araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Methylation Status of CD44 Promoter Region in Primary Lung Cancer

Summary: This project is to study the methylation status of the transcriptional regulatory region of CD44 gene in surgically resected NSCLC specimens and normal lung tissue, correlate the methylation status of promoter region with the expression of CD44 gene, and analyze if methylation is associated with survival.

Detailed description: CD44 is a cell surface receptor for the extracellular matrix hyaluronan. It mediates adhesion of cells to the extracellular matrix. Its ability to organize extracellular matrix into a medium is also used by cancer cells in their becoming metastatic. Invasive tumor cells are frequently observed to bind hyaluronate.
  CD44 gene is made up of 20 exons, at least 10 of which are variably expressed due to alternative splicing of the mRNA. The standard form, CD44s, has a coding sequence of exons 1-5 and 16-20. Variant isoforms (CD44v), all larger, arise from alternative splicing of combinations of exons 6-15 (v1-10). A variant isoform CD44 can induce metastasis of a rat pancreatic carcinoma. Studies in human tumors, however, have produced variable results. Some breast cancers demonstrate positive correlation between CD44v expression and tumor progression, while others lack any correlation. Some colorectal tumors even show an inverse correlation. CD44 has also been demonstrated to be a metastasis suppressor gene for prostate cancer. Thus, CD44 may be a marker for metastasis for some tumors, but not for others, and it may actually be a metastasis suppressor gene for yet another groups of tumors.
  For primary lung cancer, the correlation between CD44 expression and tumor metastasis has not been established. The metastasis-prone small cell lung cancer rarely showed any immunohistochemical staining for CD44s or CD44v. For non-small cell lung cancer (NSCLC), some studies showed positive correlation between immunohistochemical CD44v expression and tumor progression, while others showed no correlation. Our own study using RT-PCR, sequencing and immunohistochemical staining showed that in pulmonary adenocarcinoma, CD44v6 expression is down-regulated as the disease progressed. Based on our finding, and the observation that CD44s and CD44v expression are low in metastasis-prone small cell lung cancer, we assue that CD44 is a metastasis suppressor gene which is inactivated in lung cancers. Because in prostate cancer DNA hypermethylation has been shown to be related to the down-regulation of CD44 gene, we plan to study the methylation status of the transcriptional regulatory region of CD44 gene in primary lung cancer. We’ll study CD44 expression by immunohistochemistry, the methylation status of CD44 regulatory region by sequencing of the bisulfite-modified genomic DNA, and correlate these two findings with each other, and with histologic type, tumor staging and survival.

Eligibility: Inclusion Criteria:
  -  Non-small cell lung cancer
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Circulating Cytokines as Predictors of Radiation Induced Pulmonary Toxicity

Summary: This study is being conducted by the University of Rochester Cancer Center to determine the levels of cytokines in the blood, and to determine if blood levels of these cytokines are related to the side effects of radiation therapy combined with other treatments.


Eligibility: Inclusion Criteria:
  Patients receiving radiation therapy for lung cancer combined with surgery either pre or post RT to the chest for lung cancer not associated with atelectasis, pleural effusion.
  Patients receiving HDR Brachytherapy for lung cancer.
  Patients receiving concomitant radiation and interferon therapy for lung cancer.
  Patients receiving concomitant chemotherapy and radiation for lung cancer. Prior drug therapy does not make patients ineligible.
  Karnofsky ≥ 70 %.
  There are no age restrictions.
  Acceptable bone marrow function - WBC 2 3000/mm3, platelet count > 100,000, hematocrit ≥ 33%, hemoglobin ≥ 11 gms/dl.
  Life expectancy > 6 months.
  Patients must sign informed consent meeting all federal and institutional guidelines.
  Exclusion Criteria:
  Patients not meeting eligibility criteria stated above

Relevance to patient case: not relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Pulsed Paclitaxel And Daily Thoracic Radiotherapy For Inoperable (Stage I/II) Or Unresectable Lung Cancer

Summary: A treatment study is being conducted by the University of Rochester Cancer Center (URCC) in which patients with non-small cell lung cancer will be treated with radiation therapy and a drug called paclitaxel. Paclitaxel is a natural product with anticancer properties. The first purpose of this study is to determine the dose of paclitaxel which, when given in combination with radiation therapy, will provide the greatest effect have the least side effects. To determine this, patients will be put on the study in groups of 3. The dose for each additional group will be higher than the previous dose until the maximum tolerated dose is reached. The second purpose is to determine if radiation therapy with paclitaxel is more effective in treating lung cancer than radiation therapy alone.


Eligibility: Inclusion Criteria:
  -  Histologically confirmed lung cancer, excluding small cell carcinoma
  -  Inoperable stage I (T1-2N0) and II (T1-2N1, T3N0) disease, or stage IIIA (T3N1 andT1-3N2M0) and IIIB (TxN3M0, T4NxM0) diseases according to the American Joint Committee of Cancer criteria 1998
  -  The primary tumor must be radiographically measurable.
  -  Age > 18.
  -  Karnofsky performance status > 70.
  -  FEV1 sufficient for patients to tolerate radiation therapy which is at the discretion of the radiation oncologist, usually > 800 ml
  -  Labs: WBC > 3000; platelet count > 100,000; serum creatinine < 1.5 mg/dl or creatinine clearance >60 ml/min.
  -  Laboratory values must be obtained < 3 weeks prior to registration.
  -  A signed informed consent.
  -  Patients who failed prior chemotherapy are eligible. Patients with prior radiotherapy to the chest region are eligible as long as the normal tissue tolerance is not violated by repeat radiotherapy.
  Exclusion Criteria:
  -  Patients with medical contraindication to chemotherapy or radiotherapy.
  -  Patients with myocardial infarction within the preceding six months or symptomatic heart disease, including uncontrolled or unstable angina, uncontrolled congestive heart failure, and uncontrolled arrhythmia.
  -  Women who are pregnant.
  -  Patients with small cell carcinoma or mesothelioma

Relevance to patient case: not relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Radiofrequency Ablation of Lung Tumors

Summary: Radiofrequency ablation has achieved impressive results in the treatment of unresectable primary and metastatic liver cancer. Animal studies have demonstrated that radiofrequency can fully ablate lung tumors in animal models. We set up a prospective study to evaluate the local efficacy of radiofrequency ablation of lung neoplasms. The aim of the study is to prospectively evaluate local efficacy with a minimal follow-up of one year, tolerance, lung disease-free survival and survival after radiofrequency ablation of lung tumors (primary lung cancer or lung metastases).

Detailed description: Radiofrequency (RF) ablation has achieved impressive results in the treatment of unresectable primary and metastatic liver cancer. Animal studies have demonstrated that RF can fully ablate lung tumors in animal models. We set up a prospective study to evaluate the local efficacy of radiofrequency ablation of lung neoplasms with a minimal follow-up of one year. The primary endpoint was to determine the rate of incomplete local treatment at 1 year. The secondary endpoints were to evaluate tolerance, survival, disease-free survival and lung tumor-free survival. Patients are followed-up by CT scan examination at day 1 or 2 before discharge from the hospital, then at 2, 4, 6, 9 and 12 months and then at 2 years

Eligibility: Inclusion Criteria:
  -  Unilateral or bilateral unresectable primary or metastatic lung tumors <= 40 mm and a number of tumor <=5
  -  Tumors located more than 1 cm from the hilum, and not involving soft tissues or mediastinum.
  -  Malignancy histologically proven for pulmonary nodules in patients with no history of cancer outside the lung.
  -  Lung tumors in patients with a known distant cancer history, has to be either histologically proven or a demonstrated change in size of at least 25% in their largest diameter is required on CT during the previous year
  -  Pretreatment imaging work-up within 4 weeks of scheduled RF ablation (at least a chest CT and an abdomino-pelvic CT)
  -  If a tumor is found outside the lung, it has to be amenable to complete eradication with RF or RF plus surgery
  -  Lung spirometry within 4 weeks of treatment with a FEV1 >= 1 liter
  -  Written informed consent.
  Exclusion Criteria:
  -  Uncorrectable coagulopathy with a prothrombin time greater than 1.5 and a platelet count below 106/mm3

Relevance to patient case: not relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

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: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Identification of Serum Markers For Tumor Hypoxia in Non-Small Cell Lung Cancers

Summary: The purpose of the study is to identify a surrogate serum marker for tumor hypoxia in patients with lung cancers.


Eligibility: Inclusion Criteria:- Newly diagnosed patients with lung cancer who are undergoing surgical resection of their tumors
  Exclusion Criteria:- Patients without non-small cell lung cancer

Relevance to patient case: not relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Minimum Dose CT Post Lung Biopsy

Summary: The aim is to evaluate whether Minimum Dose CT (MnDCT) is useful in the management of patients post Lung Biopsy

Detailed description: Patients post Lung Biopsy have a chest X-ray (CXR) and a MnDCT post lung biopsy. Both studies are compared for the detection of a pneumothorax

Eligibility: Inclusion Criteria:
  -  All Patients having a lung biopsy
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Assessing the Link Between Smoke Carcinogen Biomarkers and Lung Cancer Risk - 1

Summary: Lung cancer is the leading cause of cancer death in the United States. Currently it remains impossible to predict which smokers will get cancer. Each puff of a cigarette delivers a mixture of over 60 known carcinogens. Biomarkers that quantify carcinogen levels and metabolism are a useful tool and available to use. The purpose of this study is to assess the link between tobacco smoke carcinogen biomarkers and the risk of developing lung cancer.

Detailed description: Lung cancer is the leading cause of cancer death in the United States. Approximately 90% of lung cancer is caused by cigarette smoking. While most lung cancer cases occur in smokers or ex-smokers, only 15-25% of smokers will get lung cancer. Currently it remains impossible to predict which smokers will get cancer.
  Each puff of a cigarette delivers, along with nicotine, a mixture of over 60 known carcinogens. Most of these carcinogens require metabolic activation before they can negatively affect cell DNA and cause cancer. Biomarkers that quantify carcinogen levels and metabolic activity of carcinogens are a useful tool and available to use. The purpose of this study is to assess the link between tobacco smoke carcinogen biomarkers and the risk of developing lung cancer.
  This observational case-control study will involve a random selection from a group of smokers who are participating in the Prostrate, Lung, Colon, and Ovarian Cancer (PLCO) Screen Trial. The chosen cases will include 300 incident lung cancer cases and 300 controls (participants who have had no diagnosis of lung cancer). Demographic and baseline data from the PLCO database will be obtained. Prior baseline blood samples from the PLCO trial will be obtained as well. Based on age, sex, and smoking history, participants will be grouped into triplets in order to pool their blood samples. These samples will then be analyzed to determine whether distributions of biomarker levels in lung cancer participants differ from those in non-lung cancer participants. This study will not involve recruitment of any participants, as data and samples from the PLCO trial will be used and no new blood samples will be obtained.

Eligibility: Inclusion Criteria:
  -  Screening arm participants in the Prostate, Lung, Colon, and Ovarian Screen Trial (PLCO)
  -  Reported smoking on baseline questionnaire of PLCO
  -  Contributed biorepository samples
  Exclusion Criteria:
  -  Unstable physical or mental health

Relevance to patient case: not relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Metabolomic Analysis of Lung Cancer

Summary: The purpose of this study is to learn more about the metabolic properties of lung cancer cells.

Detailed description: It has long been known that cancer cells absorb and break down substances in the body differently than healthy, non-cancer cells. This process of absorbing and breaking down substances is known as metabolism and is increased in cancer cells. Recent research suggests that this increased metabolic activity makes it easier for cancer cells to multiply. The objective of the study is to characterize the metabolism of glucose by lung tumors by serum metabolite analysis, using a variant of glucose (sugar) which makes up 1% of glucose in nature.

Eligibility: Lung Cancer Patients (Groups 1 & 2)
  Inclusion Criteria:
  -  patients with suspected, clinically diagnosed, or histologically diagnosed lung cancer. Occasionally, other cancers (including metastatic cancers to the lung) may be resected for the study as negative controls for NSCLC, as warranted by the particulars of the case.
  -  patients must have general medical conditions to allow them to undergo surgical resection of their primary tumor
  Exclusion Criteria:
  -  history of diabetes for the experimental group (surgery + glucose); patients with a history of diabetes are allowed in the control group (surgery/no glucose)
  -  known hepatitis C or HIV (AIDS)
  Healthy Subjects (Group 3)
  Inclusion Criteria:
  -  at least 30 years of age
  -  preferably be fasting for 12 hours (minimum 8 hours) prior to enrollment
  Exclusion Criteria:
  -  prior history of diagnosed lung cancer
  -  known hepatitis C or HIV (AIDS)

Relevance to patient case: not relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Effect of Flex-a-New on Osteoarthritis of the Knee

Summary: comparative trial of placebo versus flex-a-new (a food supplement) containing glucosamine an chondroitin sulfate for the symptom modification is knee osteoarthritis

Detailed description: comparative trial of placebo versus flex-a-new (a food supplement) containing glucosamine an chondroitin sulfate for the symptom modification is knee osteoarthritis

Eligibility: Inclusion Criteria:
  knee osteoarthritis grade 1 to 3 -
  Exclusion Criteria:
  ischemic heart disease with CHF -

Relevance to patient case: not relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Lung Cancer Biomarkers and Screening

Summary: RATIONALE: Screening tests that use biomarkers may help doctors find tumor cells early and plan effective treatment for lung cancer.
  PURPOSE: This clinical trial is studying biomarkers in screening participants for lung cancer.

Detailed description: OBJECTIVES:
  -  Identify and validate biomarkers for the early detection of lung cancer in individuals at low- or high-risk for smoking-related cancers.
  -  Identify preneoplastic cellular changes and lesions in these patients.
  OUTLINE: Participants are stratified according to lung cancer risk status (with or without increased risk).
  Group 1 (screening cohort): Participants complete a questionnaire and undergo pulmonary function testing, multidetector chest CT scan, sputum induction, and phlebotomy.
  Group 2 (rule-out lung cancer): Participants complete the same questionnaire and undergo the same tests and scans as in group 1. Some participants may undergo fiberoptic bronchoscopy based upon CT scan results with transbronchial or endobronchial biopsies. Some participants may undergo lung resection. Tissue samples are collected from surgery or biopsy.
  PROJECTED ACCRUAL: A total of participants will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Screening Cohort
  -  At high- or low-risk for lung cancer
  -  Smoking history ≥ 20 pack years*
  -  With or without workplace exposure to asbestos
  -  NOTE: * Participants with < 20 pack years of smoking are eligible if 50 years of age or older
  -  Rule-Out Lung cancer group
  -  Referred for evaluation of suspicious nodules with 1 of the following diagnoses:
  -  Lung cancer
  -  Nonmalignant nodules (control group)
  PATIENT CHARACTERISTICS:
  -  Not pregnant
  -  No prior malignancy except nonmelanoma skin cancer
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Cerebrospinal Fluid Levels of Erlotinib in Patients Receiving Erlotinib For Stage III Non-Small Cell Lung Cancer

Summary: RATIONALE: Determining whether erlotinib passes into the cerebrospinal fluid may help in planning treatment for some types of cancer.
  PURPOSE: This clinical trial is studying how well erlotinib is able to pass into the cerebrospinal fluid of patients receiving erlotinib for stage III non-small cell lung cancer.

Detailed description: OBJECTIVES:
  -  Determine the cerebrospinal fluid penetration of erlotinib in a subset of patients who are undergoing treatment with erlotinib for stage III non-small cell lung cancer and have no CNS metastatic disease.
  OUTLINE: This is a pilot, nonrandomized study.
  Patients will undergo single lumbar puncture (LP) to remove cerebrospinal fluid for analysis.
  After completion of study, patients will be monitored for 1 month after LP to assess for any LP-related complications.
  PROJECTED ACCRUAL: A total of 10 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Patients must be enrolled in the trial: "A Phase I/II Trial of Neoadjuvant Paclitaxel, Carboplatin and OSI-774 (Tarceva) with Concurrent Accelerated Hyperfractionation Radiation Followed by Maintenance Therapy with OSI-774 for Stage III Non-Small Cell Lung Cancer," Principal Investigator: T. Mekhail, M.D.
  -  Patient must be in maintenance therapy phase of the study and have received erlotinib for ≥ 1 week
  -  No known CNS primary or metastatic cancer at any time prior to time of enrollment
  -  No MRI evidence of pathological enhancement at the time of study entry
  PATIENT CHARACTERISTICS:
  -  Patients must use adequate birth control measures while in the study
  -  No significant side effects to erlotinib that require dose reduction or interruption
  -  None of the following medical issues which could make a lumbar puncture unsafe:
  -  Platelets < 100,000/mm³
  -  INR > 1.1
  -  Known bleeding dyscrasia
  -  Absolute neutrophil count < 1,500/mm³
  -  Ongoing systemic bacterial infection
  PRIOR CONCURRENT THERAPY:
  -  Patients on modest or anti-epileptic therapy must be on nonenzyme-inducing drug only, including any of the following:
  -  Neurontin
  -  Lamictal
  -  Depakote, Depakene
  -  Felbatol
  -  Keppra
  -  Gabitril
  -  Topimax
  -  Zonegran
  -  No concurrent enzyme-inducing anti-epileptic drugs such as phenytoin, carbamazepine, or phenobarbital
  -  No concurrent other drug known to affect the metabolism of erlotinib
  -  No concurrent anticoagulant therapy

Relevance to patient case: not relevant