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

Clinical trial: Erlotinib in Women With Previously Untreated Adenocarcinoma of the Lung

Summary: The purpose of this trial is to figure out what effects (good or bad) the investigational drug agent called Tarceva (erlotinib; OSI-774) has on women with previously untreated adenocarcinoma.

Detailed description: Patients will start taking Tarceva daily by mouth on Day 1 and will continue taking this medication daily at home, until participation in the study ends.
  Every 28 days (one cycle) while the patient is taking Tarceva, they will be examined in the outpatient clinic (blood test and physical examination) and the doctor will determine if they should continue taking Tarceva.
  After every two cycles of treatment (every 8 weeks) standard radiological testing (CT scans, MRIs, and/or x-rays) of the cancer site(s) will be done to assess the response to the Tarceva treatment.
  While the patient is on this study and at the end of the study, the patient will undergo blood and urine tests, medical history evaluation, physical exams including measures of vital signs (blood pressure, heart rate, temperature, and respiration), bone scans, tumor biopsy sample, and various radiological tests to monitor the cancer and the patients health.
  The length of time on the study depends upon how the cancer responds to Tarceva and whether or not the patient experiences unacceptable side effects.

Eligibility: Inclusion Criteria:
  -  Female
  -  Diagnosis of adenocarcinoma of the lung
  -  Patient has had at least one core biopsy of her tumor
  -  Must be willing to undergo epidermal growth factor receptor (EGFR) mutation testing of her tumor
  -  Stage IV or IIIB non-small cell lung cancer
  -  Non-smoker or former smoker. Non-smoker is defined as a person who smoked 100 or less cigarettes in her lifetime while a former smoker is defined as a person who has quit smoking one or more years ago.
  -  Three or more weeks since last radiation therapy
  -  Three or more weeks since last major surgery
  -  Must at least be able to walk and capable of taking care of herself although unable to carry out work activities
  -  Life expectancy of 8 weeks or more
  -  Blood tests that show kidneys, liver and bone marrow to be working adequately
  -  Women of child-bearing potential must agree to use adequate contraception prior to study entry and for the entire time enrolled in study
  Exclusion Criteria:
  -  Prior exposure to Tarceva (OSI-774, erlotinib)
  -  Uncontrolled central nervous system problems
  -  Prior chemotherapy regimen
  -  Difficulty swallowing
  -  A disease or disorder that interferes with ability to digest and absorb food
  -  Incomplete healing of previous oncologic or other major surgery
  -  Significant medical history or unstable medical condition such as heart failure, active infection, uncontrolled high blood pressure
  -  Pregnant or breast feeding
  -  A medical condition that could make it unsafe for patient to participate in this study

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

Clinical trial: Validation of Coregistered CT-PET Imaging in Determining Tumor Volume and Atelectasis in Patients With Operable Non-Small-Cell Lung Cancer and Tumor Associated Atelectasis

Summary: CT-PET image fusion has the potential to differentiate 'tumor' from 'atelectasis' much better than the CT-scan in patients with non-small cell lung cancer who also have atelectasis.
  This however has never been validated on a histological level. In this study patients with non small cell lung cancer and atelectasis who are eligible for surgery undergo a CT-scan and a PET-scan prior to surgery.
  The resection specimen will be compared to the preoperative imaging.


Eligibility: Inclusion Criteria:
  -Patients with non small cell lung cancer and atelectasis, who are eligible for surgery.
  Exclusion Criteria:
  -  age < 18 years
  -  pregnancy

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

Clinical trial: Genetic Epidemiological Study of Lung Cancer in Taiwan and Clinical Applications

Summary: Lung adenocarcinoma in Chinese females is hypothesized to be determined by both genetic and environmental factors. In this grant proposal, we propose to map the loci of susceptibility genes of female lung adenocarcinoma based on multiplex families recruited in Taiwan. We focus on a unique pathological type of a unique population in order to reduce heterogeneity of the genetic background. Compared with western women, female Chinese population has a high prevalence of lung adenocarcinoma. Our reasoning is that if we focus on a specific sub-type, which has a familial basis, we will increase the probability of identifying genes associated with female lung adenocarcinoma. The primary goal of this study is to identify the genetic and environmental determinants of female lung adenocarcinoma, and study the relationship between gene polymorphisms and clinical manifestation profiling of lung cancer.

Detailed description: This research proposal intends to integrate epidemiologists, biostatisticians, clinicians, molecular biologists/geneticists to identify susceptible genes for lung cancer, especially for female lung adenocarcinoma, and to study the relationship between gene polymorphisms and clinical outcomes of lung cancer patients. Our objective is to find gene markers for developing useful screening tools for the high risk group in order to prevent or early detect lung cancer, especially female lung adenocarcinoma.
  The specific aims of this subproject include:
  1. Establish and maintain the research network that will recruit and follow up the subjects and families for the GEFLAC study; keeping control of the progress of the study.
  2. Coordinate all the subprojects such as integrating genotyping data with clinical data and environment data.
  3. Continue to employ the candidate gene approach to examine the contribution of specific genes to the lung cancer.
  4. Generate genotyping data for candidate genes in the exploring stage and prioritize SNPs of candidate genes for large scale studies.
  5. Identify susceptible genes/candidate genes to develop multiplex PCR for screening.

Eligibility: Inclusion Criteria:
  -  lung adenocarcinoma
  Exclusion Criteria:
  -

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

Clinical trial: Study to Evaluate the Clinical Benefit Response in Cancer Patients With Advanced Disease With AMT2003 Versus Placebo

Summary: The purpose of the study is to evaluate the efficacy and the safety of AMT2003 in cancer patients with advanced disease.
  The primary evaluation criterion is clinical benefit response.

Detailed description: The study will include patients with a variety of solid tumors (i.e. esophageal, colon, pancreatic, bronchial, gastric, hepatocellular, gall bladder, prostate and gynaecological carcinomas.)
  The clinical benefit response - CBR, is an end point that provides a clinical measure for symptom improvement in patients. The key evaluation parameters for CBR will be assessment of pain, the ability to perform daily activities and weight change.

Eligibility: Inclusion Criteria:
  -  Cancer confirmed by histology or cytology
  -  At least one measurable lesion
  -  Advanced disease refractory to standard therapy or for which no standard therapy exists
  -  Life expectancy at least 3 months
  Exclusion Criteria:
  -  Known secondary neoplasia or central nervous system (CNS) metastases, acute or chronic leukemia, lymphoma or multiple myeloma
  -  Body weight below 45 kg
  -  Female patients who are pregnant or breast feeding or adults of reproductive potential not employing effective birth control methods
  -  Concurrent severe or uncontrolled medical disease
  -  Acute or chronic liver disease
  -  Confirmed diagnosis of HIV
  -  Insulin dependent diabetes mellitus/abnormal glucose tolerance test (GTT)/latent diabetes mellitus type I or II
  -  Chemotherapy or radiotherapy less than 4 weeks prior to entry
  -  Surgery less than 2 weeks prior to entry (or not recovered from effects of surgery)
  -  Participation in a clinical trial less than 30 days prior to entry into this study

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

Clinical trial: AVE0005 (VEGF Trap) in Patients With Recurrent Symptomatic Malignant Ascites

Summary: The primary objective of this study was to compare the time between paracenteses before and after administration of Aflibercept (ziv-aflibercept, AVE0005, VEGF trap, ZALTRAP®) in ovarian cancer participants with symptomatic malignant ascites.
  The secondary objectives were to further assess efficacy and safety of Aflibercept treatment, and the exploratory objectives were to assess pharmacokinetics, immunogenicity and health-related quality of life.

Detailed description: The study consisted of:
  -  A 30-day screening phase prior to Day 1
  -  Day 1 registration and pre-treatment paracentesis
  -  Aflibercept administration within 1-day of registration
  -  Two-week study treatment cycles (for efficacy data, the cut-off date was 6 months post-registration
  -  A 60-day post-treatment follow-up phase
  During the study, participants were treated with Aflibercept study treatment through the duration of the study unless they met one the following criteria for discontinuation:
  -  Participant (or legal representative) chose to withdraw from treatment
  -  The investigator or sponsor thought that continuation of the study would be detrimental to the participants well-being
  -  Participant had intercurrent illness that prevented further administration of investigational product (IP)
  -  Participant had more than 2 IP dose reductions
  -  Participant had unacceptable adverse events (AEs)
  -  Participant had arterial thromboembolic events, including cerebrovascular accidents, myocardial infarctions, transient ischemic attacks, new onset angina, or worsening of preexisting angina
  -  Participant required surgical intervention for intestinal obstruction or gastrointestinal perforation

Eligibility: Participants that met the following criteria were eligible.
  Inclusion Criteria:
  -  Symptomatic malignant ascites resulting from advanced ovarian epithelial cancer (including fallopian tube and primary peritoneal adenocarcinoma) that required at least 3 previous therapeutic paracenteses at a frequency of 1 to 4 paracenteses per month for management.
  -  Platinum resistant disease defined by relapse or progression of disease during or after treatment, or drug intolerance.
  -  Topotecan- and/or liposomal doxorubicin-resistant disease defined by relapse or progression of disease during or after treatment, or drug intolerance.
  Exclusion Criteria:
  -  Peritoneovenous or other type of shunt that was placed for the management of ascites
  -  Prior treatment with a VEGF or VEGF receptor inhibitor
  -  Uncontrolled hypertension
  The above information is not intended to contain all considerations relevant to participation in a clinical trial.

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

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: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: Pyrosequencing of the BRAFV600E Mutation

Summary: To investigate the diagnostic efficiency of pyrosequencing for the mutant BRAF allele in ultrasound (US)-guided fine needle aspiration biopsies (FNAB) of thyroid incidentalomas.


Eligibility: Inclusion Criteria:
  -  Patients with thyroid nodule larger than 1 cm, or nodule smaller than 1 cm that required further evaluation because of suspicious ultrasound findings
  Exclusion Criteria:
  -  Patients who refuse participation.

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

Clinical trial: The Character of Perfusion Parameters Derived From MDCT Between Adenocarcinoma and Squamous Cell Carcinoma of Lung in the Treatment Course of Radiation Therapy

Summary: Lung cancer is one of the leading causes of cancer-related death in Taiwan. Recently, there are more treatment methods available which result in increased patient survival. Although adenocarcinoma and squamous cell carcinoma were both categorized as non-small cell lung cancer (NSCLC), the recent advancement of target therapy implied that these two histologies behave differently (Shah NT, et al. 2005; Sandler A, et al. 2006). Radiation therapy is an important method for locally advanced non-resectable non-small cell lung cancer (NSCLC). Computed tomography (CT) is the mainstay for evaluating lung cancer. The advance of multi-row detector CT (MDCT) provides volumetric acquisition within a breath hold, and enables detailed evaluation of tissue and organ perfusion with excellent resolution. Using this new technique with image post processing, excellent spatial resolution and functional perfusion information can be obtained simultaneously. Therefore, the purpose of this study is to explore not only the longitudinal change of lung cancer eligible for radiation therapy (including concurrent, sequential chemoradiotherapy and high-dose radiation therapy) but also comparison of adenocarcinoma and squamous cell lung cancers using perfusion MDCT. Total twenty patients with histopathologically proved adenocarcinoma or squamous cell carcinoma will be enrolled in this study and receive longitudinal study for perfusion MDCT evaluation before, during radiation therapy and in early and late phases after complete radiation therapy. Dynamic perfusion will be used for processing the image data, and quantitative parameters such as tumor blood volume and permeability etc will be derived. From this study, we expect to understand the change of tumor vascularity after radiation therapy and characters of treatment response of adenocarcinoma and squamous cell carcinoma in addition to the change of tumor size.


Eligibility: Inclusion Criteria:
  -  Ages 18 and up
  -  Males and females
  Exclusion Criteria:
  -  Pregnancy

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

Clinical trial: Genetic Identification (ID) of Segmental Dysplastic Nevi

Summary: The investigators' goal is to identify the mutation in the gene that is responsible for the development of segmental dysplastic nevi. To identify the gene the investigators may use a candidate gene approach (i.e. sequence specific genes that are thought to be involved: NRAS, BRAF, etc) or a genome-wide approach trying to implicate regions in the genome (Loss-of-heterozygosity or copy number changes on comparative genomic hybridization).

Detailed description: Dysplastic (atypical) melanocytic (DMN) nevi have been identified as being potential precursors of melanoma and markers for patients at risk of developing primary melanoma1. In addition, having an increased number of nevi is associated with increased risk1. DMN are present in 2-5% of white adults in the U.S. population and international studies have documented up to 18% prevalence2. These lesions may be present in at least 17% of white adults with melanoma and 20-50% of melanomas may arise in nevi and atypical nevi2. The exact gene(s) involved in the development of nevi have yet to be elucidated.
  Segmental dysplastic nevi are nevi that are restricted to one area of the body3. This condition is much rarer than the occurrence of dysplastic nevi, but nonetheless, may involve the same genetic mutation. The pattern of distribution in SDN is thought to result from mosaicism, i.e. the part of the body that expresses the dysplastic nevi has a mutation in a gene, however, the rest of the body does not contain this same mutation. Other mosaic disorders that have been studied in greater detail than SDN have been shown to be caused by a single gene mutation4. It appears that SDN is no different and that it too is caused by a mutation in a single gene, however, this gene is not yet known.
  In this study we will perform a genetic analysis of tissue from a patient known to have SDN. With the information we gather from this analysis, we may be able to find the gene responsible for the development of dysplastic nevi.
  Primary Research Objective:
  To investigate the genetic mutation involved in the development of dysplastic nevi by examining a patient with SDN.

Eligibility: Inclusion Criteria:
  -  Patient with a positive history of segmental dysplastic nevi
  Exclusion Criteria:
  -  None

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

Clinical trial: Positron Emission Tomography and Computed Tomography in Planning Treatment for Patients Undergoing 3-Dimensional Conformal Radiation Therapy for Non-Small Cell Lung Cancer That Cannot Be Removed by Surgery. ICORG 06-35

Summary: RATIONALE: Diagnostic procedures, such as positron emission tomography and computed tomography, may help learn the extent of disease and allow doctors to plan 3-dimensional conformal radiation therapy.
  PURPOSE: This phase II trial is studying the side effects of positron emission tomography and computed tomography and to see how well it works in planning treatment for patients undergoing 3-dimensional conformal radiation therapy for non-small cell lung cancer that cannot be removed by surgery.
  This is a clinical study, as the patient will be treated using the PET-CT-GTV: - The pilot study is investigating the technological feasibility - The Phase II study will be a 2-stage Phase II study

Detailed description: Pilot Study- Primary Objectives:
  -  Prospective evaluation of the technical feasibility of integrating PET-CT fusion in St Luke's Hospital
  -  Rate of PET-CT Scan based treatment delivery
  Pilot Study- Secondary Objectives:
  -Comparison of GTV, PTV and OAR DVHs between conventional 3-DCRT plan and PET-CT based 3-DCRT plan.
  Phase II Study- Primary Objective:
  -The safety of PET-CT scan based radiotherapy, with regard to loco-regional disease control.
  Phase II Study- Secondary Objectives:
  -Comparison of GTV, PTV and OAR DVHs between conventional 3-DCRT plan and PET-CT based 3-DCRT plan.

Eligibility: Inclusion Criteria:
  -  Histologically proven (biopsy or cytology) NSCLC (SCC, Adenocarcinoma, Large Cell)
  -  TNM clinical non-operable stage I/II and non-resectable stage IIIa/b without pleural effusion
  -  Measurable disease
  -  No other malignancy, except non-melanomatous skin cancer, within 5 years prior to participation in this study; the disease-free interval from any prior carcinoma must be continuous
  -  Patient suitable for radical 3-DCRT
  -  ECOG-Performance status ≤ 2 / KPS > or equal to 60
  -  Weight loss <10% within the 3 months prior to diagnosis
  -  No prior radiotherapy to the thorax
  -  Patient is suitable for lung-board immobilisation
  -  No chemotherapy received prior to planning PET-CT scan
  -  Age 18 and over
  -  Provision of written informed consent
  Exclusion Criteria:
  -  Evidence of any other significant clinical disorder or laboratory finding that makes it undesirable for the patient to participate in the trial or if it is felt by the research / medical team that the patient may not be able to comply with the protocol.
  -  FEV1 < 1

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

Clinical trial: A Phase II Trial of Afatinib(BIBW 2992) in Third-line Treatment for Patients With Stage IIIB/IV Adenocarcinoma of the Lung Harbouring Wild-type Epidermal Growth Factor Receptor[EGFR]

Summary: To explore the efficacy of BIBW 2992 defined by the objective response rate (Complete Response, Partial Response) as determined by Response Evaluation Criteria in Solid Tumours[RECIST] 1.1 in the patients with advanced (stage IIIB or IV) adenocarcinoma of the lung harbouring wild-type EGFR.


Eligibility: Inclusion criteria:
  1. Pathologically confirmed stage IIIB/IV adenocarcinoma in non-small cell lung cancer[NSCLC]
  2. Progressive disease following a second-line cytotoxic chemotherapy including at least one platinum-containing regimen
  3. A known wild-type EGFR status
  4. Patients 18 years of age or older
  Exclusion criteria:
  1. More than two prior cytotoxic chemotherapy treatment regimens for relapsed or metastatic disease
  2. Prior treatment with EGFR targeting small molecules or antibodies
  3. Radiotherapy or surgery within 4 weeks prior to study entry
  4. Active brain metastasis
  5. Known pre-existing interstitial lung disease
  6. History or presence of clinically relevant cardiovascular abnormalities
  7. Cardiac left ventricular function with resting ejection fraction of less than 50%
  8. Absolute neutrophil count[ANC] < 1,500/mm3
  9. Platelet count <100,000/mm3
  10. Creatinine clearance<60ml/min or serum creatinine >1.5 times upper limit of normal
  11. Women of childbearing potential, or men who are able to father a child, unwilling to use a medically acceptable method of contraception during the trial
  12. Pregnancy or breast-feeding

Relevance to patient case: not relevant