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: Non-Invasive Biomarkers For Early Detection Of Lung Cancers

Summary: Recent studies have shown that low-dose chest CT scans can detect lung cancers in high-risk populations (age >50yo, >30 pack-years of tobacco use), and can lower cancer mortality. Unfortunately, the vast majority of "positive" findings on these CT scans are benign (>95%). Currently, an inordinate amount of expensive follow-up testing is required for these patients to try to prove who among them truly has a cancer.
  Several new emerging non-invasive and potentially cheaper tests are now being investigated to help differentiate patients with cancers versus just benign lung nodules. These new tests include a new type of sputum analysis, a breath analysis, a blood test measuring certain tumor markers, a blood test looking for auto-antibodies, and a standard PET/CT scan. Each of these tests have different sensitivity and specificity rates when looking for lung cancer, and it is unclear which test is best.
  This study will employ a panel of all 5 of these non-invasive tests on an initial cohort of 50 patients with recently diagnosed lung cancer to try to measure the sensitivity of the tests. A follow-on study will then perform the same panel of tests on 300 lung nodule patients to see which test, or combination of tests, gives the best overall accuracy in terms of predicting who really has lung cancer. It is hoped that the use of such a panel could lead to dramatically decreased need for expensive and morbid invasive testing for this population.

Detailed description: The study revolves around specifying the exact signatures and accuracy associated with discriminating between benign and malignant SPNs for each of the biomarkers in the specific high risk cohort under the NLST screening protocol. To help identify and quantify these signatures, we will evaluate specifically the volatile signature in the exhaled breath, the accuracy of LuCED sputum detection, the profile of tumor markers and the specifications of auto-antibodies through immunoassays and Orbitrap technology, and the PET/CT in patients already diagnosed with lung cancer.

Eligibility: Inclusion Criteria:
  -  newly diagnosed cancer, prior to treatment
  Exclusion Criteria:
  -  prior treatment for this cancer
  -  a history of any other 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: Specimen Banking From Patients With Lung Cancer

Summary: The primary objective of the protocol is to develop a comprehensive specimen banking program from patients with lung cancer for future translation research, which will enable the investigators to detect lung cancer earlier, develop better therapies and explore screening and prevention strategies.

Detailed description: The aims of the study are as follows: 1) to continue to unravel the complex biology of lung cancer 2) to identify early detection and prognostic markers to guide therapeutic decision 3) to define markers of response and/or resistance to drug therapy, and 4) to identify new therapeutic and prevention targets.

Eligibility: Inclusion Criteria:
  1. Subjects who are undergoing further testing for the diagnosis or treatment of lung cancer.
  2. Oral and written informed consent
  Exclusion Criteria:
  1. Any individual who does not give oral and written consent for participation

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: The Diagnosis of Biliary Tract Neoplasm by Diffusion Weighted Imaging and Magnetic Resonance Cholangiopancreatography

Summary: Researching the diagnostic significance of Biliary Tract Neoplasm under combining DWI sequence with MRCP versus MRCP only separately.

Detailed description: The purpose of the study is to evaluate the usefulness of diffusion weighted imaging(DWI) combined with MRCP of 3-T magnetic resonance imaging (MRI) in the evaluation of suspected malignant bile duct diseases.People with suspected Biliary Tract Neoplasm based on clinical symptoms(such as jaundice and thinness with unknown reasons)and CA-199 value raises are included.Diagnosis divided into two steps: the first one，only provide conventional MR sequences and MRCP images to make a diagnosis; the second step,provide the DWI images additionally, combining the image data before to make a diagnosis.Hypothesis is that DWI sequence should be regularly added into MRCP examination for improving diagnosis rate of Biliary Tract Neoplasm.

Eligibility: Inclusion Criteria:
  -  Informed consent
  -  Suspected Biliary Tract Neoplasm based on clinical symptoms(such as jaundice and thinness with unknown reasons)and CA-199 raises（＞37U/mL）
  -  No evidence of clinical symptoms or CA-199 increase by non-bile duct cancerous factors(hepatitis,cholangeitis,stones)
  -  Age ≥ 16
  Exclusion Criteria:
  -  Previous Biliary Tract Neoplasm surgery
  -  Contraindication for MRI (such as pacemaker or inner ear implant)
  -  Claustrophobia
  -  Age < 16

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: Dysregulation of the C/EBPa Pathway in Human Lung Cancer and Search for New Biomarkers and/or Therapeutic Targets

Summary: The overall goal of this research is to enhance the investigators understanding of the pathways involved in lung cancer, and to identify new biomarkers and/or therapeutic targets. By comparing gene expression between normal lung tissue and tumors growing in lung-specific C/EBPa KO mice, the investigators have identified the Bmi-1 proto-oncogene as being abnormally upregulated in C/EBPa-deleted tumors. Subsequently, the investigators have validated this observation in human lung cancer, implicating the investigators KO mice are an effective discovery tool for lung cancer research. Through similar approaches, the investigators have already identified (Sonic Hedgehog, SHH), and plan to identify other pathways which are abnormally regulated in C/EBPa-/- tumors. In parallel, the investigators will proceed to define the clinical relevance of the SHH pathway and the other newly-discovered molecular aberrations, by analyzing their expression and correlate it to C/EBPa expression on the samples of patients with NSCLC at NUHS. If the investigators preliminary data on Bmi-1 will be confirmed, this proto-oncogene may generate useful correlates that could be used in diagnosis and treatment of lung cancer, as well as identify new prognostic/predictive markers in lung cancer. Similarly, SHH pathway-components may behave as potential biomarkers and therapeutic tools for C/EBPa-related lung cancers.
  This proposal seeks to test the hypothesis that pathways which are dysregulated in lung tumors growing in a lung-specific C/EBPa KO model can be utilized as discovery tools to identify genes involved in human lung cancer pathogenesis.


Eligibility: Inclusion Criteria:
  Patients with 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: Detection of Chromosomal Aberrations in Non-small Cell Lung Cancer (NSCLC) Using Fluorescent in Situ Hybridization (FISH) (ALK Test)

Summary: The purpose of the study is the identification of chromosomal aberrations in non-small cell lung cancer (NSCLC) .
  The imaging system is intended for diagnostic use as an aid to the pathologist in the detection, counting and classifying ALK FISH stained lung samples.

Detailed description: The ALK Break Apart FISH test detects chromosomal aberrations via fluorescence in situ hybridization (FISH) in formalin-fixed paraffin-embedded (FFPE) non-small cell lung cancer (NSCLC) tissue specimens. The FDA approved ALK kit is designed to detect rearrangements involving the ALK gene (2p23). Results from the ALK Kit are intended for use, in conjunction with and not in lieu of current standard diagnostic procedures, as an aid for the pathologist in the identification of patients eligible for treatment with XALKORI® (crizotinib).

Eligibility: Inclusion Criteria:
  -  Well stained slides with bright FISH signals
  Exclusion Criteria:
  -  Very old slides that were already bleached

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: Strategies for Maintenance Therapies in Advanced Non Small Cell Lung Cancer

Summary: In France, lung cancer is responsible for more than 30000 each year. Progress was made in treatment of lung cancer in the last five years due to targeted therapies and to strategical evolutions consisting in a best adjustment of treatments. Maintenance strategies is one of this strategical evolution. It is based on maintaining continuous therapeutical pression in order to preserve the therapeutical benefit obtained by the first line (induction chemotherapy). Several clinical trials showed that maintenance strategies increase the duration of controlled disease.
  There is two types of maintenance strategies:
  -  Continuous maintenance : prolongation of the treatment initially associated with platin until progression
  -  Switch maintenance : introduction of a new treatment after the end of induction chemotherapy
  The aim of this study is to compare two maintenance strategies
  -  A continuous maintenance by pemetrexed
  -  A switch maintenance or a continuous maintenance according to the response of induction chemotherapy.


Eligibility: Inclusion Criteria:
  -  Non-squamous NSCLC histologically or cytologically confirmed
  -  Stage IV with a cytologically or histologically confirmation for an unique metastasis
  -  No EGFR activating mutation or indeterminate EGFR mutational status
  -  At least one measurable lesion
  -  Age between 18 and 70
  -  PS 0 or 1
  Exclusion Criteria:
  -  squamous cell lung cancer, small cell lung cancer , neuroendocrine cell lung cancer
  -  Knowledge of ALK gene rearrangement
  -  Symptomatic central nervous system metastases or requiring immediate cerebral radiotherapy
  -  Superior venous cave syndrome except if treated by implantation of a prosthesis
  -  Previous anti-tumoral treatment
  -  Concomitant radiotherapy

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: Vitamin D Loading Dose in Advanced Lung Cancer

Summary: Hypovitaminosis D is highly prevalent in people with lung cancer, and may have adverse clinical consequences. The long and variable pharmacokinetic half-life of vitamin D makes prompt vitamin D replacement problematic. This is an open, one-armed therapeutic intervention using a loading dose of vitamin D that will be predicted to increase plasma 25-hydroxyvitamin D concentrations of every patient well into the normal range (> 100 nmol/L) within 2 or 3 weeks and monitored after 2 and 3 weeks of loading and maintenance dose. Preliminary data will also be obtained to identify potentially clinical important outcome benefits for future investigation. The outcomes are
  1. plasma 25OHD concentration
  2. Vitamin D binding protein and other plasma concentrations
  3. Mood and symptom


Eligibility: Inclusion Criteria:
  1. Any patient with advanced lung cancer whether or not receiving specific anti-cancer therapy
  2. Mentally competent (but need not be fluent in French or English if capable neutral translator available)
  3. Self report of reduced food intake and/or involuntary weight loss of any extent at time of enrollment: does not have to be documented
  Exclusion Criteria:
  1. Current diagnosis of primary hyperparathyroidism
  2. Nephrocalcinosis
  3. Current or suspected active tuberculosis, histoplasmosis, sarcoidosis, or other granulomatous disease
  4. Current using a vitamin D supplement providing > 1000 IU/day
  5. Current prescribed calcitriol in any dose
  6. History of extensive sunlight exposure (> 30 min summer sunlight exposure per day for more than 5 days per week) in previous 3 months
  7. Expected to die within next 2 months
  8. 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: 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: 52-year-old male with Lung cancer. Genetic variant: EML4-ALK Fusion transcript. Other conditions: Hypertension, Osteoarthritis.

Clinical trial: Chest Imaging, Breath, and Biomarkers in a Screening Trial

Summary: The investigators would like to see if lung cancer screening with chest x-rays,computer aided detection (CAD)and a lose dose CT scan can detect lung cancer in early stages when it is more responsive to treatment. The investigators would also like to see if early detection will reduce the incidence of symptomatic advanced lung cancer compared to no screening in former and current smokers with or without a family history of lung cancer who are 40-75 years old.

Detailed description: The fight against lung cancer is waged on three major fronts: prevention, detection and treatment. Our goal is to determine if chest x-rays,computer aided detection (CAD)and a CT scan can detect disease earlier when treatment is more effective. If we improve the detection of disease, we will see if screening reduces the incidence of symptomatic advanced lung cancer relative to no screening in people at high risk to develop lung cancer.

Eligibility: Inclusion Criteria:
  -  ages 40-75 years
  -  If ages 40-59, then one of the following criteria needs to be met:
  -  Current or ex-smoker with >25 pack years and a family history of lung cancer(parent or sibling) OR
  -  current or ex-smoker with > 25 pack years and COPD OR
  -  current or ex-smoker with a > 35 pack year history
  -  If ages 60-75, then one of the following additional criteria needs to be met:
  -  Current or ex-smoker with >25 pack years and a family history of lung cancer (parent or sibling) OR
  -  Current or ex-smoker with >25 pack years and COPD OR
  -  Current or ex-smoker with a >30 pack year history
  -  Subject is able to return to Cleveland Clinic for annual follow-up screening
  -  Subject is willing to sign a medical release form
  Exclusion Criteria:
  -  Current health requires oxygen
  -  Have had a chest x-ray or CT of the chest within the last 6 months
  -  Previous pneumonectomy
  -  Lobectomy of the lung within the last 5 years
  -  Diagnosed malignancy within the last 5 years, excluding non-melanoma skin cancer, carcinoma in situ of the cervix and localized prostate cancer
  -  A medical condition that would prevent treatment for lung cancer
  -  Within the last 6 weeks, one of the following has occured:
  -  A new cough or chronic cough that has gotten worse
  -  Either new shortness of breath, or any worsening of shortness of breath
  -  A cough producing blood
  -  Constant chest pain
  -  Respiratory infection, pneumonia, or cold
  -  Unintentional and unexplained weight loss greater than 5% of total body weight

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: Long-term Follow-up of the Anterior Lumbar Interbody Fusion Procedure.

Summary: During the period 1989-1999, a number of patients underwent an ALIF-procedure. Anterior Lumbar Interbody Fusion procedure (ALIF) is a type of lumbar spinal fusion. The approach of the lumbar region is by incision of the abdominal wall. The intervertebral disc is removed and replaced by a bone graft. These patients form the population of this study. The goal of this study is to evaluate their current medical condition and to determine the clinical outcome.
  The clinical result will be stipulated by means of standardized questionnaires (VAS-score, Oswestry low Back Pain Questionnaire and SF-36)


Eligibility: Inclusion Criteria:
  -  An Anterior Lumbar Interbody Fusion procedure between 1999 and 2005
  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: Phase 1b/2 Trial of AMG386 With Pemetrexed and Carboplatin in Non-Small Cell Lung Cancer

Summary: The purpose of this phase 1b/2 study is to estimate the treatment effect of study drug measuring progression free survival.

Detailed description: To evaluate the incidence of adverse events and clinical laboratory abnormalities defined as dose-limiting toxicity in subjects with metastatic non-squamous non-small cell lung cancer (NSCLC) treated with AMG 386 in combination with pemetrexed and carboplatin

Eligibility: Inclusion Criteria:
  -  Histologically confirmed, unresectable stage IV non-squamous non small cell lung cancer (NSCLC)
  -  Radiographically evaluable disease (measurable or non-measurable) per RECIST 1.1 with modifications
  -  Adequate hematological, renal, and hepatic function, normal coagulation profile, calculated CrCL ≥ 45 mL/min
  -  Other criteria may apply
  Exclusion Criteria:
  -  Any prior chemotherapy or targeted therapy for non-squamous NSCLC
  -  Subjects with adenosquamous histology or any histology subtype containing greater than 10% squamous cells
  -  Subjects with an epidermal growth factor receptor (EGFR) mutation sensitive to treatment with a tyrosine kinase inhibitor (TKI)
  -  Subjects with known anaplastic lymphoma kinase (EML4-ALK) translocations
  -  History or presence of central nervous system metastases
  -  Central (chest) radiation therapy within 28 days prior to enrollment/randomization, radiation therapy to any other site(s) within 14 days prior to enrollment/randomization
  -  History of pulmonary hemorrhage or gross hemoptysis within 6 months
  -  History of arterial or venous thromboembolism within 12 months
  -  History of clinically significant bleeding within 6 months
  -  Clinically significant cardiovascular disease within 12 months
  -  Other criteria may apply

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: A Study to Evaluate the Safety, Tolerability and Pharmacokinetics of Multiple Subcutaneous Injections of ABT-981 in Patients With Osteoarthritis of the Knee

Summary: To assess the safety, tolerability and pharmacokinetics of ABT-981 in patients with osteoarthritis of the knee.

Detailed description: This is a phase 1, randomized, double-blind, placebo-controlled, multiple ascending dose study. Thirty-six patients with osteoarthritis of the knee will be selected to participate. Patients will be randomized to receive either ABT-981 or placebo. ABT-981 or placebo will be administered as subcutaneous (under the skin) injections in four dosing groups. Subjects will be administered subcutaneous injections of ABT-981 for up to 8 weeks.

Eligibility: Inclusion Criteria:
  -  Adult male or female, 40 to 70 years of age, inclusive.
  -  History of symptomatic osteoarthritis (OA) of the knee joint for at least 3 months, with typical Osteoarthritis (OA) symptoms
  -  Radiographic Osteoarthritis (OA) of Kellgren-Lawrence (K-L) grade 1, 2 or 3
  -  Patients assessment of Osteoarthritis (OA) pain intensity of the study joint is between 40 and 80 on the 0 - 100 mm VAS scale
  -  Other than Osteoarthritis (OA) of the study joint, patient should be in general good health
  Exclusion Criteria:
  -  Radiographic OA of Kellgren-Lawrence grade 4 or chronic opioid user due to severe knee OA
  -  History of allergic reaction or significant sensitivity to any constituents of the study drug and acetominophen or history of anaphylactic reaction to any agent
  -  Significant trauma or surgery to the study joint within the last year or arthroscopy within 6 months, or, scheduled for major surgery to the study joint
  -  Diagnosis of rheumatoid arthritis, other autoimmune disorders or any arthritis other than Osteoarthritis (OA) of the knee.
  -  Any uncontrolled medical illness including unstable treatment or therapy.

Relevance to patient case: not relevant