araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: EUS Evaluation of CBD Diameter in Malignant Obstructive Jaundice

Summary: The main objective of the study is to evaluate the size of the common bile duct (CBD) in a large cohort of patients with jaundice secondary to pancreatic head or distal bile duct malignancy undergoing diagnostic EUS for tissue acquisition or evaluation of resectability and to establish factors associated with a dilation of the CBD greater than 15mm.

Detailed description: Rationale: The size of the common bile duct (CBD) may influence the type of stent used and the type of the procedure performed in cases of EUS-guided biliary drainage. However, no data of the size of the CBD in patients with jaundice presenting with a pancreatic head mass or with a distal cholangiocarcinoma/ carcinoma of the ampulla of Vater are available.
  Objectives: To evaluate the size of the CBD in a large cohort of patients with jaundice secondary to pancreatic head or distal bile duct malignancy undergoing diagnostic EUS for tissue acquisition or evaluation of resectability and to establish factors associated with a dilation of the CBD greater than 15mm.
  Study design: International prospective observational multicenter trial. Study population: Patients ≥18 years old, referred for EUS-guided tissue sampling or evaluation of resectability of a pancreatic, a distal bile duct lesion or a carcinoma of the ampulla of Vater determining obstructive jaundice.
  Intervention: EUS examination Main study parameters/endpoints: measurement of the CBD in patients with an obstructive distal biliary mass. Determine the factors associated with a CBD greater than 15mm Nature and extent of the burden and risks associated with participation, benefit and group relatedness: Measurement of the CBD during EUS examination does not add additional risks to the procedure.

Eligibility: Inclusion Criteria:
  -  Patients with jaundice and a pancreatic head mass lesion referred for EUS-guided tissue acquisition or staging
  -  Patients with jaundice and a distal CBD lesion suggestive of cholangiocarcinoma or a carcinoma of the ampulla of Vater referred for EUS-guided tissue acquisition or staging
  -  Serum bilirubin level ≥3 mg/dL
  -  Age ≥18 years
  -  Written informed consent
  Exclusion Criteria:
  -  Presence of altered anatomy from previous gastric surgery (Billroth II or Roux-en-Y anastomosis)
  -  Previously performed sphincterotomy, biliary plastic stent or metal stent placement
  -  Previous percutaneous drainage of the bile duct
  -  Pregnancy
  -  Inability to sign the informed consent

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: Mouthwash Containing Propolis, Clove Oil and Chlorhexidine Improving the Caries Risk of High Risk Patients

Summary: This study is conducted to determine if using a mouthwash containing propolis, clove oil and chlorhexidine will improve the caries risk of high risk patients in comparison to using a mouthwash containing chlorhexidine only.

Detailed description: A total of 64 patients will be assigned in this study. Patients will be randomly divided into two groups according to type of mouthwash (A) where group A1 patients will use chlorhexidine mouthwash as control group while group A2 patients will use chlorhexidine with propolis and clove oil mouthwash as intervention group with 32 patients in each group. Each group will be further divided into two groups according to times of application (T) where T1 represents patients using the mouthwash once daily for one week every month for 6 months and T2 where patients will use the mouthwash twice daily for one week every month for 6 months with 16 patients in each subgroup.

Eligibility: Inclusion Criteria:
  -  Patients should be over 18 years of age.
  -  Patients should be with high caries risk assessment.
  Exclusion Criteria:
  -  Patients with a compromised medical history.
  -  Severe or active periodontal disease.
  -  Patients with a diseased salivary gland
  -  History of allergies or other adverse reactions to chlorhexidine, propolis, bee stings, or clove
  -  Patients on any antibiotics during the past month

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: Neoadjuvant mFOLFOXIRI for Potentially Resectable Cholangiocarcinoma

Summary: Previous reports suggest benefit of neoadjuvant chemotherapy/chemoradiation treatment for borderline resectable cholangiocarcinoma. This study is a single center prospective phase II study of neoadjuvant chemotherapy with mFOLFOXIRI in patients with borderline resectable cholangiocarcinoma.

Detailed description: Previous reports suggest benefit of neoadjuvant chemotherapy/chemoradiation treatment for borderline resectable cholangiocarcinoma.
  This study is a single center prospective phase II study of neoadjuvant chemotherapy with mFOLFOXIRI in patients with borderline resectable cholangiocarcinoma.
  This phase 2 trial was designed to enroll 25 patients with BRCC who were assigned to mFOLFOXIRI neoadjuvant chemotherapy. The primary endpoint was the overall response rate.

Eligibility: Inclusion Criteria:
  1. ≥ 18 years old at the time of informed consent
  2. Diagnosed with cholangiocarcinoma and the disease is measurable by RECIST 1.1 criteria
  3. ECOG performance status of 0 or 1
  4. No distant metastasis
  5. The disease is either resectable or potentially resectable
  6. Patients must have adequate organ function as defined by the following laboratory values at study entry:
  Hemoglobin ≥ 8 g/dL (transfusions are acceptable) ANC ≥ 1.5 x 109/L Platelets ≥ 100 x 109/L AST/ALT ≤ 3 x ULN Total bilirubin ≤ 2.5 mg/dL Creatinine clearance ≥ 50 mL/min (estimated by Cockcroft-Gault or measured)
  7. Women of childbearing potential definition (WOCBP) and men must agree to use adequate contraception prior, to study entry, for the duration of study participation, and 3 months after the end of treatment.
  8. WOCBP must have a negative serum or urine pregnancy test prior to initiation of treatment.
  Exclusion Criteria:
  1. > 75 years old
  2. Prior therapy for cholangiocarcinoma with either surgery, radiation or chemotherapy
  3. Other malignancies except for the following: adequately treated cervical carcinoma in situ and treated basal cell carcinoma.
  4. Hypersensitivity to 5FU, oxaliplatin (or other platinum agents), irinotecan (or to their excipients).
  5. Pregnant or lactating women.
  6. Psychological, familial, sociological or geographical condition potentially hampering compliance with the study protocol and follow-up schedule; those conditions should be discussed with the patient before registration in the trial.
  7. Liver disease including but not limited to cirrhosis, primary sclerosing cholangitis, future liver remnant of less than 20-30%
  8. Comorbidity including but not limited to active clinically serious infections, congestive heart failure, life-threatening arrhythmia
  9. known HIV positive
  10. Baseline peripheral neuropathy/paresthesia grade ≥ 2.

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: Fluorescence Image Guided Surgery in Cholangiocarcinoma

Summary: Cholangiocarcinoma is an epithelial cell malignancy arising from varying locations within the biliary tree and is difficult to diagnose due to the often-silent clinical nature. The best chance of long-term survival and potential cure is surgical resection with negative surgical margins, but many patients are unresectable due to locally advanced or metastatic disease at diagnosis. Because cholangiocarcinoma is difficult to diagnose at an early stage and extends diffusely, most patients have unresectable disease at clinical presentation, and prognosis is very poor (5-year survival is 0-40% even in resected cases)
  There is a need for better visualization of tumor tissue, lymph nodes and resection margins during surgery for perihilar cholangiocarcinoma (PHCC). Optical molecular imaging of PHCC associated biomarkers is a promising technique to accommodate this need. The biomarkers Vascular Endothelial Growth Factor (VEGF-A), Epidermal Growth Factor Receptor (EGFR) and c-MET are all overexpressed in PHCC versus normal tissue and are proven to be valid targets for molecular imaging. Currently, tracers that target these biomarkers are available for use in clinical studies. In previous studies with other tumor types, the investigators tested the tracer bevacizumab-IRDye800CW for the biomarker VEGF-A with very promising results. Since all markers show roughly similar expression in ex vivo studies, the initial study will be performed with bevacizumab-IRDye800CW as the investigators have the most experience with this tracer. The investigators hypothesize that the tracer bevacizumab-IRDye 800CW accumulates in PHCC tissue, enabling visualization using a NIR intraoperative camera system and ex vivo NIR endoscopy. In this pilot study, the investigators will determine if it is possible to detect PHCC intraoperatively and by ex vivo NIR endoscopy using bevacizumab 800CW, and which tracer dose gives the best target-to-background ratio. The most optimal tracer dose will be selected for a future phase II trial.

Detailed description: See brief summary

Eligibility: Inclusion Criteria:
  -  Patients with clinical suspicion of PHCC who are scheduled to undergo surgical intervention with curative intent
  -  WHO performance score 0-2.
  Exclusion Criteria:
  -  Medical or psychiatric conditions that compromise the patient's ability to give informed consent.
  -  Other invasive malignancy
  -  Pregnant or lactating women.
  -  History of infusion reactions to bevacizumab or other monoclonal antibody therapies.
  -  Inadequately controlled hypertension with or without current antihypertensive medications
  -  Within 6 months prior to inclusion: myocardial infarction, TIA, CVA pulmonary embolism, uncontrolled chronic hepatic failure, unstable angina pectoris.

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: Cholangioscopy in Primary Sclerosing Cholangitis (PSC)

Summary: To demonstrate the clinical utility of the addition of per oral cholangioscopy (POCS) to standard endoscopic retrograde cholangiopancreatography (ERCP) with brushing cytology for diagnosis and early detection of cholangiocarcinoma in patients diagnosed with primary sclerosing cholangitis (PSC).

Detailed description: The primary objective of this study is to demonstrate the clinical utility of the addition of per oral cholangioscopy (POCS) to standard ERCP with brushing cytology for diagnosis and early detection of cholangiocarcinoma in patients diagnosed with primary sclerosing cholangitis (PSC).

Eligibility: Inclusion Criteria:
  1. Confirmed diagnosis of PSC
  2. Clinical indication for ERCP per local standard of practice, such as suspicion of potential malignancy based on worsening cholestatic values or clinical presentation (such as itching, cholangitis) or new biliary stricture on trans-abdominal imaging (MRI/MRCP, US or CT) or suspicious cytology
  3. Diameter of bile ducts deemed sufficient to accommodate the cholangioscopy system based on baseline imaging performed within 3 months prior to scheduled ERCP
  4. Written informed consent from patient to participate in the study, including compliance with study procedures.
  Exclusion Criteria:
  1. Contraindication for an ERCP or POCS
  2. History of liver transplantation
  3. Mass/metastasis extrinsic to the bile duct identifiable on diagnostic imaging
  4. History of iatrogenic bile duct trauma, including biliary surgery within 6 months of enrollment
  5. INR > 1.5 or platelets count < 50,000
  6. Age < 18 years
  7. Pregnant women or women trying to become pregnant

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: MEN1611 With Trastuzumab (+/- Fulvestrant) in Metastatic Breast Cancer

Summary: The main purpose of this open-label, dose-escalation, phase Ib study is to identify the appropriate dose of MEN1611 to be used in combination with Trastuzumab with/without Fulvestrant for the treatment of advanced or metastatic HER2-positive breast cancer

Detailed description: This Phase Ib study will investigate the safety and anti-tumor activity of daily oral doses MEN1611 in combination with Trastuzumab with/without Fulvestrant in female patients affected by advanced or metastatic HER2-positive breast cancer. Fulvestrant will be added to the post-menopausal patients with hormone-sensitive disease.
  MEN1611 is an investigational drug which blocks a protein called PI3K (phosphoinositide 3-kinase) involved in cancer cells growth. The Maximum Tolerated Dose (MTD) of MEN1611 given as single agent was assessed in a phase I trial in patients with advanced solid tumors.
  This Phase IB will start with a dose escalation part (Step 1) to identify the MTD of MEN1611 given in combination with Trastuzumab with/without Fulvestrant.
  The study will continue with a cohort expansion (Step 2) to investigate the anti-tumor activity of the selected MEN1611 dose level considered to be tolerable by a Safety Review Committee.

Eligibility: Main Inclusion Criteria:
  -  Histologically confirmed invasive adenocarcinoma of the breast
  -  Known HER2+ breast cancer
  -  Advanced or metastatic breast cancer harbouring PIK3CA mutation on tissue sample
  -  > 2 lines of anti-HER2 based regimens with at least 1 regimen with trastuzumab
  -  Radiological documented evidence of progressive disease
  -  Life expectancy ≥ 12 weeks
  -  Eastern Cooperative Oncology Group (ECOG) performance status ≤ 2
  Main Exclusion Criteria:
  -  Previous treatment with PI3K inhibitors
  -  Brain metastases untreated, unless treated > 4 weeks and only if clinically stable and not receiving corticosteroids
  -  History of clinically significant bowel disease
  -  ≥ grade 2 diarrhoea
  -  History of significant, uncontrolled, or active cardiovascular disease
  -  Any serious and/or unstable pre-existing psychiatric or neurologic illness or other conditions that could interfere with patient's safety
  -  Not controlled diabetes mellitus (glycated haemoglobin [HbA1c] >7%) and fasting plasma glucose >126 mg/dL
  -  Concurrent chronic treatment with steroids, as immunosuppressant, or another immunosuppressive agent

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: Window of Opportunity Study of IPI-549 in Patients With Locally Advanced HPV+ and HPV- Head and Neck Squamous Cell Carcinoma

Summary: The purpose of this study is to investigate how effective the study drug IPI-549 is against types of cancers. IPI-549 is considered experimental because it is not approved by the US Food and Drug Administration (FDA) for the treatment of cancer.
  Patients will be treated with 3 weeks of IPI-549, a specific PI3Kγ inhibitor. Tumor tissue for research purposes through core biopsies will be obtained prior to initiation of IPI-549 and at surgery.

Detailed description: This is a phase 2 window of opportunity trial in patients with locally advanced head and neck cancer. A key objective is to provide the first proof that macrophage phenotype switching can be accomplished in humans and lay the groundwork for future trials of this novel approach to immune therapy. Patients who are candidates for surgical resection will be enrolled and treated with 3 weeks of IPI-549, a specific PI3Kγ inhibitor. Tumor tissue for research purposes through core biopsies will be obtained prior to initiation of IPI-549 and at surgery.
  The study team hypothesizes that mRNA signatures of immune response will be increased in IPI-549-treated patients. For the efficacy endpoints, RECISTv1.1 will be used.

Eligibility: Inclusion Criteria:
  -  Have locally advanced that is amenable to surgical resection
  -  Must be able to swallow tablets
  -  Must be able to undergo a core tumor biopsy.
  -  Must have adequate organ function.
  Exclusion Criteria:
  -  Diagnosis of cutaneous squamous cell carcinoma (SCC) or Epstein-Barr virus (EBV) related nasopharynx cancer.
  -  Planned major surgery within 4 weeks prior to initiation of study drug
  -  Patients treated with chemotherapy, biologic therapy, or other investigational agent within < 28 days of starting study drug
  -  History of infection with human immunodeficiency virus (HIV), hepatitis B, or hepatitis C virus (HCV)
  -  On going treatment with chronic immunosuppressants (e.g., cyclosporine) or systemic steroids
  -  Prior surgery or gastrointestinal dysfunction that may affect drug absorption (e.g. gastric bypass surgery, gastrectomy)
  -  Female subjects who are pregnant or breastfeeding
  -  Concurrent active malignancy other than nonmelanoma skin cancer, carcinoma in situ of the cervix, or prostate intraepithelial neoplasia

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: WGS of Korean Idiopathic Bronchiectasis

Summary: Whole genome sequencing of Korean patients with idiopathic bronchiectasis and their family will perform to identify disease-causing variants.

Detailed description: Idiopathic bronchiectasis may be a manifestation of genetic diseases such as cystic fibrosis, primary ciliary dyskinesia, etc. Diagnosis of these rare genetic diseases is crucial not only because some of the rare diseases developed already effective treatment options, but also the detection of syndrome enables us to detect other organ damages before the deterioration of them.
  Several diagnostic tools have been developed; however, the genetic panel has limited screening efficacy due to the genetic heterogeneity of diseases. Even more, especially in Korea, the incidence of idiopathic bronchiectasis caused by the genetic disease is rare, most clinics have limited to assess specialized diagnostic tools such as the specialized genetic panels, sweat chloride test, and the electromagnetic detection tools for ciliary movement.
  Whole genome sequencing may be an excellent solution to identify the neglected genetic diseases causing idiopathic bronchiectasis and explore the heterogeneity of disease-causing variants in Korean patients.

Eligibility: Inclusion Criteria:
  -  If the patient has bronchiectasis proved by computed tomography (CT).
  -  The clinical features of the patient are suitable for ciliary dysfunction disease (primary ciliary dyskinesia, cystic fibrosis), alpha1-antitrypsin deficiency, and primary immune deficiency (hyper-immunoglobulin E syndrome, hypogammaglobulinemia, activated phosphoinositide 3-kinase (PI3K) delta syndrome, bare lymphocyte syndrome)
  -  The patient has no apparent medical events causing bronchiectasis.
  Exclusion Criteria:
  -  If the patient does not agree or withdraw
  -  If the patient has any clear etiology causing bronchiectasis including AIDS, malignancy, receiving immunosuppressant or chemotherapy.

Relevance to patient case: not relevant
Patient case: 62-year-old male with cholangiocarcinoma; genetic feature: PIK3CA (1047H)

Clinical trial: Volumetric Laser Endomicroscopy's (VLE) Diagnostic Accuracy Validation Study: Impact on Clinical Management Study

Summary: The purpose of this study is to assess the interobserver agreement (IOV) for pancreatico-biliary Volumetric Laser Endomicroscopy (VLE) de-identified clips using the new VLE criteria.
  This is an Interobserver study to validate VLE criteria for indeterminate biliary and pancreatic duct strictures and evaluate impact on clinical management.

Detailed description: Objective: Validate diagnostic impact of VLE diagnostic accuracy on clinical management
  Primary Objectives:
  1. Interobserver study for criteria validation and accuracy, Positive predictive value (PPV) and Negative predictive value (NPV), sensitivity and specificity.
  2. Evaluation of VLE diagnostics on clinical management (increased accuracy/faster detection)
  3. Determination of learning curve to standardize credentialing for endoscopists to use and interpret VLE imaging for biliary/pancreatic treatment management.
  B. Hypotheses / Research Question(s) The new VLE criteria for biliary and pancreatic duct strictures increase accuracy, thus leading to substantial impact on clinical management (Screening and Treatment)
  Study Design (2 phase):
  -  Phase 1: Primary Objective 1 and 2 part of the study will be completed.
  -  Phase 2: Primary Objective 3 of the study will be conducted within 1 month.
  Study Timeline: 3 months post WIRB approval. Sample size: 40 VLE Clips of at least 20 seconds featuring one or more the VLE criteria. All clips will have confirmed diagnosis for accuracy analysis. All clips will be de-identified. All clips will be removed from RedCAP and other secure cloud storage upon completion of study.
  Clips will be supplied by NinePoint Medical, the company behind VLE OCT. All VLE clips will be from a dataset of clips collected from adults > 18 and who underwent Endoscopic retrograde cholangiopancreatography (ERCP) with indeterminate biliary stricture indications. The clips are chosen based on the quality of the clips, duration, final diagnosis and presence of either benign or malignant criteria.
  Investigators: Up to 30 Expert and non-expert endoscopists currently using VLE

Eligibility: Inclusion Criteria:
  VLE clips featuring indeterminate biliary or pancreatic duct stricture with confirmed diagnosis on pathology -
  Exclusion Criteria:
  -

Relevance to patient case: not relevant