araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 48-year-old male with Lung adenocarcinoma. Genetic variant: MET Amplification. Other conditions: Emphysema.

Clinical trial: Development of a Model to Predict Progression-Free Survival After Erlotinib in Patients With Non-Small Cell Lung Cancer

Summary: RATIONALE: Studying samples of tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer. It may also help doctors predict how patients respond to treatment with erlotinib.
  PURPOSE: This laboratory study is developing a model to predict progression-free survival after erlotinib in patients with non-small cell lung cancer.

Detailed description: OBJECTIVES:
  -  Assess mesenchymal and epithelial markers in tissues from patients with non-small cell lung cancer treated with erlotinib hydrochloride on clinical trial ECOG-E3503.
  -  Determine the loss of epithelial markers (E-cadherin) and gain of mesenchymal markers (vimentin/cytokeratin co-expression) in these patients.
  -  Assess whether mesenchymal and epithelial markers are predictive of progression-free survival (PFS) of these patients.
  -  Identify a single nucleotide polymorphism profile via whole genome mapping and other known biomarkers to predict PFS of these patients.
  OUTLINE: Tissue samples are analyzed by whole genome mapping for single nucleotide polymorphism (SNP) rate and by signal detection rate and by quantitative immunohistochemistry for mesenchymal (vimentin/cytokeratin) and epithelial (E-cadherin) marker transitions. After biomarker identification and gene mapping are complete, a model to predict progression-free survival in these patients is developed.
  PROJECTED ACCRUAL: A total of 137 samples will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of non-small cell lung cancer, including any of the following subtypes:
  -  Adenocarcinoma
  -  Squamous cell carcinoma
  -  Bronchoalveolar carcinoma
  -  Carcinoid
  -  Stage IIIB or IV or recurrent disease
  -  Must have received treatment with erlotinib hydrochloride on clinical trial ECOG-E3503
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 48-year-old male with Lung adenocarcinoma. Genetic variant: MET Amplification. Other conditions: Emphysema.

Clinical trial: Lapatinib Resistance in Patients With Breast Cancer

Summary: RATIONALE: Studying samples of tumor tissue and blood from patients with cancer in the laboratory may help doctors learn more about cancer and the development of drug resistance in patients.
  PURPOSE: This research study is looking at lapatinib resistance in patients with breast cancer.

Detailed description: OBJECTIVES:
  -  To identify secondary ErbB2 mutations in tumor tissue samples from patients with ErbB2-positive breast cancer treated with lapatinib ditosylate.
  -  To investigate ErbB2 copy number changes and expression levels.
  -  To determine abnormalities of other pathways (e.g., c-MET and PI3K) as potential mechanisms of resistance.
  OUTLINE: Previously collected tumor tissue samples* are obtained for genetic analysis studies. Samples are analyzed for secondary ErbB2 mutations by nested PCR; ErbB2 copy number changes by quantitative PCR and standard histological FISH; and ErbB2 expression levels by quantitative RT-PCR and IHC. Patients also undergo blood sample collection for extraction of DNA (as normal control DNA) and isolation of EpCAM-positive circulating tumor cells using immunomagnetic cell separation technology. Additional research studies may include mutational and amplification analysis of the c-MET and PI3K pathways.
  NOTE: *Patients may undergo biopsy if a post-treatment tumor tissue sample is unavailable.

Eligibility: DISEASE CHARACTERISTICS:
  -  Pathologically confirmed invasive breast cancer
  -  ErbB2-positive disease
  -  Has received or is currently receiving lapatinib ditosylate
  -  Documented clinical benefit while receiving lapatinib ditosylate (e.g., stable disease of ≥ 12 weeks duration OR a radiographic response)
  -  Must have tumor tissue samples available for research studies
  -  Hormone receptor status not specified
  PATIENT CHARACTERISTICS:
  -  Menopausal status not specified
  -  Not pregnant*
  -  Coagulation profile normal*
  -  Platelet count > 100,000/mm³* NOTE: *For patients requiring a post-treatment biopsy
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics
  -  Concurrent chemotherapy or trastuzumab (Herceptin®) allowed
  -  No concurrent anticoagulants, including warfarin or low-molecular weight heparin*
  -  No concurrent antiplatelet therapy, including aspirin, clopidogrel, or other antiplatelet agents* NOTE: *For patients requiring a post-treatment biopsy

Relevance to patient case: not relevant
Patient case: 48-year-old male with Lung adenocarcinoma. Genetic variant: MET Amplification. Other conditions: Emphysema.

Clinical trial: Ultra Structure Of Peritoneum At Electronic Microscopy In Control Subjects And Patients With Gastric Cancer

Summary: Peritoneal metastases appear in a great proportion of patients affected by gastric carcinoma. Involved mechanisms are poorly understood though experimentally it has been demonstrated that neoplastic cells exfoliated from primary tumor can only implant and proliferate in areas of damaged peritoneum. Objectives: to study ultra-structure of peritoneal surface by electronic microscopy in control subjects and in patients with early or locally advanced gastric cancer looking for spontaneous changes in peritoneal surface not related with surgical injury.

Detailed description: 18 out of 32 cases were eligible for analysis. Four patients operated on for benign diseases served as control and 14 patients with operable local gastric adenocarcinoma (4 mucosa/submucosa/muscular y 10 serosa lesions) were studied. At the beginning of surgery, a 2 x 2 cm. sample from macroscopically normal visceral peritoneum at mesenterium root was carefully obtained, washed with saline and fixed in glutaraldehyde solution. Besides a sample of peritoneal washing fluid was studied to exclude patients with free cancer cells. Peritoneal tissue was fixed during 24 hours and then all samples were evaluated by electronic microscope.

Eligibility: Inclusion Criteria:
  -  patients with operable local gastric adenocarcinoma
  Exclusion Criteria:
  -  previous abdominal surgery
  -  previous open or blunt abdominal trauma
  -  history of inflammatory bowel disease or Typhoid Fever, Gallstone disease, chemotherapy or radiotherapy, or any other abdominal condition that could alter peritoneal integrity.
  -  All other gastric malignancies such as lymphomas, GIST, carcinoids

Relevance to patient case: not relevant
Patient case: 48-year-old male with Lung adenocarcinoma. Genetic variant: MET Amplification. Other conditions: Emphysema.

Clinical trial: TS Gene Polymorphism Predicts Effect in Patients With Advanced Lung Cancer

Summary: The investigators performed a multicenter, open trial of using TS gene polymorphism to predict advanced lung adenocarcinoma effect to pemetrexed combined with cisplatin regiment as first-line treatment.

Detailed description: 1. Main eligibility criteria were histologic or cytologic proof of advanced non-small-cell lung cancer (NSCLC) primary treatment, normal organ function, and Eastern Cooperative Oncology Group performance status 0 to 2.
  2. All Patients were delivered to pemetrexed 500 mg/m2 and cisplatin 75 mg/m2 for not less than 4 cycle, administered intravenously every 3 weeks. Response assessment was performed every 6 weeks; toxicity assessment was performed every 3 weeks.
  3. Primary end point was time to progression (TTP); secondary end points were objective response rate (ORR), overall survival (OS), and toxicity.
  4. The study was designed to evaluate TS(thymidylate synthase) gene polymorphism as a predictor for advanced lung adenocarcinoma effect to pemetrexed combined with cisplatin regiment as first-line treatment.
  5. Polymorphisms of thymidylate synthase were investigated in peripheral WBC（white blood cell）of all patients.

Eligibility: Inclusion Criteria:
  -  histologic or cytologic proof of advanced lung adenocarcinoma
  -  primary treatment
  -  normal organ function
  -  Eastern Cooperative Oncology Group performance status 0 to 2
  Exclusion Criteria:
  -  Symptomatic patients with brain metastases
  -  Major organ dysfunction and severe heart disease

Relevance to patient case: not relevant
Patient case: 48-year-old male with Lung adenocarcinoma. Genetic variant: MET Amplification. Other conditions: Emphysema.

Clinical trial: Radiation Therapy to the Brain or Observation in Preventing Brain Metastases in Patients With Advanced Non-Small Cell Lung Cancer

Summary: RATIONALE: Radiation therapy to the brain may be effective in preventing brain metastases in patients with advanced non-small cell lung cancer. It is not yet known whether radiation therapy is more effective than observation in patients with advanced non-small cell lung cancer.
  PURPOSE: This randomized phase III trial is studying radiation therapy to the brain to see how well it works compared with observation in preventing brain metastases in patients with advanced non-small cell lung cancer.

Detailed description: OBJECTIVES:
  Primary
  -  Determine the effectiveness of prophylactic cranial radiotherapy in patients with advanced non-small cell lung cancer that is responsive to gefitinib or erlotinib hydrochloride.
  Secondary
  -  Determine the progression-free survival in patients treated with this regimen.
  -  Determine the overall survival in patients treated with this regimen.
  -  Determine the safety and tolerability of this regimen in these patients.
  -  Determine the psycho-neurological effects of this regimen in these patients.
  -  Determine the quality of life of patients treated with this regimen.
  OUTLINE: This is a multicenter study. Patients are stratified according to prior chemotherapy regimens (first line vs second line), and disease response status (complete response or partial response vs stable disease). Patients are randomized to 1 of 2 treatment groups.
  -  Group 1: Patients undergo prophylactic brain radiotherapy.
  -  Group 2: Patients undergo observation. Patients complete quality of life (HVLT, K-ADL, EORTC QLQ-C30, and EORTC-BN20) questionnaires periodically.
  After completion of study therapy, patients are followed up periodically.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically confirmed non-small cell lung cancer
  -  Stage IIIB or IV disease
  -  Must have had ≥ 8 weeks of gefitinib or erlotinib hydrochloride therapy
  -  At least 12 weeks of complete response or partial response since starting gefitinib or erlotinib hydrochloride
  -  Stable disease allowed provided 1 of the following criteria is met:
  -  EGFR mutation (exon 19 or 21)
  -  Having ≥ 2 of the following 3 factors:
  -  Female
  -  Never smoked
  -  Histologically confirmed adenocarcinoma of the lung
  -  No evidence of brain metastases by CT scan or MRI within the past 4 weeks
  PATIENT CHARACTERISTICS:
  -  ECOG performance status 0-2
  -  ANC ≥ 1,500/mm^3
  -  Platelet count ≥ 150,000/mm^3
  -  Bilirubin < 1.5 mg/dL
  -  Serum creatinine < 1.5 times upper limit of normal
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics
  -  Received 1 or 2 prior systemic chemotherapy regimens

Relevance to patient case: not relevant
Patient case: 48-year-old male with Lung adenocarcinoma. Genetic variant: MET Amplification. Other conditions: Emphysema.

Clinical trial: DNA Chip Based Prognosis of Lung Cancer

Summary: The purpose of the study is to determine whether a DNA chip, designed by Medical Prognosis Institute (MPI), can provide an accurate prognosis for survival of NSCLC (adeno-, squamous and large cell lung cancer).


Eligibility: Inclusion Criteria:
  1. A histological diagnosis of primary NSCLC stage Ia
  2. Surgical removal of the tumor
  3. Age between 18 and 75 years
  4. Ability to understand and the willingness to sign a written informed consent document.
  Exclusion Criteria:
  1. A primary NSCLC stage Ia diagnosis that is changed to not primary NSCLC or NSCLC stage Ib-IV after surgery.
  2. Adjuvant treatment with chemotherapy.
  3. Prior history of cancer in the past 5 years or breast cancer at any time.
  4. Life expectancy less than 3 years in the opinion of the investigator due to concurrent illnesses.

Relevance to patient case: not relevant
Patient case: 48-year-old male with Lung adenocarcinoma. Genetic variant: MET Amplification. Other conditions: Emphysema.

Clinical trial: Unilateral Versus Bilateral Endoscopic Lung Volume Reduction A Comparative Case Study

Summary: Patients with bilateral heterogeneous pulmonary emphysema benefit to differing degrees from unilateral ELVR with complete lobe closure in comparison with incomplete bilateral treatment.

Detailed description: Patient enrolment and data acquisition is to be carried out on a prospective basis. It is planned to enrol a total of 20 patients with bilateral heterogeneous pulmonary emphysema. All patients will undergo treatment at one study centre in Heidelberg. Patients will be considered for both unilateral and bilateral treatment with intrabronchial valves (IBV) on the basis of their emphysema distribution. Patients will be randomised to two treatment arms. 10 patients receive unilateral or bilateral treatment in each case.

Eligibility: Inclusion Criteria:
  -  age > 40 inhomogeneous emphysema FEV1 between 20-40% DLCO between 20-40% 6MWT > 150 m
  Exclusion Criteria:
  -  pregnant homogeneous disease FEV1 < 20%

Relevance to patient case: not relevant
Patient case: 48-year-old male with Lung adenocarcinoma. Genetic variant: MET Amplification. Other conditions: Emphysema.

Clinical trial: Safety, Tolerability and Pharmacokinetics of Cobimetinib in Combination With Pictilisib in Patients With Locally Advanced or Metastatic Solid Tumors

Summary: This is an open-label, multicenter, Phase Ib dose-escalation study designed to assess the safety, tolerability and pharmacokinetics of oral dosing of cobimetinib and pictilisib administered in combination in patients with locally advanced or metastatic solid tumors.


Eligibility: Inclusion Criteria:
  -  Histologically or cytologically documented, locally advanced or metastatic solid tumors for which standard therapy either does not exist or has proven ineffective or intolerable
  -  Evaluable disease or disease measurable per Response Evaluation Criteria in Solid Tumors (RECIST)
  -  Life expectancy greater than or equal to (>=) 12 weeks
  -  Adequate hematologic and end organ function
  -  Agreement to use an effective form of contraception for the duration of the study
  Exclusion Criteria:
  -  History of prior significant toxicity from another mitogen-activated protein kinase (MEK) pathway inhibitor requiring discontinuation of treatment
  -  History of prior significant toxicity from another phosphoinositide 3-kinase (PI3K) pathway inhibitor requiring discontinuation of treatment
  -  Allergy or hypersensitivity to components of the cobimetinib or pictilisib formulations
  -  Palliative radiotherapy within 2 weeks prior to first dose of study drug treatment in Cycle 1
  -  Experimental therapy within 4 weeks prior to first dose of study drug treatment in Cycle 1
  -  Major surgical procedure or significant traumatic injury within 4 weeks prior to first dose of study drug treatment in Cycle 1, or anticipation of the need for major surgery during the course of study treatment
  -  Prior anti-cancer therapy within 28 days before the first dose of study drug treatment in Cycle 1
  -  History of diabetes requiring daily medication, or history of Grade >= 3 fasting hyperglycemia
  -  Current severe, uncontrolled systemic disease
  -  History of clinically significant cardiac or pulmonary dysfunction
  -  History of malabsorption or other condition that would interfere with enteral absorption
  -  Clinically significant history of liver disease (including cirrhosis), current alcohol abuse, or current known active infection with human immunodeficiency virus (HIV), hepatitis B virus, or hepatitis C virus
  -  Any condition requiring anticoagulants, such as warfarin, heparin, or thrombolytics
  -  Active autoimmune disease
  -  Uncontrolled ascites requiring weekly large volume paracentesis for 3 consecutive weeks prior to enrollment
  -  Pregnancy, lactation, or breastfeeding
  -  Known brain metastases that are untreated, symptomatic, or require therapy to control symptoms
  -  No other history of or ongoing malignancy that would potentially interfere with the interpretation of the pharmacodynamic or efficacy assays

Relevance to patient case: not relevant
Patient case: 48-year-old male with Lung adenocarcinoma. Genetic variant: MET Amplification. Other conditions: Emphysema.

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
Patient case: 48-year-old male with Lung adenocarcinoma. Genetic variant: MET Amplification. 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: 48-year-old male with Lung adenocarcinoma. Genetic variant: MET Amplification. Other conditions: Emphysema.

Clinical trial: A Study of Mycophenolate Mofetil (CellCept) in Lung Transplant Recipients

Summary: This open-label, single center study will assess the pharmacokinetics, efficacy and safety of mycophenolate mofetil in lung allograft recipients. Participants will be split into 2 groups according to the original disease: Group A (cystic fibrosis) and Group B (chronic obstructive pulmonary disease [COPD], emphysema, idiopathic pulmonary fibrosis, alpha-1 antitrypsin deficiency [A1AD]). All participants will receive mycophenolate mofetil orally, 1.5 grams (g) twice daily (BID) from Day 2 to 30 post transplantation, and 1 g BID from Day 31 to 90 post transplantation. Anticipated time on study treatment is 90 days, and target sample size is 50-100 individuals.


Eligibility: Inclusion Criteria:
  -  primary single or bilateral lung allograft
  -  original disease cystic fibrosis, COPD, emphysema, idiopathic pulmonary fibrosis or A1AD
  Exclusion Criteria:
  -  lung allograft retransplantation
  -  multiple organ transplantation
  -  severe gastrointestinal disorder
  -  malignancies or history of malignancy

Relevance to patient case: not relevant
Patient case: 48-year-old male with Lung adenocarcinoma. Genetic variant: MET Amplification. 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