araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: Lung Cancer Mutation Consortium Protocol

Summary: The primary objective of this protocol is to determine the frequency of oncogenic mutations in 1000 patients with advanced adenocarcinoma of the lung. The linked clinical and mutational analyses will be used to determine the frequency of each mutation, its association with clinical features and outcome, and its association with other mutations. As future therapeutic protocols specific for these mutations are developed, patients may be notified of their eligibility for these studies. Future translational studies may be used to: a) unravel the complex biology of lung cancer; b) identify prognostic markers; c) define predictive markers of response/resistance to new therapies; d) identify new targets. A secondary goal is to establish a consortium of sites that have the capability of conducting multiple mutation testing in a Clinical Laboratory Improvement Amendments (CLIA) certified lab.


Eligibility: Inclusion Criteria:
  1. Subjects (=> 18 years of age) who are undergoing further evaluation for the diagnosis or treatment of advanced adenocarcinoma of the lung.
  2. Diagnosed May 2012 or later
  3. Oral and written informed consent.
  Exclusion Criteria:
  1. Lung cancer histologies other than adenocarcinoma
  2. Lack of adequate tissue.

Relevance to patient case: not relevant
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: Clinical Validation of a Microfluidic Device for Isolation and Molecular Characterization of Circulating Tumor Cells

Summary: To evaluate the efficiency of a microdevice for circulating tumor cells isolation and to correlate the circulating titre with response and progression.

Detailed description: -  Validate the clinical use of a mircofluidic device to capture circulating timor cells from a broad range of tumor types
  -  Characterize and identify these circulating tumor cells and demostrate cell viability with this capture method
  -  Apply this technology in clinically relevant settings and correlate to response to treatment and disease progression
  -  Elucidate predictive and pharmacodynamic biomarkers in the context of early phase trials of novel therapeutics

Eligibility: Inclusion Criteria:
  -  Patients with newly diagnosed metastatic disease planned for palliative chemotherapy
  -  Tumor types as specified: non smokers with lung adenocarcinoma, undifferentiated EBV-ISH positive nasopharyneal carcinoma, breast cancer, colorectal cancer, prostate cancer, gastric cancer
  -  Informed consent given for the purposes of blood sampling for this study
  -  Measurable disease by RECIST criteria of at least 1cm is preferred but not a sine qua non for study accrual
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: Frailty Index and Geriatric Assessment in Predicting Toxicity to Front-Line Chemotherapy in Treating Patients With Stage IV Non-Small Cell Lung Cancer

Summary: This phase II trial is studying how well a frailty index and geriatric assessment works in predicting toxicity to front-line chemotherapy in treating patients with stage IV non-small cell lung cancer. A frailty index and geriatric assessment prior to treatment may help identify a better treatment regimen

Detailed description: PRIMARY OBJECTIVE:
  I. To determine the correlation of the data from the frailty index and geriatric assessment tool with the level of toxicity encountered in the first two cycles of therapy.
  OUTLINE:
  Patients complete a frailty index and geriatric assessment prior to beginning chemotherapy. Patients receive standard-of-care chemotherapy comprising carboplatin intravenously (IV) and paclitaxel IV on day 1. Treatment repeats every 21 days for up to 2 courses.

Eligibility: Inclusion Criteria:
  Pathological documentation of non-small cell lung cancer Stage IV disease Prior adjuvant chemotherapy for the earlier stages of non-small cell lung cancer is allowed Patients with brain metastases are allowed on protocol only if they have received brain irradiation and are neurologically stable Patients with other malignancies are allowed on protocol unless they are receiving active treatment (surgery, radiation, chemotherapy or immunotherapy) for the other malignancy Ability to understand and the willingness to sign a written informed consent document
  Exclusion Criteria:
  Prior palliative chemotherapy Pregnant and/or lactating women Prior radiation therapy other than brain irradiation for brain metastases

Relevance to patient case: not relevant
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: Bronchoscopic Thermal Vapor Ablation (BTVA) for Lung Volume Reduction

Summary: To assess the safety and efficacy of BTVA for the treatment of patients with heterogeneous upper lobe emphysema.

Detailed description: All subjects meeting the eligibility criteria and who provide written informed consent will be enrolled. Immediately prior to BTVA treatment, an initial bronchoscopy will be performed to evaluate the baseline condition of the airways and to confirm anatomy of the lung segments targeted for BTVA treatment. Up to 3 segments in either the right or left upper lobe will be treated with a vapor dose of 10 calories per gram of lung tissue (10 cal/g). Targeted lobe for treatment will be based on lobar disease severity.

Eligibility: Inclusion Criteria:
  1. Age: > 40 and ≤ 75 years old
  2. Diagnosis of heterogeneous emphysema with upper lobe predominance
  3. FEV1 < 45% predicted
  4. TLC > 100% predicted
  5. RV > 150% predicted
  6. 6-minute walk test > 140 meters
  7. mMRC ≥ 2 (mMRC)
  8. Non-smoking for 3 months
  9. Optimized medical management and completed pulmonary rehabilitation
  Exclusion Criteria:
  1. Known α-1-antitrypsin deficiency
  2. BMI < 15 kg/m2 or > 35 kg / m2
  3. History of pneumothorax within previous 18 months
  4. History of heart and / or lung transplant, lung volume reduction surgery (LVRS), median sternotomy, bullectomy, and/or lobectomy
  5. Respiratory infections or recurring COPD exacerbations > 3 hospitalizations in past 12 months or active infection
  6. History of the (EF) ≤ 40%; Stroke; Unstable Myocardial Ischemia; FEV1 < 15% predicted; DLCO < 20% predicted; of pulmonary hypertension; indwelling pacemaker or implantable cardiac defibrillator (ICD); pregnancy or breastfeeding

Relevance to patient case: not relevant
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: AeriSeal System for Lung Volume Reduction

Summary: The purpose of this study is to evaluate the safety and efficacy of AeriSeal treatment in patients with advanced emphysema.

Detailed description: The purpose of this study is to evaluate the safety and efficacy of AeriSeal treatment in patients with advanced homogeneous and heterogeneous emphysema.

Eligibility: Inclusion Criteria:
  -  Patients must have a diagnosis of advanced emphysema as defined by FEV1/FVC<70% predicted, FEV1 of <50% predicted, TLC > 100% predicted, and RV > 135% predicted.
  -  Patients must have persistent symptoms despite medical therapy and either not be candidates for Lung Volume Reduction Surgery (LVRS) or have elected not to undergo LVRS.
  -  Patients must be > 40 years of age, have symptoms despite medical therapy, and have none of the prespecified co-morbid conditions that could influence study outcomes or their ability to tolerate bronchoscopy.

Relevance to patient case: not relevant
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

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: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: A Study of the Use of Chartis Assessment System to Optimize Subject Selection for Endobronchial Lung Volume Reduction.

Summary: Use of the Chartis® Assessment System prior to EBV Treatment

Detailed description: This is a multi-center study which will enroll up to 120 patients. Subjects will undergo a Chartis Assessment prior to EBV treatment. The Chartis assessment will determine the presence or absence of collateral ventilation, a potential determining factor in the success of EBV therapy. This study is not randomized; all subjects are eligible to receive EBV Treatment, regardless of Chartis Assessment outcome. Follow-up data will only be collected on those patients that meet the Chartis inclusion criteria.

Eligibility: Inclusion Criteria:
  -  Heterogeneous emphysema
  -  Able to obtain a Chartis value during Assessment
  Exclusion Criteria:
  -  Any co-existing major medical problems that would not make it possible for the subject to tolerate a bronchoscopic procedure.

Relevance to patient case: not relevant
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: Bronchoscopic Thermal Vapor Ablation (BTVA) for Lung Volume Reduction

Summary: To establish and confirm the safety and clinical utility of BTVA applied unilaterally for lung volume reduction in patients with upper lobe predominate heterogeneous severe emphysema.

Detailed description: All subjects meeting the eligibility criteria and who provide written informed consent will be enrolled. Up to 3 segments in either the right or left upper lobe will be treated with a vapor dose of 10 calories per gram of lung tissue (10 cal/g). Targeted lobe for treatment will be based on lobar disease severity.

Eligibility: Inclusion Criteria:
  1. Age: > 40 and ≤ 75 years old
  2. Diagnosis of heterogeneous emphysema with upper lobe predominance
  3. FEV1 < 45% predicted
  4. TLC > 100% predicted
  5. RV > 150% predicted
  6. 6-minute walk test > 140 meters
  7. mMRC ≥ 2 (mMRC)
  8. Non-smoking for 3 months
  9. Optimized medical management and completed pulmonary rehabilitation
  Exclusion Criteria:
  1. Known α-1-antitrypsin deficiency
  2. BMI < 15 kg/m2 or > 35 kg / m2
  3. History of pneumothorax within previous 18 months
  4. History of heart and / or lung transplant, lung volume reduction surgery (LVRS), median sternotomy, bullectomy, and/or lobectomy
  5. Respiratory infections or recurring COPD exacerbations > 3 hospitalizations in past 12 months or active infection
  6. History of the (EF) ≤ 40%; Stroke; Unstable Myocardial Ischemia; FEV1 < 15% predicted; DLCO < 20% predicted; pulmonary hypertension; indwelling pacemaker or implantable cardiac defibrillator (ICD); pregnancy or breastfeeding

Relevance to patient case: not relevant
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: A Non-interventional Survey on the EGFR (Epidermal Growth Factor Receptor) Mutation Status in Completely Resected Chinese Non-Small Cell Lung Cancer (NSCLC) Patients With Adenocarcinoma Histology

Summary: This is a descriptive observational study. The primary objective is to explore the EGFR gene mutation status in early stage NSCLC with adenocarcinoma histology after complete resection. The patients should be histological confirmed adenocarcinoma of the lung, have received complete resection and tested for EGFR mutation in regular medical practice.


Eligibility: Inclusion Criteria:
  -  Histological diagnosed as adenocarcinoma type of non-small cell lung cancer
  -  Have completed lung cancer operation
  -  The tumour EGFR gene mutation status test was performed as regular medical practice
  Exclusion Criteria:
  -  Patients who disagree to participate this study

Relevance to patient case: not relevant
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: Study on Phenotypic Characterization of Combined Pulmonary Fibrosis and Emphysema

Summary: This study is to evaluate the expression of biological markers in induced sputum and peripheral blood T lymphocytes of patients with combined pulmonary fibrosis and emphysema (CPFE). The features of CPFE would be observed, including pulmonary function tests and fractional exhaled nitric oxide （FENO）.

Detailed description: A new disease including concomitant upper-lobe emphysema and lower-lobe fibrosis in radiology has been defined as (combined pulmonary fibrosis and emphysema, CPFE). CPFE has distinct clinical characteristics with the emphysema and the pulmonary fibrosis, including gender, age, clinical manifestation, pulmonary function tests and prognosis.
  Normally Th1/Th2 is balanced. However, patients with emphysema had a significantly higher expression of Th1. On the other hand, higher expression of Th2 is involved in the development of pulmonary fibrosis. The expressions of Th1 and Th2 were proved to play a central role in pathogenesis of emphysema and pulmonary fibrosis, while are still unknown in patients of combined pulmonary fibrosis and emphysema. The study would observe the Th1/Th2 expression, pulmonary function tests , fractional exhaled nitric oxide （FENO）and other features in CPFE patients.

Eligibility: Inclusion Criteria:
  1. IPF-alone group: 10 patients meeting the IPF diagnosis criteria without emphysema.
  2. CPFE group: 15 patients with CT presentation of concomitant upper-lobe emphysema and lower-lobe fibrosis.
  3. Emphysema-alone group: 15 patients with their CT diagnosis of emphysema without fibrosis.
  4. Control: 20 healthy sex- and age-matched volunteers including nonsmokers and smokers. None of the healthy volunteers with a history of respiratory diseases.
  Exclusion Criteria:
  1. Age > 90 or < 50
  2. Treated with corticosteroids or other immunomodulatory drugs
  3. Some known causes of interstitial lung disease such as collagen vascular disease, drug-induced lung disease, occupational disease.
  4. An exacerbation in 4 weeks
  5. Subjects had a history of allergic diseases.

Relevance to patient case: not relevant
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: An Investigational Drug, Crizotinib (PF-02341066), Is Being Studied In Tumors, Except Non-Small Cell Lung Cancer, That Are Positive For Anaplastic Lymphoma Kinase (ALK)

Summary: This is a Phase 1 trial evaluating the safety and efficacy of crizotinib in patients with tumors except non-small cell lung cancer that are positive for ALK.


Eligibility: Inclusion Criteria:
  -  histologically or cytologically proven diagnosis of malignancy other than NSCLC
  -  positive for translocation or inversion event involving the ALK gene locus
  -  positive for ALK amplification events
  -  positive for ALK activating point mutations
  Exclusion Criteria:
  -  mutations of amplifications involving the c-Met gene but not the ALK gene
  -  concurrent treatment on another therapeutic clinical trial
  -  prior therapy specifically directed against ALK

Relevance to patient case: possibly relevant
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: A Chinese Randomized Crossover Study of Erlotinib Versus Docetaxel/Cisplatin in Previously Untreated Stage IIIB/IV Lung Adenocarcinoma With EGFR Mutations

Summary: Objective: the objective of this study in china is to clarify, whether the overall survival is different between previously untreated stage IIIB/IV lung adenocarcinoma with EGFR mutations receiving first-line erlotinib plus second-line docetaxel/cisplatin and those receiving first-line docetaxel/cisplatin plus second-line erlotinib .


Eligibility: Inclusion Criteria:
  -  Male and female patients aged over 18 years
  -  Histologically proven lung adenocarcinoma
  -  clinical stage IIIB/IV
  -  ECOG performance status 0-2
  -  Had no prior anticancer agent, radiation or surgical therapy for lung adenocarcinoma
  -  At least one measurable lesion (according to RECIST)
  -  Provision of written informed consent
  -  Life expectancy of at least 12 weeks
  Exclusion Criteria:
  -  History of malignant disease.
  -  Evidence of clinically active interstitial lung diseases (patients with chronic, stable, radiographic changes who are asymptomatic need not be excluded)
  -  Expected life expectancy less than 2 months
  -  As judged by the investigator, any evidence of severe or uncontrolled systemic disease (e.g. unstable or uncompensated respiratory, cardiac, hepatic, or renal disease)
  -  Aspartate aminotransferase (AST/SGOT) or alanine aminotransferase (ALT/SGPT) ≥ 2.5 x ULN if no demonstrable liver metastases (or >5 x in presence of liver metastases)
  -  Evidence of any other significant clinical disorder or laboratory finding that makes it undesirable for the subject to participate in the study
  -  Pregnancy or breast-feeding women (women of child¬bearing potential). Women of childbearing potential must practice acceptable methods of birth control to prevent pregnancy.

Relevance to patient case: not relevant
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: Non Small Cell Lung Cancer Evaluation According to Pre-determined Drug-targeting Tumor Markers

Summary: Evaluate chemotherapy related tumor markers on non small cell lung cancer by fluorescent in situ hybridization and immunohistochemistry, targets to be studied include EGFR, c-MET, topoisomerase II, p53, topoisomerase I, thymidylate synthase, ERCC1, tau, c-myc, RRM1, class III tubulin. These targets have been chosen because they are targets for chemotherapeutic agents that are currently used in clinical management of these diseases. In total 50 specimen will be studied, approximately one third have mutations/deletions of the EGFR gene.To attempt to establish a correlation between the pre-selected tumor markers and response to chemotherapy, and thus to be able to create a clinically useful classification that would provide clinical guidance for selection of the most effective chemotherapy for a individual patient, and thus be able to logically design more effective clinical trials for the future.


Eligibility: Inclusion Criteria:
  -  Patients with histologically confirmed lung cancer who received standard platinum-containing doublet chemotherapy followed by EGFR tyrosine kinase inhibitors.
  Exclusion Criteria:
  -  non

Relevance to patient case: not relevant
Patient case: 64-year-old female with Lung adenocarcinoma. Genetic variant: ALK Fusion. Other conditions: Emphysema.

Clinical trial: A Clinical Trial Testing The Efficacy Of Crizotinib Versus Standard Chemotherapy Pemetrexed Plus Cisplatin Or Carboplatin In Patients With ALK Positive Non Squamous Cancer Of The Lung

Summary: This study will evaluate the anti-cancer effects of crizotinib when compared with standard chemotherapy in patients with ALK positive lung cancer.


Eligibility: Inclusion Criteria:
  -  Proven diagnosis of locally advanced not suitable for local treatment, recurrent and metastatic non-squamous cell carcinoma of the lung
  -  Positive for translocation or inversion events involving the ALK gene locus
  -  No prior systemic treatment for locally advanced or metastatic disease; Patients with brain metastases only if treated and neurologically stable with no ongoing requirement for corticosteroids
  -  Evidence of a personally signed and dated informed consent document and willingness and ability to comply with scheduled visits, treatment plans, laboratory tests, and other study procedures including completion of patient reported outcome [PRO] measures.
  -  18 years of age or older with the exception of India which has an upper age limit of 65 years old
  Exclusion Criteria:
  -  Current treatment on another therapeutic clinical trial.
  -  Prior therapy directly targeting ALK.
  -  Any of the following within the 3 months prior to starting study treatment: myocardial infarction, severe/unstable angina, coronary/peripheral artery bypass graft, congestive heart failure, or cerebrovascular accident including transient ischemic attack. - - Appropriate treatment with anticoagulants is permitted.
  -  Ongoing cardiac dysrhythmias of NCI CTCAE Grade >=2, uncontrolled atrial fibrillation of any grade, or QTc interval >470 msec.
  -  Pregnancy or breastfeeding.
  -  Use of drugs or foods that are known potent CYP3A4 inducers/inhibitors Concurrent use of drugs that are CYP3A4 substrates with narrow therapeutic indices.
  -  Known HIV infection
  -  Known interstitial lung disease or interstitial fibrosis
  -  Other severe acute or chronic medical conditions (including severe gastrointestinal conditions such as diarrhea or ulcer) or psychiatric conditions, or laboratory abnormalities that would impart, in the judgment of the investigator and/or sponsor, excess risk associated with study participation or study drug administration, and which would, therefore, make the patient inappropriate for entry into this study

Relevance to patient case: possibly relevant