araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: A Study Comparing Trametinib and Dabrafenib Combination Therapy to Dabrafenib Monotherapy in Subjects With BRAF-mutant Melanoma

Summary: This is a two-arm, double-blinded, randomized, Phase III study comparing dabrafenib (GSK2118436) and trametinib (GSK1120212) combination therapy to dabrafenib administered with a trametinib placebo (dabrafenib monotherapy). Subjects with histologically confirmed cutaneous melanoma that is either Stage IIIC (unresectable) or Stage IV, and BRAF V600E/K mutation positive will be screened for eligibility. Subjects who have had prior systemic anti-cancer treatment in the advanced or metastatic setting will not be eligible although prior systemic treatment in the adjuvant setting will be allowed. Approximately 340 subjects will be randomized 1:1 (combination therapy: dabrafenib monotherapy). Subjects will be stratified by lactate dehydrogenase (LDH) level (> the upper limit of normal (ULN) versus less than or equal to the ULN) and BRAF mutation (V600E versus V600K). The primary endpoint is investigator-assessed, progression-free survival for subjects receiving the combination therapy compared with those receiving dabrafenib monotherapy. Subjects will be followed for overall survival; crossover will not be permitted.


Eligibility: Inclusion Criteria:
  -  Histologically confirmed cutaneous melanoma that is either Stage IIIC (unresectable) or Stage IV (metastatic), and determined to be BRAF V600E/K mutation-positive using the bioMerieux (bMx) investigational use only (IUO) THxID BRAF Assay (IDE: G120011). The assay will be conducted by a central reference laboratory. Subjects with ocular or mucosal melanoma are not eligible.
  -  The subject must have a radiologically 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 counts
  Exclusion Criteria:
  -  Prior treatment with a BRAF or a MEK inhibitor
  -  Prior systemic anti-cancer treatment for Stage IIIC (unresectable) or Stage IV (metastatic) melanoma. Prior systemic treatment in the adjuvant setting is allowed. (Note: Ipilimumab treatment must end at least 8 weeks prior to randomization.)
  -  The subject has received major surgery or certain tyes of cancer therapy with 21 days of starting treatment
  -  Current use of prohibited medication listed in the protocol
  -  Left ventricular ejection fraction less than the lower limit of normal
  -  Uncontrolled blood pressurl
  -  History or current evidence of retinal vein occlusion or central serous retinopathy
  -  Brain metastases unless previously treated with surgery or stereotactic radiosurgery and the disease has been stable for at least 12 weeks
  -  The subject is pregnant or nursing

Relevance to patient case: not relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: Mutation Analysis and Copy Number Changes of KRAS and BRAF Gene in Taiwanese Cases of Biliary Tact Adenocarcinoma

Summary: Cholangiocarcinoma is a fatal malignant neoplasm originating from biliary tracts and constitutes about 5-10% of primary liver cancers, characterized by a poor prognosis. High prevalence in southeast and eastern Asia has been observed. At present, the cellular and molecular mechanisms leading to oncogenesis of cholangiocarcinoma remain unclear.
  The RAS gene product has a key role in controlling cell growth and differentiation through its intrinsic GTPase activity. Point mutations that activate the RAS protein and its downstream cascade have been observed in human tumors. Both KRAS and BRAF are members of the RAS-RAF-MEK-ERK-MAP kinase pathway which mediates cellular response to growth signals. Somatic KRAS mutations are found at high rates in leukemia, colon cancer, pancreatic cancer and lung cancer. Studies from European and Japanese groups have recently described that activating KRAS/ BRAF mutations may play a role in the carcinogenesis of cholangiocarcinoma of the biliary tracts, but our preliminary data demonstrated low frequency of KRAS and BRAF mutation in the same tumor as well as the results from Thailand. In this study, the investigators hypothesize copy number changes rather than genetic mutation of either KRAS or BRAF genes may be the key findings of Taiwanese cases of the adenocarcinoma from the biliary tracts.


Eligibility: Inclusion Criteria:
  -  The patients diagnosed as biliary tact adenocarcinoma.

Relevance to patient case: not relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: Clinicopathological Features of NSCLC Patients Associated With the Chromosome 2p (EML4-ALK)

Summary: Because ALK-positive lung cancer constitutes less than 5% of all lung cancers, it is critically important to select those patients who are more likely to have the ALK mutation. Clinical characteristics of patients with mutations in the target gene should also be known, so that the incidence of a given target mutation is established in a specific population. There is not incidence known in Mexican population, but it is believed it is greater.

Detailed description: Lung adenocarcinoma studies. The only inclusion criterion was the availability of tissue for biomarker studies. To identify ALK rearrangements, fluorescence in situ hybridization (FISH) studies were performed on 3 to 4 mm thick paraffin sections from NSCLCs. The commercially labeled Vysis LSI ALK Dual Color (split-apart), break-apart rearrangement probe (Abbott Molecular, Abbott Park, IL) was used to detect any rearrangement involving the ALK gene. The probe hybridizes to band 2p23, on either side of the ALK gene breakpoint. Criteria for probe signal interpretation in at least 200 interphase nuclei were as follow: 1) separated green and orange signals or single red signals identified cells with rearranged ALK; 2) overlapping of red and green signals (yellowish) indicated cells in which ALK was not rearranged.
  FISH-positive samples for ALK rearrangement were defined as having cells with a clearly separated pair of probe signals, or with >15% of cells having loss of the 5´(centromeric) probe. The higher threshold for loss is necessary because parts of probes can be lost during sectioning.
  The aim of our study is to evaluate the utility of IHC with 5A4 and RT-qPCR in the detection of ALK rearrangements in NSCLC compared with the current method of choice, FISH. Further, we report on the demographics, and clinicopathologic features of ALK-rearranged NSCLC in a Latin-American population.
  Clinical details of these patients were included in a database. Further results will be analyzed with the program SPSS17

Eligibility: Inclusion Criteria:
  -  The only inclusion criterion was the availability of tissue for biomarker studies.
  Exclusion Criteria:
  -  Disease Progression

Relevance to patient case: not relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: LDK378 in Crizotinib naïve Adult Patients With ALK-activated Non-small Cell Lung Cancer

Summary: A single-arm, open-label, two-stage multicenter, phase II study. Patients were pre-screened for ALK positive status. Treatment with LDK378 at 750 mg qd was continued until the patient experienced unacceptable toxicity that precluded further treatment, discontinued treatment at the discretion of the investigator or patient, started a new anticancer therapy and/or died. LDK378 was continued beyond RECIST defined progressive disease (PD) as assessed by the investigator, if in the judgment of the investigator, there was evidence of clinical benefit. Patients who discontinued the study medication in the absence of progression continued to be followed for tumor assessment until the time of PD as assessed by the investigator. Male and female patients aged 18 or over with ALK-rearranged non-small cell cancer (NSCLC) were screened for eligibility. Patients had to have received no prior crizotinib, and had to be chemotherapy-naïve or been pretreated with cytotoxic chemotherapy (up to three prior lines).


Eligibility: Key Inclusion criteria:
  -  Histologically or cytologically confirmed diagnosis of stage IIIB or IV NSCLC that carried an ALK rearrangement, as per the FDA-approved Vysis ALK break-apart FISH assay (Abbott Molecular Inc.)
  -  Age 18 years or older at the time of informed consent.
  -  Patients must have NSCLC that had progressed during or after the last chemotherapy regimen received prior to the first dose of LDK378, if chemotherapy was received
  -  Patients must have been chemotherapy-naive or had received 1-3 lines of cytotoxic chemotherapy to treat their locally advanced or metastatic NSCLC
  -  Patients must have had a tumor tissue sample available, collected either at the time of diagnosis of NSCLC or any time since.
  -  Patients must have recovered from all toxicities related to prior anticancer therapies to grade ≤ 2, except for patients with grade 2 nausea/vomiting and/or grade 2 diarrhea despite optimal supportive therapy who were not allowed to participate in the study.
  Key Exclusion criteria:
  -  Prior treatment with crizotinib, or any other ALK inhibitor investigational agent, for NSCLC
  -  Patients with known hypersensitivity to any of the excipients of LDK378.
  -  Patients with symptomatic central nervous system (CNS) metastases who were neurologically unstable or had required increasing doses of steroids within the 2 weeks prior to study entry to manage CNS symptoms.
  -  History of carcinomatous meningitis.
  -  Presence or history of a malignant disease other than NSCLC that has been diagnosed and/or required therapy within the past 3 years.
  -  Clinically significant, uncontrolled heart disease.

Relevance to patient case: not relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: Serum Free Fatty Acid Metabolite Biomarkers of Lung Cancer

Summary: This study aims to evaluate the performance of serum free fatty acids as biomarkers for the identification of lung cancer.

Detailed description: We will compare the concentration of free fatty acids and their metabolites between patients with lung cancer and control pulmonary patients without known cancer. The diagnostic accuracy will be assessed for potential predictors.

Eligibility: Inclusion Criteria:
  -  Age from 40 to 80
  -  Lung adenocarcinoma with pathological diagnosis
  -  Lung squamous cell carcinoma with pathological diagnosis
  -  Control patients should have at least one of the following criteria: (1) current or ex-smoker with at least a 10 pack-year history, (2) a first-degree relative with a history of lung cancer, or (3) a clinical diagnosis of COPD.
  Exclusion Criteria:
  - Lung cancer patient without serum sample before the initiation of treatment

Relevance to patient case: not relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: Low-Dose Acetylsalicylic Acid in Treating Patients With Stage I-III Non-Small Cell Lung Cancer

Summary: This pilot clinical trial studies low-dose acetylsalicylic acid in treating patients with stage I-III non-small cell lung cancer. Studying samples of urine and blood from patients with cancer in the laboratory may help doctors learn more about changes in biomarkers that occur during treatment with acetylsalicylic acid

Detailed description: PRIMARY OBJECTIVES:
  I. To determine whether ASA (acetylsalicylic acid) 325 mg inhibits prostaglandin E2 (PGE2) biosynthesis in patients with early stage non-small cell lung cancer (NSCLC). Cyclooxygenase (COX) catalytic activity will be determined by measuring the metabolite of PGE2, 11alpha-hydroxy-9,12-dioxo-2,3,4,5-tetranor-prostane-1,20 dioic acid (PGE-M) in urine pre- and post-ASA 325 mg as a surrogate of systemic PGE2 biosynthesis.
  SECONDARY OBJECTIVES:
  I. To determine whether COX-2 protein has a slow turnover in adenocarcinoma of the lung. COX turnover will be determined by measuring urinary PGE-M levels daily for 7 days after discontinuing ASA 325 mg. COX-2 and Prostaglandin expression will also be measured in tumor samples of patients taken at the time of surgery.
  OUTLINE:
  Patients receive acetylsalicylic acid orally (PO) for 7 days and urine is collected for 7 days post therapy.

Eligibility: Inclusion Criteria:
  -  Have confirmed (stage IIIb-IV) or recurrent non-small cell lung cancer, adenocarcinoma histology
  -  Understand and voluntarily sign an informed consent document prior to any study related assessments or procedures are conducted
  -  Anticipated that they will complete all study procedures
  -  Ability to swallow pills
  -  No aspirin in the last 7 days
  Exclusion Criteria:
  -  Know allergy to aspirin or other nonsteroidal anti-inflammatory drugs
  -  History of allergic reaction to aspirin or other non-steroidal anti-inflammatory drugs, including ibuprofen
  -  Any other concomitant serious illness or organ system dysfunction which in the opinion of the investigator would either compromise patient safety

Relevance to patient case: not relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: Comparison of In-House Methods and Cobas BRAF V600 Mutation Assay in Melanoma Tumor Samples

Summary: This non-interventional study will compare the Cobas BRAF V600 mutation assay with in-house methods used in molecular laboratories for the assessment of the BRAF mutation status in melanoma tumor samples. No patients will be enrolled in this study. Data will be collected for approximately 6 months.


Eligibility: Inclusion Criteria:
  No patients are enrolled. Use of tumor samples only.
  -  Histologically proven melanoma tumor sample
  -  Any type of tumor sample: biopsy or surgical specimen of primary tumor or metastasis
  -  Tumor samples must be fixed and paraffin-embedded.
  Exclusion Criteria:
  No patients are enrolled. Use of tumor samples only.
  -  Fixative unknown

Relevance to patient case: not relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: A Pharmacokinetics Study to Investigate the Effect of Vemurafenib on Digoxin in Patients With BRAFV600 Mutation-Positive Metastatic Melanoma

Summary: This open-label, multi-center, three-period, one sequence study will investigate the effect of vemurafenib on the pharmacokinetics of digoxin in patients with unresectable BRAFV600-mutation positive metastatic melanoma or other malignant tumor type that harbors a V600-activating mutation of BRAF without acceptable standard treatment options. Patients will receive multiple doses of vemurafenib in Periods B and C and a single dose of digoxin in Periods A and C. Eligible patients will have the option to continue treatment with vemurafenib as part of an extension study (NCT01739764). The anticipated time on study treatment is approximately 36 days.


Eligibility: Inclusion Criteria:
  -  Male or female patients >= 18 years old
  -  Patients with either unresectable Stage IIIc or Stage IV metastatic melanoma positive for the BRAFV600 mutation or other malignant tumor type that harbors a V600-activating mutation of BRAF, as determined by results of cobas® 4800 BRAF V600 mutation test or a DNA sequencing method, and who have no acceptable standard treatment options
  -  Eastern Cooperative Oncology Group (ECOG) performance status 0 to 2
  -  Life expectancy >= 12 weeks
  -  Full recovery from the effects of any major surgery or significant traumatic injury within 14 days prior to the first dose of study treatment
  -  Adequate hematologic and end organ function
  -  Female patients of childbearing potential and male patients with partners of childbearing potential must agree to always use two effective methods of contraception
  -  Negative serum pregnancy test within 7 days prior to commencement of dosing in women of childbearing potential
  Exclusion Criteria:
  -  Prior treatment with vemurafenib or other BRAF inhibitor within 42 days of first dose of study drug
  -  Prior anti-cancer therapy within 28 days before the first dose of study drug
  -  History of clinically significant cardiac or pulmonary dysfunction
  -  History of symptomatic congestive heart failure of any New York Heart Association class or serious cardiac arrhythmia requiring treatment
  -  History of myocardial infarction within 6 months prior to first dose of study drug
  -  Current dyspnea at rest, owing to complications of advanced malignancy or any requirement for supplemental oxygen to perform activities of daily living
  -  History of congenital long QT syndrome or QTc > 450 ms
  -  Current digoxin therapy or anticipated requirement to take digoxin therapy during the study
  -  Active central nervous system lesions
  -  Uncontrolled or poorly controlled diabetes
  -  Current severe, uncontrolled systemic disease

Relevance to patient case: not relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: Safety and Efficacy of LEE011 and LGX818 in Patients With BRAF Mutant Melanoma.

Summary: To evaluate the safety, tolerability and efficacy of LEE011 and LGX818 when administered orally to patients with BRAF mutant melanoma.

Detailed description: In response to developments in the treatment of melanoma, the sponsor reviewed the data from the ongoing study and decided to halt further enrollment of patients in the Phase Ib part of the study. Consequently, the Phase II part of the study was not performed. Early termination of the study was not due to any safety concerns.

Eligibility: Inclusion Criteria:
  -  Age ≥18 years.
  -  Diagnosis of locally advanced or metastatic melanoma along with written documentation of BRAF V600 mutation.
  -  ECOG performance status of 0 - 2.
  -  Patients enrolled into Phase Ib must have evidence of evaluable and/or measurable disease as determined by RECIST v1.1.
  -  Patients enrolled into Phase II (BRAFi naïve and resistant) must have evidence of measurable disease as determined by RECIST v1.1.
  -  Archival tumor tissue must be obtained for patients enrolled in Phase Ib and Phase II arm 1a/b- BRAFi naïve patients. If an archival tumor tissue is not available, a fresh tumor sample is acceptable.
  -  For patients enrolled in the phase II arm 2, patients must agree to undergo a fresh tumor biopsy unless one was collected prior to study entry but at the time of disease relapse from the most recent BRAFi treatment.
  Exclusion Criteria:
  -  Symptomatic brain metastases.
  -  Symptomatic or untreated leptomeningeal disease.
  -  Patients with inadequate laboratory values during screening.
  -  In the phase II BRAFi naïve arms (1a/b), prior exposure to CDK4/6 inhibitor (e.g., PD 0332991)
  -  Impaired cardiac function or clinically significant cardiac diseases.
  -  Impairment of gastro-intestinal (GI) function or GI disease that may significantly alter the absorption of LEE011 or LGX818.
  -  Patients with concurrent severe and/or uncontrolled concurrent medical conditions.
  -  Previous or concurrent malignancy.
  -  Major surgery < 2 weeks before starting study treatment
  -  Known diagnosis of human immunodeficiency virus (HIV) or hepatitis C.
  Other protocol-defined inclusion/exclusion criteria may apply.

Relevance to patient case: not relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: Circulating Melanoma Cells in Metastatic Patients Treated With Selective BRAF Inhibitors

Summary: The purpose of this study, is to evaluate Circulating Melanoma Cell (CMC) changes in Metastatic Melanoma (MM) patients, undergoing treatment with selective inhibitors of mutated BRAF.

Detailed description: This is an observational prospective pilot study aimed to investigate the association between changes of total and apoptotic CMC count and disease progression in MM patients undergoing treatment with selective inhibitors of mutated B-RAF.

Eligibility: Inclusion Criteria:
  -  Fourth stage Melanoma patients with both measurable and not measurable lesions undergoing treatment with selective B-RAF inhibitors will be included. To determine the prevalence of CMC-positive patients in IV stage Melanoma, patients without mutated B-RAF undergoing chemotherapy and/or vaccines will be also enrolled at baseline, as part of study protocols approved and activated in the participating centers.
  -  Informed written consent.
  Exclusion Criteria:
  -  Inadequate compliance to multiple blood draws (baseline, 15 days, 1th month, 4th month, and/or at progression) as scheduled in this adjunctive biologic study for patients carrying B-FAF mutation; inadequate compliance to adjunctive blood draws, as scheduled at baseline for BRAF wild-type
  -  Previously exposure to immunological treatment.

Relevance to patient case: not relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: Impact of Methylation Alterations in Colon Cancer: Epidemiology and Prognosis

Summary: We conducted a preliminary study in 2010 using the innovative Illumina GoldenGate (methylation assay) which has enabled us to characterize the level of methylation of 807 potential markers on a series of 200 adenocarcinomas of the colon (C18) and rectosigmoid junction (C19) resected between 1998 and 2001. The results, validated by pyrosequencing, allowed us to establish a panel of 12 markers to assess the level of methylation. The aim of this project is to validate the prognostic value of this panel in a second cohort of patients with adenocarcinomas (stage I to IV) resected between 2002 and 2006 in public and private hospitals (n=685).
  This study relies on an original collection of surgical specimens of colorectal cancers resected in public and private hospitals among patients resident in the département of Côte-d'Or and followed by the cancer registry of Burgundy. Samples obtained from each cancer and from adjacent normal mucosa are stored in liquid nitrogen in the Ferdinand Cabane Biological Resources Centre(certified S 96900). Annotations are collected by the cancer registry staff from multiple sources (pathologists, gastroenterologists, oncologists and radiotherapists).
  Pyrosequencing will be used to quantify the level of methylation. The percentage of methylated allele for each marker on cancerous DNA and the ratio of methylated markers to the number of markers analyzed will be determined. The molecular status of MSI, BRAF, KRAS, and PI3K will be taken into consideration.
  To study the prognosis, relative and relapse free-survival will be calculated. A multivariate relative survival analysis will be performed to determine independent prognostic factors taking into account the characteristics of patients and tumours and epigenetic and molecular alterations. Epigenetic alterations will be described according to age group, sex and subsite. The epigenetic phenotypes will be evaluated according to already known molecular status using logistic regression models.


Eligibility: Inclusion Criteria:
  -  Adenocarcinomas of the colon (C18) and rectosigmoid junction (C19)
  -  Resident in Côte-d'Or
  -  Treated by surgical resection
  Exclusion Criteria:
  -  Rectal cancer
  -  Cancer on Crohn's disease and ulcerate colitis
  -  Hereditary colon cancer (HNPCC, familial polyposis)

Relevance to patient case: not relevant