteer who is age- and sex-matched for patients who were diagnosed with melanoma before October 2005
  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: Germline Mutations in Patients With Head and Neck Cancer and a Family History of Cancer

Summary: RATIONALE: Studying gene mutations in samples of DNA from patients with head and neck cancer and a family history of cancer may help doctors learn more about the development of cancer in families.
  PURPOSE: This clinical trial is studying germline mutations in patients with head and neck cancer and a family history of cancer.

Detailed description: OBJECTIVES:
  -  Measure the incidence of p16^INK4a germline mutations in patients with squamous cell carcinoma of the head and neck and a family history of cancer.
  -  Determine biologic activity of identified p16^INK4a germline mutations.
  OUTLINE: DNA specimens are collected for genetic and mutation analysis and examined by PCR and flow cytometry. The activity of cells with p16 mutations is determined by cell cycle arrest functional assay.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of squamous cell carcinoma (SCC) of the head and neck
  -  Must have ≥ 1 first-degree relative with any of the following cancers:
  -  Non-small cell lung cancer
  -  Melanoma
  -  Pancreatic cancer
  -  SCC of the head and neck
  -  Lymphoma (controls)
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant