araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 38-year-old male with Liposarcoma. Genetic variant: CDK4 Amplification. Other conditions: GERD.

Clinical trial: A Comparative Study of Proton-pump Inhibitor Tests for Chinese Reflux Patients in Relation to the CYP2C19 Genotypes

Summary: Backgrounds & Aims: Proton-pump inhibitor (PPI) test has been proposed as a valuable tool in the diagnosis of gastroesophageal reflux disease (GERD) in Western populations. We assumed that a higher prevalence of poor metabolizers in Chinese population might affect the diagnostic accuracy of a PPI test.
  Methods: In this open-label, randomized trial, patients with symptoms suggestive of GERD were randomly assigned to receive a 2-week test with daily rabeprazole 40-mg or daily pantoprazole 80-mg after diagnostic endoscopy. Therapeutic response was assessed with a five-grade daily record. Genotypes of cytochrome P450 (CYP) 2C19 polymorphism were determined.

Detailed description: As described above

Eligibility: Inclusion Criteria:
  -  Consecutive patients with symptoms suggesting GERD will be enrolled from gastroenterology outpatient clinics in our academic institute. The typical GERD symptom was defined as heartburn and/or regurgitation at least 3 episodes per week in recent 3 months.
  Exclusion Criteria:
  -  Those who were under maintenance PPI treatment, have a medical contraindication to PPI therapy, report a history of peptic ulcer disease or gastrointestinal surgery, malignancy proven by endoscopy, or unwilling or unable to provide informed consent.

Relevance to patient case: not relevant
Patient case: 38-year-old male with Liposarcoma. Genetic variant: CDK4 Amplification. Other conditions: GERD.

Clinical trial: Gastroesophageal Reflux Disease (GERD) Segmentation: Document How Swiss General Practitioners (GPs) Allocate Their GERD Patients to the Three GERD Patient Segments

Summary: Document how Swiss GPs allocate their GERD patients to the three GERD patient segments (according to King et al.) and how treated GERD patients are affected by their GERD treatment


Eligibility: Inclusion Criteria:
  -  Previously diagnosed GERD patients
  -  on treatment for at least 2 weeks
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 38-year-old male with Liposarcoma. Genetic variant: CDK4 Amplification. Other conditions: GERD.

Clinical trial: National Survey on Gastroesophageal Reflux Disease (GERD) Patients

Summary: The purpose of this observational study is to assess the impact of abdominal fat on severity and frequency of GERD symptoms .


Eligibility: Inclusion Criteria:
  -  Male or female > or = 18 years old
  -  Patient with symptomatic GERD
  -  Without PPI or H2 antagonist treatment during the 3 previous months
  -  Agree to take part in this study
  Exclusion Criteria:
  -  Pregnant women

Relevance to patient case: not relevant
Patient case: 38-year-old male with Liposarcoma. Genetic variant: CDK4 Amplification. Other conditions: GERD.

Clinical trial: Waist Circumference Versus Body Mass Index to Predict Severity of Gastroesophageal Reflux Disease

Summary: Gastroesophageal reflux disease (GERD) is a common and important disorder. Previous studies have demonstrated the association of obesity with GERD, and now obesity is regarded as a risk factor for GERD. Moreover, body mass index (BMI), an indicator of general obesity, correlates with severity of symptoms and degree of erosive esophagitis. Waist circumference, an indicator of abdominal obesity, has stronger correlation with intra-abdominal pressure and low-grade inflammatory state when compared with BMI. Nevertheless the association of waist circumference with severity of GERD has not been studied.
  The primary aim of this study is to compare BMI with waist circumference for their independent association with severity of GERD. The secondary aim is to evaluate independent risk factors of severity of GERD.

Detailed description: This is a cross-section observational study. Outpatients presenting with acid reflux or heart burn are interviewed with standardized questionnaire to quantify severity of symptoms. The eligible patients undergo upper endoscopy to diagnose erosive esophagitis and further classify the degree of erosions according to Los-Angels classification. Enrolled patients receive anthropometric measurements to record body weight, body height and waist circumference on the day of enrollment.
  Two outcomes are studied: the severity of GERD symptoms and the Los-Angels Classification of erosive esophagitis.

Eligibility: Inclusion Criteria:
  -  age more than 20 years old and less than 70 years old
  -  typical gastroesophageal reflux symptoms (heart burn and acid reflux)
  -  outpatient
  -  complete upper gastrointestinal endoscopy
  Exclusion Criteria:
  -  age less than 20 years or more than 70 years old
  -  receive medication for reflux disease (including proton pump inhibitor, histamine type 2 receptor blocker, prokinetic agents) in previous one month
  -  pregnant women
  -  history of abdominal surgery
  -  severe comorbidity with cirrhosis, end-stage renal disease, heart failure
  -  no written informed consent

Relevance to patient case: not relevant
Patient case: 38-year-old male with Liposarcoma. Genetic variant: CDK4 Amplification. Other conditions: GERD.

Clinical trial: Safety and Efficacy the Medigus SRS Endoscopic Stapling System in Gastroesophageal Reflux Disease (GERD)

Summary: The study is designed to test the safety and efficacy of the Medigus SRS endoscopic stapling system for the treatment of GERD.
  The system allows the operator to staple the stomach to the esophagus,in order to restore the gastroesophageal flap valve. The effect of the stapling is similar to a common operation for GERD (partial fundoplication) but is done through the mouth, and incision into the abdomen is not needed.
  The hypothesis of the study is that the treatment will be effective in improving GERD related quality of life by 50% or more in the majority of the subjects, and that the procedure will be as safe as surgery.


Eligibility: Inclusion Criteria:
  -  History of GERD related symptoms for at least 2 years.
  -  Recent objective evidence of GERD, demonstrated by a 24h pH acid exposure test.
  -  History of daily intake of proton pump inhibitors (PPIs) for at least 6 months, with significant relief of symptoms (i.e., difference in GERD Health Related Quality of Life (GERD HRQL) scores on and off PPI > =6).
  -  GERD-HRQL ≥20 off of PPI's
  Exclusion Criteria:
  -  Hiatal hernia > 3 cm or a paraesophageal hernia
  -  Barrett's esophagus or grade IV esophagitis
  -  Esophageal stricture, ring or web causing symptoms of dysphagia
  -  Grade I Flap valve according Hill's classification
  -  History of co-morbidity

Relevance to patient case: not relevant
Patient case: 38-year-old male with Liposarcoma. Genetic variant: CDK4 Amplification. Other conditions: GERD.

Clinical trial: Prevalence of EED and Quality of Life Evaluated by Gastroesophageal Reflux Disease (GERD)-Q in Korean GERD Patients

Summary: The purpose of this study is to asses the EED symptom prevalence in Koran GERD patients with typical reflux symptom and to evaluate quality of life with the scales including Gerd Q.


Eligibility: Inclusion Criteria:
  -  GERD patients who have experienced heartburn or acid regurgitation during past 7 days
  -  GERD patients who have already undergone endoscopy before enrolment
  Exclusion Criteria:
  -  Involvement in the planning and conduct of the programme
  -  The person who took the medicine such as PPI or H2RA during the last 7 days
  -  Severe systemic disease

Relevance to patient case: not relevant
Patient case: 38-year-old male with Liposarcoma. Genetic variant: CDK4 Amplification. Other conditions: GERD.

Clinical trial: ADX10059 as an add-on Therapy to Proton Pump Inhibitors (PPIs) in Patients With Gastroesophageal Reflux (GERD)

Summary: The purpose of this study is to evaluate the effect of ADX10059 in patients with gastroesophageal reflux disease who are partial responders to proton pump inhibitors


Eligibility: Inclusion Criteria:
  -  diagnosis of typical GERD
  -  partial responder to a stable standard clinical symptoms control dose of PPI therapy
  -  body mass index ≤ 32 kg/m2
  Exclusion Criteria:
  -  exclusively atypical symptoms of GERD
  -  symptoms that have been shown not to be associated with GERD
  -  erosive oesophagitis
  -  treated with a dose of PPI greater than the dose indicated for clinical symptom control of GERD
  -  hiatus hernia > 3 cm
  -  current diagnosis of co-existing psychiatric disease
  -  known clinical significant allergy or known hypersensitivity to drugs
  -  is pregnant or breast-feeding
  -  has received sodium valproate or topiramate within 30 days of Screening
  -  has a history of a significant medical condition that may affect the safety of the patient or preclude adequate participation in the study

Relevance to patient case: not relevant
Patient case: 38-year-old male with Liposarcoma. Genetic variant: CDK4 Amplification. Other conditions: GERD.

Clinical trial: National Survey on GERD Patients (Adults and Children)

Summary: To describe GERD digestive expression according to ages: - children (from 0 to 23 months) and (24 months and more)- adults (from 18 to 29 years old), (from 30 to 39 years old), (from 40 to 49 years old), (from 50 to 59 years old), (more than 60 years old)


Eligibility: Inclusion Criteria:
  -  Adults : - Male or female > or = 18 years old - With at least one GERD typical clinical sign (pyrosis and / or acid regurgitations).- Not receiving any GERD treatment within the 3 previous months.
  -  Children :- Male or female < 18 years old - With GERD digestive clinical signs during the consultation (receiving treatment or not)- Whose parents or legal guardian gave oral approval to the child participation in the survey.
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 38-year-old male with Liposarcoma. Genetic variant: CDK4 Amplification. Other conditions: GERD.

Clinical trial: GENSARC 2008 : Medical Economic Evaluation of the Molecular Detection by FISH (Fluorescent in Situ Hybridization) and by PCR (Polymerase Chain Reaction) of Sarcomas Specific Translocations and Amplifications .

Summary: The clinical and histological diagnosis of sarcomas is often very difficult. The identification of chromosomal and molecular anomalies, such as amplifications, deletions or fusion genes is a powerful help for establishing a correct diagnosis of sarcomas and their benign counterparts. However, the cost of the cytogenetic and molecular techniques for the detection of these alterations is often a limitation to their use. The aim of our study is to evaluate the direct cost of the molecular techniques in comparison to the cost that would be generated by an appropriate therapy and care management of the patient in case of an erroneous diagnosis.


Eligibility: Inclusion Criteria:
  -  patients with biopsy or excision of sarcoma (suspected or diagnosed)
  -  sampling reviewed by pathologists
  -  frozen sampling
  -  clinical data available
  Exclusion Criteria:
  -  opposition of patient

Relevance to patient case: not relevant
Patient case: 38-year-old male with Liposarcoma. Genetic variant: CDK4 Amplification. Other conditions: GERD.

Clinical trial: Structured Treatment of Gastroesophageal Reflux in a Company Health Care Setting, -Effect on Quality of Life, Symptoms and Productivity

Summary: The study aims to evaluate if a GERD treatment programme, in accordance with current regional recommendations, in a company health care setting, has an impact on health related quality of life (HRQoL), symptoms, and productivity in GERD patients.


Eligibility: Inclusion Criteria:
  -  Female and/or male aged > 18 years
  -  Diagnosis of GERD confirmed
  -  Prescription of GERD treatment or already receiving GERD treatment
  Exclusion Criteria:
  -  Any symptom suggesting a need for further investigation
  -  Previous participation in the present study
  -  Current participation in a clinical study or participation in a clinical study during the last 30 days

Relevance to patient case: not relevant
Patient case: 38-year-old male with Liposarcoma. Genetic variant: CDK4 Amplification. Other conditions: GERD.

Clinical trial: Gastroesophageal Reflux Disease (GERD) Before and After Gastric Bypass

Summary: The hypothesis of this study was that gastric bypass (GBP) ameliorates gastroesophageal reflux disease (GERD) in morbidly obese patients.

Detailed description: The investigators studied the impact of this surgical procedure on GERD in patients with morbid obesity.
  Esophageal syndromes were evaluated according to the Montreal Consensus, where troublesome symptoms were defined as score ≥ 2 on a validated questionnaire of symptoms for Portuguese language along with esophageal syndromes with injury assessed through upper endoscopy.
  Esophageal acid exposure was determined through 24h pH monitoring. Increased acid exposure was characterized when total esophageal pH < 4 for at least 4% of the total monitoring time.

Eligibility: Inclusion Criteria:
  -  Morbid obesity
  -  Acceptance to undergo open gastric bypass
  Exclusion Criteria:
  -  Prior gastroesophageal surgery
  -  Achalasia

Relevance to patient case: not relevant
Patient case: 38-year-old male with Liposarcoma. Genetic variant: CDK4 Amplification. Other conditions: GERD.

Clinical trial: Diagnosis and Response to Treatment Using a Reliable Gastroesophageal Reflux Disease (GERD) Questionnaire: An In Clinical Practice Study

Summary: The purpose of the study is to determine the applicability and utility of Gerd Q in the diagnosis of GERD and in the assessment of treatment response.


Eligibility: Inclusion Criteria:
  -  Patients of either gender aged between 18-79 years of age
  -  Patients must be having symptoms of gastroesophageal reflux disease
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 38-year-old male with Liposarcoma. Genetic variant: CDK4 Amplification. Other conditions: GERD.

Clinical trial: Study Evaluating the Efficacy and Safety of IPI 504 in Patients With Advanced Dedifferentiated Liposarcoma

Summary: The primary objective of the study is to determine the safety profile and overall response rate of IPI 504 in patients with advanced dedifferentiated liposarcoma.


Eligibility: Inclusion Criteria:
  -  At least 18 years of age at the time of signing informed consent.
  -  Histologic diagnosis of dedifferentiated liposarcoma.
  -  Available archival pathology specimen or tissue sample from a new biopsy for confirmation of diagnosis by central pathology reading.
  -  At least one prior chemotherapy regimen for dedifferentiated liposarcoma.
  -  No more than 2 prior chemotherapy regimens for dedifferentiated liposarcoma. Note: Any number of non-chemotherapy regimens is permitted.
  -  Measurable disease on computed tomography (CT) or magnetic resonance imaging (MRI) as defined by RECIST (version 1.1) with at least one measurable lesion.
  -  Eastern Cooperative Oncology Group (ECOG) performance status: 0 or 1.
  -  Life expectancy ≥6 months.
  Exclusion Criteria:
  -  Prior treatment with any heat shock protein 90 (Hsp90) inhibitor.
  -  Surgery, radiotherapy, or lesion ablative procedure to the only area of measurable disease
  -  Patients with prior hepatic resections or hepatic-directed therapy
  -  Use of a medication or food that is a clinically relevant CYP3A inhibitor or inducer within 2 weeks prior to dosing.

Relevance to patient case: not relevant
Patient case: 38-year-old male with Liposarcoma. Genetic variant: CDK4 Amplification. Other conditions: GERD.

Clinical trial: Phase III Trial to Evaluate the Elortinib vs Gefitinib in Advanced NSCLC With EGFR Exon 19 or 21 Mutations

Summary: This is a randomized controlled trial to compare efficacy and safety between erlotinib and gefitinib in advanced NSCLC harboring EGFR exon 19 or 21 mutations.Eligible patients were randomized to receive erlotinib or gefitinib in any line settings.The primary endpoint was progression-free survival (PFS).

Detailed description: Patients with stage IV NSCLC who have EGFR exon 19 or 21 mutations will randomized to received oral erlotinib 150mg or gefitinib 250mg once daily until disease progression or unacceptable toxicity. Method of direct DNA sequencing of tumor tissue is used to analysis EGFR mutation status of exons 18-21. The response will be evaluated by RECIST criteria first month,second month and then repeat every 3 months after the beginning of the treatment weeks.

Eligibility: Inclusion Criteria:
  -  Histologically or cytologically confirmed stage IIIB (wet) or IV NSCLC.
  -  Patients with positive EGFR exon19 or exon21 mutation as confirmed by direct sequencing histologically.
  -  Signing the informed consent form.
  -  The vital organ functions are tolerant to therapy.
  -  Have recovered to CTCAE2 grade below from toxicity of previous chemotherapy and radiotherapy
  -  PS 0-2 scores.
  -  Functional reserve of bone marrow is adequate, e.g. white blood cell count ≥3.0×109/L, planet count ≥90×109/L, and HB≥80×109/L.
  -  Serum bilirubin is 2 times less than the upper limit of normal (ULN), ALT and AST are 3 times less than ULN; for liver metastases, ALT and AST need to be 5 times less than ULN; creatinine should be 2 times less than ULN.
  Exclusion Criteria:
  -  Informed consent is not provided.
  -  Women of pregnancy or breastfeeding.
  -  Have difficulty in swallowing.

Relevance to patient case: not relevant
Patient case: 38-year-old male with Liposarcoma. Genetic variant: CDK4 Amplification. Other conditions: GERD.

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: 38-year-old male with Liposarcoma. Genetic variant: CDK4 Amplification. Other conditions: GERD.

Clinical trial: Transoral Incisionless Fundoplication (TIF) Registry Study for Treatment of Gastroesophageal Reflux Disease (GERD)

Summary: The study objective is to evaluate the safety and efficacy of TIF among a broad range of GERD patients treated in routine clinical practice at multiple centers across the United States.

Detailed description: Primary Effectiveness Endpoint: Typical and atypical GERD symptom elimination (scores ≤ 2 to each question) or clinically significant improvement (≥ 50% reduction in total scores) at 6-month follow-up compared to baseline.
  Secondary Effectiveness Endpoints: GERD symptom elimination or clinically significant improvement at 12-month follow-up, 24-month follow-up and 36-month follow-up; complete discontinuation of PPIs; normalization of esophageal acid exposure; significant reduction in reflux episodes; healing of reflux esophagitis; reduction of hiatal hernia; safety supported by low incidence of serious adverse events.

Eligibility: Inclusion Criteria:
  -  Age 18-75 years
  -  GERD for > 1 year
  -  History of daily PPIs use for > 6 months
  -  Moderate to severe typical or atypical GERD symptoms off PPIs
  -  Complete (responders) or partial (nonresponders) symptom control on PPIs
  -  Deteriorated gastroesophageal junction (Hill grade II or III)
  -  Proven gastroesophageal reflux by either endoscopy, ambulatory pH or barium swallow testing
  -  Willingness to undergo pH/impedance testing, if required
  -  Willingness to cooperate with the postoperative diet for 6 weeks
  -  Availability for follow up visits at 6 months and 12 months
  -  Willingly and cognitively signed informed consent
  Exclusion Criteria:
  -  BMI > 35
  -  Incompletely reducible hiatal hernia with residual of > 5 mm
  -  Esophagitis grade D
  -  Barrett's Esophagus > 2 cm
  -  Esophageal ulcer
  -  Fixed esophageal stricture or narrowing
  -  Portal hypertension and/or varices
  -  Active gastro-duodenal ulcer disease
  -  Gastric outlet obstruction or stenosis
  -  Gastroparesis or delayed gastric emptying confirmed by solid-phase gastric emptying study, if patient complains of postprandial satiety during assessment
  -  Coagulation disorder
  -  History of any of the following: resective gastric or esophageal surgery, antireflux surgery with anatomy unsuitable for TIF procedure per physician judgment, cervical spine fusion, Zenker's diverticulum, esophageal epiphrenic diverticulum, achalasia, scleroderma or dermatomyositis, eosinophilic esophagitis, or cirrhosis
  -  Pregnancy or plans of pregnancy in the next 12 months
  -  Enrollment in another device or drug study that may confound the results

Relevance to patient case: not relevant