araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 67-year-old male with melanoma; genetic feature: BRAF (V600E), NRAS (Q61R)

Clinical trial: A Pilot Study to Evaluate Optical Spectroscopy of Pigmented Skin Lesions

Summary: The incidence of malignant melanoma has increased dramatically in recent decades. In 1930, the lifetime risk of an individual in the United States developing melanoma was 1 in 1,500. This has been exponentially increasing over the years with the risk estimated to be 1 in 75 in 2000 . According to the American Cancer Society, approximately 59,580 new cases of melanoma will be diagnosed in the United States in 2005 and about 7,770 people are expected to die of the disease.

Detailed description: The researcher ucan use special imaging devices to obtain information about a typical mole and melanoma and use this information to determine the different between malignant and benign melanized lesions. The imaging devices are, Modified Two Layer Diffuse Optical Spectroscopy,multi-spectral imaging, and Spatially Modulated Quantitative Spectroscopy can use to measure atypical moles and melanoma and correlate the results of the biopsy tissue histology.
  The imaging devices can quantify melanin, oxy and deoxy hemoglobin concentration, water, lipid and reduced scattering coefficients and can compare results to histopathologic. Atypical moles and melanoma have a different optical profile based on physiological parameters compared to benign nevus.

Eligibility: Inclusion Criteria:
  -  18 years or older.
  -  Have atypical mole/s and melanoma
  Exclusion Criteria:
  -  Age less than 18 years old.
  -  have NO atypical mole/s and melanoma

Relevance to patient case: not relevant
Patient case: 67-year-old male with melanoma; genetic feature: BRAF (V600E), NRAS (Q61R)

Clinical trial: Feasibility and Functionality of fPAM Imaging in Melanoma

Summary: Melanoma is a cutaneous malignancy that has the potential for local (skin) and regional (lymph node) recurrence. These recurrences may be difficult to detect in their earliest stages. We are attempting to use novel form of skin imaging that uses ultrasound combined with laser to identify these recurrences early, when they may be most amenable to treatment. This imaging will detect melanoma pigment below the surface of the skin and in the draining lymph nodes, as well as new blood vessel formation that occurs with these loco-regional metastases.

Detailed description: recruiting healthy individuals with pigmented lesions and individuals with melanoma and pigmented lesions

Eligibility: Inclusion Criteria:
  -  Adult patients (> 18 yrs of age) with recently diagnosed or a history of, Stage I - III melanoma who are able to give informed consent.
  Exclusion Criteria:
  -  Patients with melanomas < 1mm.
  -  Pregnant females.
  -  Children and young adults < 18 yrs of age and patients who are unable to give informed consent.

Relevance to patient case: not relevant
Patient case: 67-year-old male with melanoma; genetic feature: BRAF (V600E), NRAS (Q61R)

Clinical trial: PEAK: Panitumumab Plus mFOLFOX6 vs. Bevacizumab Plus mFOLFOX6 for First Line Treatment of Metastatic Colorectal Cancer (mCRC) Patients With Wild-Type Kirsten Rat Sarcoma-2 Virus (KRAS) Tumors

Summary: The primary objective of this study is to estimate the treatment effect on progression-free survival (PFS) of panitumumab relative to bevacizumab in combination with mFOLFOX6 chemotherapy as first-line therapy in patients with tumors expressing wild-type KRAS, unresectable mCRC.


Eligibility: Inclusion Criteria:
  -  Histologically or cytologically-confirmed adenocarcinoma of the colon or rectum in patients with unresectable metastatic (M1) disease
  -  Patients with at least 1 uni-dimensionally measurable lesion of at least 10 mm per modified Response Evaluation Criteria in Solid Tumors (RECIST) guidelines
  -  Wild-type KRAS tumor status confirmed by an Amgen approved central laboratory or an experienced laboratory (local laboratory) per local regulatory guidelines using a validated test method
  -  Eastern Cooperative Oncology Group (ECOG) score of 0 or 1
  -  Men or women 18 years of age or older
  -  Adequate hematologic, renal, hepatic, metabolic, and coagulation function
  Exclusion Criteria:
  -  History of prior or concurrent central nervous system (CNS) metastases
  -  Prior chemotherapy or other systemic anticancer therapy for treatment of metastatic colorectal carcinoma
  -  Clinically significant cardiac disease
  -  Clinically significant peripheral sensory neuropathy
  -  Active inflammatory bowel disease
  -  Recent gastroduodenal ulcer to be active or uncontrolled
  -  History of interstitial lung disease
  -  Recent pulmonary embolism, deep vein thrombosis, or other significant venous event
  -  Pre-existing bleeding diathesis and/or coagulopathy with exception of well-controlled anticoagulation therapy
  -  Recent major surgical procedure, open biopsy, or significant traumatic injury not yet recovered from prior major surgery.

Relevance to patient case: not relevant
Patient case: 67-year-old male with melanoma; genetic feature: BRAF (V600E), NRAS (Q61R)

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: possibly relevant
Patient case: 67-year-old male with melanoma; genetic feature: BRAF (V600E), NRAS (Q61R)

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: possibly relevant
Patient case: 67-year-old male with melanoma; genetic feature: BRAF (V600E), NRAS (Q61R)

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: 67-year-old male with melanoma; genetic feature: BRAF (V600E), NRAS (Q61R)

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

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

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

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

Relevance to patient case: possibly relevant
Patient case: 67-year-old male with melanoma; genetic feature: BRAF (V600E), NRAS (Q61R)

Clinical trial: A Study of Vemurafenib (RO5185426) in Comparison With Dacarbazine in Previously Untreated Patients With Metastatic Melanoma (BRIM 3)

Summary: This randomized, open-label study evaluated the efficacy, safety and tolerability of vemurafenib (RO5185426) as compared to dacarbazine in previously untreated patients with metastatic melanoma. Patients were randomized to receive either vemurafenib 960 mg orally twice daily or dacarbazine 1000 mg/m2 intravenously every 3 weeks. Study treatment was continued until disease progression or unacceptable toxicity occurred. The data and safety monitoring board recommended that patients in the dacarbazine group be allowed to cross over to receive vemurafenib, and the protocol was amended accordingly on January 14, 2011, as both overall survival and progression-free survival endpoints had met the prespecified criteria for statistical significance in favor of vemurafenib.


Eligibility: Inclusion Criteria:
  -  adults, >/=18 years of age
  -  metastatic melanoma, stage IIIC or IV (AJCC)
  -  treatment-naïve (no prior systemic anticancer therapy)
  -  positive for BRAF V600E mutation
  -  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 central nervous system metastases
  -  history of carcinomatous meningitis
  -  severe cardiovascular disease within 6 months prior to study drug administration
  -  previous malignancy within 5 years prior to study, except for basal or squamous cell carcinoma of the skin, melanoma in-situ, or carcinoma in-situ of the cervix

Relevance to patient case: not relevant
Patient case: 67-year-old male with melanoma; genetic feature: BRAF (V600E), NRAS (Q61R)

Clinical trial: Study to Determine the Effectiveness of GSK1120212 in BRAF Mutation-positive Melanoma Previously Treated With or Without a BRAF Inhibitor

Summary: MEK113583 is a Phase II open-label, multi-site study to investigate the objective response rate, safety, and pharmacokinetics of GSK1120212 in subjects with BRAF mutation-positive melanoma who were previously treated with or without a BRAF inhibitor. GSK1120212 is a potent and highly selective inhibitor of MEK activation and kinase activity.


Eligibility: Inclusion Criteria:
  -  Metastatic cutaneous melanoma that was previously treated with: (Cohort A) a BRAF inhibitor either with or without other prior therapy. (Cohort B) at least 1 prior chemotherapy or immunotherapy, without treatment with a BRAF inhibitor.
  -  Documented positive BRAF mutation (V600E, V600K, or V600D).
  -  Subjects must provide archived tumor tissue or undergo fresh tumor biopsy prior to enrollment.
  -  The subject must have a radiographically measurable tumor.
  -  The subject is able to carry out daily life activities without significant difficulty (ECOG performance status score of 0 or 1).
  -  Able to swallow and retain oral medication.
  -  Sexually active subjects must use acceptable methods of contraception during the course of the study.
  -  Adequate organ system function and blood cell counts.
  Exclusion Criteria:
  -  The subject has had major surgery or received certain types of cancer therapy within 21 days before starting the study.
  -  Previous treatment with a MEK inhibitor.
  -  Current use of a prohibited medication listed in the protocol.
  -  Uncontrolled glaucoma.
  -  Brain metastasis, unless previously treated with surgery or stereotactic radiosurgery, and the disease has been stable for at least 2 months prior to enrollment.
  -  Current severe or uncontrolled systemic disease.
  -  History of clinically significant heart, lung, or eye/vision problems.
  -  Significant unresolved side effects from previous anti-cancer therapy.
  -  The subject is pregnant or breastfeeding.

Relevance to patient case: possibly relevant
Patient case: 67-year-old male with melanoma; genetic feature: BRAF (V600E), NRAS (Q61R)

Clinical trial: A Pharmacokinetic/Pharmacodynamic Study of RO5185426 in Previously Treated Patients With Metastatic Melanoma

Summary: This open-label study will assess the pharmacokinetics, efficacy and safety of RO5185426 administered as 240mg tablets in previously treated patients with metastatic melanoma. Patients will be randomized to receive one of four dose-levels of RO5185426 [RG7204; PLEXXIKON; PLX4032] orally twice daily on days 1 to 15 (morning dose). Starting on day 22, treatment with RO5185426 may be resumed at a dose of 960 mg twice daily and continued until disease progression. Target sample size is <100 patients.


Eligibility: Inclusion Criteria:
  -  adult patients, >/=18 years of age
  -  histologically confirmed metastatic melanoma, stage IIIc or IV (AJCC)
  -  failure of at least one prior standard of care regimen
  -  positive for BRAF V600E mutation (by Roche CoDx BRAF mutation assay)
  -  ECOG performance status 0 or 1
  -  adequate hematologic, renal and liver function
  Exclusion Criteria:
  -  active CNS lesions on CT/MRI within 28 days prior to enrollment
  -  history of spinal cord compression o carcinomatous meningitis
  -  anticipated or ongoing anti-cancer therapies other than those administered in this study
  -  previous treatment with BRAF inhibitor (sorafenib allowed) or MEK inhibitor
  -  severe cardiovascular disease within 6 months prior to study
  -  previous malignancy within the past 5 years except for basal or squamous cell carcinoma of the skin, melanoma in-situ and carcinoma in-situ of the cervix

Relevance to patient case: definitely relevant
Patient case: 67-year-old male with melanoma; genetic feature: BRAF (V600E), NRAS (Q61R)

Clinical trial: Neoadjuvant Treatment of Colon Cancer

Summary: This study will investigate
  -  the effect of preoperative combination chemotherapy in patients with locally advanced colon cancer with mutation in the KRAS, BRAF or PIK3CA gene
  -  the effect of preoperative combination chemotherapy in combination with biological treatment in patients without mutation in the KRAS, BRAF or PIK3CA gene.


Eligibility: Inclusion Criteria:
  -  Histologically verified locally advanced T3 or T4 colon cancer assessed by CT scan
  -  Analysis of KRAS, BRAF, PIK3CA
  -  Age ≥18 år
  -  Performance status ≤ 2
  -  Hematology
  -  ANC ≥ 1.5x10^9/l. Thrombocytes ≥ 100x10^9/l.
  -  Biochemistry
  -  Bilirubinaemia ≤ 3 x UNL. ALAT ≤ 5 x UNL
  -  Consent to translational research
  -  Fertile women must present a negative pregnancy test and use secure birth control during and 3 months after treatment.
  -  Written and orally informed consent.
  Exclusion Criteria:
  -  Clinically significant cardiovascular disease (including myocardial infarction, unstable angina, symptomatic congestive heart failure, serious uncontrolled cardiac arrhythmia) ≤ 1 year before enrollment, active severe infections or other concurrent disease.
  -  Peripheral neuropathy NCI grade >1
  -  Other malignant disease within 5 years prior to enrollment, except basal cell squamous carcinoma of the skin and cervical carcinoma-in-situ
  -  Other investigational treatment within 30 days prior to treatment start
  -  History of interstitial lung disease e.g. pneumonitis or pulmonary fibrosis or evidence of interstitial lung disease on baseline chest CT scan.
  -  Bleeding tumors
  -  Hypersensitivity to one or more of the substances

Relevance to patient case: not relevant
Patient case: 67-year-old male with melanoma; genetic feature: BRAF (V600E), NRAS (Q61R)

Clinical trial: Using High Resolution Function Imaging To Detect Melanoma and Dysplastic Nevi

Summary: A novel infrared imaging tool to aid in the clinical detection of atypical pigmented lesions and melanoma is developed. Goals include evaluation of the utility of high-resolution infrared scanning of cutaneous lesions in the diagnosis of pigmented lesions and the identification of high-risk lesions and melanomas.


Eligibility: Inclusion Criteria:
  -  Patients seen in the high-risk pigmented lesion clinic, who posses a pigmented lesion with a clinical indication for biopsy
  Exclusion Criteria:

Relevance to patient case: not relevant