araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 61-year-old male with melanoma; genetic feature: BRAF amplification

Clinical trial: Studying Tumor Tissue Samples From Patients With Melanoma Who Have Undergone Sentinel Lymph Node Biopsy

Summary: RATIONALE: Studying samples of tumor tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer. It may also help the study of cancer in the future.
  PURPOSE: This laboratory study is looking at tumor tissue samples from patients with melanoma who have undergone sentinel lymph node biopsy.

Detailed description: OBJECTIVES:
  -  Develop a predictive model for sentinel lymph node biopsy positivity in patients with melanoma who have undergone sentinel lymph node biopsy.
  -  Develop a survival model for relapse based on sentinel lymph node biopsy positivity.
  -  Assess the genetic determinants in primary melanomas that predict a metastatic phenotype and thereby improve understanding of the biology of the metastases in melanoma.
  OUTLINE: This is a retrospective, case-controlled, multicenter study. Patients are stratified according to Breslow thickness of the tumor (0.75-1.50 mm vs 1.51- 4 mm vs > 4 mm) and gender.
  Archived tumor tissue is analyzed by immunohistochemistry (IHC) for AP2, vascular endothelial growth factor, MMP 2, MCM4, and others, if feasible. Sentinel node biopsies are analyzed by IHC for CD31, LYVE-1, and D2-40 expression. RNA and DNA are also extracted for genetic expression studies and mutation analysis (e.g., BRAF, NRAS, PTEN, CDKN2A).
  Patient data related to relapse and recurrence is collected, if available.
  Peer reviewed and funded or endorsed by Cancer Research UK
  PROJECTED ACCRUAL: A total of 1,000 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Confirmed diagnosis of cutaneous melanoma
  -  Breslow thickness > 0.75 mm
  -  Has undergone sentinel lymph node biopsy
  -  No primary melanoma that has not originated in the skin
  -  No multiple primary melanomas
  -  Currently under clinical followup OR discharged from follow up within the past 3 months
  PATIENT CHARACTERISTICS:
  -  No other malignancy except for nonmelanoma skin cancer or cervical carcinoma in situ
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 61-year-old male with melanoma; genetic feature: BRAF amplification

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

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


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

Relevance to patient case: possibly relevant
Patient case: 61-year-old male with melanoma; genetic feature: BRAF amplification

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: not relevant
Patient case: 61-year-old male with melanoma; genetic feature: BRAF amplification

Clinical trial: Ultraviolet Light Exposure and Immunosuppression in Cutaneous Melanoma

Summary: This project seeks to understand differences in the serum vitamin D levels and immune status in cutaneous malignant melanoma patients with different UV exposure histories in New Mexico.

Detailed description: It is well established that ultraviolet radiation (UV) exposure is related to the development of melanoma. There is also evidence that immune reactions are altered after UV exposure in the skin (locally) and perhaps throughout the body (systemically). Additionally, while the role of vitamin D and melanoma development has not been fully established, UV-B exposure is essential for vitamin D production in the skin. Increased sun exposure is also related to the presence of solar elastosis, which might protect (1) or improve survival from melanoma. Thus, melanoma represents a unique model for studying UV exposure, the immune system, and vitamin D. Malignant melanoma is an antigenic cancer; therefore, the role of UV exposure-induced immunosuppression and vitamin D production in the recognition, destruction and growth inhibition of cancerous melanocytes is worth further study.
  To underscore the importance of this project, the Scientific Advisory Committee of the Melanoma Research Foundation and the Steering Committee of the Society of Melanoma Research have indicated a need to collect more human data on the host immune response mechanisms in melanoma and also to focus on the skin as a whole microenvironment, moving away from only in vitro experiments.

Eligibility: Inclusion Criteria:
  -  Resident of New Mexico
  -  Age between the 1 and 95
  -  Newly diagnosed with cutaneous invasive melanoma; any stage permitted (ICDO C44.0-9) between September 1, 2008 and December 31, 2011.
  -  SSM (superficial spreading melanoma) and NM (nodular melanoma) histological subtypes are allowed
  -  Access to a telephone or be able to participate in a personal interview at the clinic
  -  Physically and mentally competent to complete a 1-hour telephone or personal interview
  Exclusion Criteria:
  -  Ocular melanoma, LMM (lentigo maligna melanoma) or ALM (acral lentigo melanoma), and mucosal melanoma cases.
  -  No access to a telephone or is not able to meet with the interviewer.

Relevance to patient case: not relevant
Patient case: 61-year-old male with melanoma; genetic feature: BRAF amplification

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: possibly relevant
Patient case: 61-year-old male with melanoma; genetic feature: BRAF amplification

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: 61-year-old male with melanoma; genetic feature: BRAF amplification

Clinical trial: A Retrospective Study of Biomarkers in Non-Small Cell Lung Cancer

Summary: The purpose of this study is:
  1. To characterize the types and frequency of molecular alterations to the epidermal growth factor receptor (EGFR) pathway, FGFR4 and EML-ALK in Asian patients with non-small cell lung cancer
  2. To identify candidate biomarkers of importance in the EGFR and estrogen pathways
  Most, if not all, human malignancies including lung cancer are caused by somatic alterations of the genome, leading to activation of oncogenes or inactivation of tumor suppressor genes and their resultant oncogenic effects. In addition to mutations, increased chromosomal copy number (by amplification or polysomy) and DNA methylation are other mechanisms of oncogene activation and tumour suppressor gene inactivation respectively.
  Little is known about the relationship between these oncogenes of the EGFR family and the recently described oncogenes FGFR4 and fusion gene EML4-ALK. Recent data suggests molecularly defined subgroups of non-small cell lung cancer (NSCLC) exist and can be used to predict for sensitivity to targeted agents (erlotinib or gefitinib) or cytotoxic chemotherapy (pemetrexate, gemcitabine, platinum agents). The findings that estrogen receptors are present in lung tumours and that estrogen can stimulate growth and proliferation of lung cancers in vitro and in vivo are provocative. Further studies to evaluate the role of estrogens and other sex hormones in lung cancer are warranted.
  A further understanding of the molecular indicators of lung cancer prognosis and treatment prediction would improve drug development and patient treatment selection.
  Archived paraffin-embedded and fresh frozen NSCLC tumor tissue will be obtained via the Department of Pathology and the National University Tissue Repository respectively. Clinico-pathological characteristics will be obtained from the case records, Pathology and Tissue Repository. DNA will be isolated using standard techniques. Sequencing of genes in the EGFR signaling pathway: EGFR, KRAS, ErbB2, ErbB3, MET, PI3K, and BRAF as well as FGFR4. Unstained slides from the paraffin-embedded tissue will be obtained and subjected to fluoresce in vitro hybridization (FISH) for breakpoints in the EML4 and ALK genes as previously described. For cases that have been snap-frozen, RNA will be extracted and EML4-ALK fusions will be confirmed using RT-PCR and pre-specified primers. To analyse the expression of proteins of putative relevance to EGFR function (such as EGFR, ErbB2, ErbB3, AKT, MET, STAT, ERK, MAPK, cyclin D1, C/EBPa), downstream effects of EGFR: cell proliferation (Ki-67), angiogenesis (CD34, VEGF-A), apoptosis (bcl-2), metastasis, and hormonal influence (oestrogen and progesterone receptors, aromatase), TMA technology will be utilised. The status of the tumor suppressor genes PTEN and C/EBPa will be analysed.


Eligibility: Inclusion Criteria:
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 61-year-old male with melanoma; genetic feature: BRAF amplification

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: possibly relevant
Patient case: 61-year-old male with melanoma; genetic feature: BRAF amplification

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: 61-year-old male with melanoma; genetic feature: BRAF amplification

Clinical trial: Biomarkers in Blood Samples From Patients With Refractory Non-Small Cell Lung Cancer Previously Treated With Sorafenib Tosylate

Summary: RATIONALE: Studying samples of blood from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer.
  PURPOSE: This research study is studying biomarkers in blood samples from patients with refractory non-small cell lung cancer previously treated with sorafenib tosylate.

Detailed description: OBJECTIVES:
  -  To determine the mutation rates of BRAF, KRAS, and EGFR in patients with non-small cell lung cancer treated with sorafenib tosylate on protocol ECOG-2501.
  -  To determine the association between BRAF, KRAS, or EGFR mutation status and clinical benefits in patients treated with this regimen.
  OUTLINE: This is a multicenter study.
  DNA is isolated from archived plasma samples and analyzed for BRAF, KRAS, and EGFR mutations.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of refractory non-small cell lung cancer
  -  Received sorafenib tosylate on protocol ECOG-E2501
  -  Available blood specimens
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 61-year-old male with melanoma; genetic feature: BRAF amplification

Clinical trial: KRAS Mutation and Incidence of the Colorectal Carcinoma in Martinique Between 2007 and 2009

Summary: -  There is no data at present concerning the KRAS mutation in patients from Martinique with colorectal cancer. Despite the fact that the incidence of this disease continues to increase there is no recent data to confirm it. This study has a descriptive purpose, allowing a comparison of the population from Martinique to other populations.
  -  A study of incidence of colorectal cancer, overseen by the Association from Martinique for the Epidemiological Search on Cancer (AMREC), also leads to a better knowledge of the local characteristics of the colorectal cancer.
  -  These two descriptive characteristics of colorectal cancer in Martinique will be useful data for the health professionals to provide their patients better care.

Detailed description: -  The colorectal carcinogenesis is complex. It influences among others, the EGFR (Epidermal Growth Factor Receptor) which activation leads to tumoral proliferation, differentiation and invasion. The binding of the EGF (Epidermal Growth Factor) or of another ligand to the EGFR is responsible for the activation of the Ras- Raf and Pi3k pathways.
  -  The mutation of the genes KRAS, BRAF or PIK3CA results in their continuous activation, independently of the activation or of the pharmacological blocking of EGFR. The most frequently found mutation affects the KRAS gene (20 to 50 % of the cases). 90 % of these mutations are situated on codons 12 and 13 of this gene (70 % codon 12 and 30 % codon 13). These mutations are responsible for a decrease of the GTPase activity of the ras protein, which stays then in active conformation bound to the GTP. This leads to the blocking of the pathway and to the inactivity of the pharmacological blocking of EGFR.

Eligibility: Inclusion Criteria:
  -  for the study of the KRAS mutation: 250 patients drawn by lots among the cases of colorectal carcinoma diagnosed between January 1st, 2007 and December 31st, 2009 in Martinique
  -  for the study of incidence: patient for whom was diagnosed a colorectal carcinoma between January 1st, 2007 and December 31st, 2009
  -  patient unopposed and in free agreement to participate in this study
  -  patient having his main home in Martinique at the time of the diagnosis
  -  patient 18 years old and over
  Exclusion Criteria:
  -  patient whose diagnosis is prior to 2007 and later in 2009
  -  patient having shown opposition to the participation in this study
  -  patient minor or under guardianship
  -  patient not having his main home in Martinique at the time of the diagnosis

Relevance to patient case: not relevant