araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 11-year-old male with Peutz-Jeghers syndrome; genetic feature: STK11

Clinical trial: Prospective Study of BK Virus Disease After Allogeneic Hematopoietic-cell Transplantation: Defining BK Disease's Natural History, Clinical Spectrum, Immunology, and Outcomes

Summary: This research study is evaluating the reactivation of BK virus in patients who have undergone allogeneic hematopoietic-cell transplantation.

Detailed description: Every year, more than 25,000 patients worldwide receive lifesaving bone marrow transplantations with hematopoietic-cells from another person. It is estimated that over 75% of these patients will develop an infectious complication, of which approximately one third can be life-threatening. A significant proportion of these infections are caused by opportunistic viruses, such as BK virus.
  This virus establishes latent infection in most individuals, but does not normally cause disease. It can reactivate after hematopoietic-cell transplantation and represents the second most common viral infection in this patient population. BK virus is associated with kidney failure and a decreased chance of survival after hematopoietic-cell transplantation. There are no effective antiviral treatments for this disease.
  Despite being the second most common cause of clinical disease hematopoietic-cell transplantation, very little is known about this virus. To address this knowledge gap, the investigators aim to study patients with confirmed BK virus disease post allogeneic hematopoietic-cell transplantation.
  As part of this study, regular urine and blood tests will be done to understand how the virus behaves over time and which organs it affects. Blood and urine samples will also be obtained to study how the immune system rebuilds itself after hematopoietic-cell transplantation. Finally, an ultrasound of the kidneys and the bladder will be done to evaluate for any presence of disease in these organs.

Eligibility: Inclusion Criteria:
  -  Adult ≥18 years old
  -  All adult patients who undergo allo-HCT will be eligible for the study, regardless of age, underlying disease, conditioning regimen, or GVHD prophylaxis regimen
  Exclusion Criteria:
  -  Adults unable to consent
  -  Individuals who are not yet adults (infants, children, teenagers)
  -  Pregnant women
  -  Prisoners

Relevance to patient case: not relevant
Patient case: 11-year-old male with Peutz-Jeghers syndrome; genetic feature: STK11

Clinical trial: Blood Markers of Early Pancreas Cancer

Summary: Identifying biomarkers of early pancreatic ductal adenocarcinoma (PDAC) could facilitate screening for individuals at higher than average risk and expedite the diagnosis in individuals with symptoms and substantially improve an individual's chance of surviving the disease.
  The investigators propose a longitudinal study of subjects at higher than average risk of PDAC in order to generate clinical data and bank serial blood specimens.

Detailed description: Patients diagnosed with pancreatic ductal adenocarcinoma (PDAC) have only an 8% chance of surviving 5 years after diagnosis. Most PDAC is advanced and not amenable to curative therapies at the time of diagnosis, owing to lack of symptoms in early disease, nonspecific symptoms when they do develop resulting in a delay in diagnosis. Identifying biomarkers of early PDAC could facilitate screening for individuals at higher than average risk and expedite the diagnosis in individuals with symptoms and substantially improve an individual's chance of surviving the disease.
  The investigators propose a longitudinal study of subjects at higher than average risk of PDAC in order to generate clinical data and bank serial blood specimens. Subjects will include individuals with family history of pancreas cancer, individuals with cystic pancreas lesions or chronic pancreatitis, and individuals with new-onset diabetes. Identifying specific biomarkers - blood markers and/or a clinical "prodrome" - in participants who go on to develop PDAC could improve the diagnostic approach outcomes for patients diagnosed with PDAC.

Eligibility: Inclusion Criteria:
  General inclusion criteria:
  1. Age ≥19
  2. Able to provide written, informed consent
  Exclusion Criteria:
  General exclusion criteria:
  1. Personal history of PDAC
  2. Currently receiving treatment for a cancer diagnosis (excluding long-term hormonal therapy)
  3. Pre-diabetes on metformin for ≥ 3 years

Relevance to patient case: not relevant
Patient case: 11-year-old male with Peutz-Jeghers syndrome; genetic feature: STK11

Clinical trial: Diagnostic and Prognostic Value of Miss-1 Study in Children and Adult With Nephrotic Syndrome MISSNEPHROTIQUE

Summary: The nephrotic syndrome is a rare disease defined by a proteinuria >3g/24h and a hypoalbuminemia < 30g/L. Genetic and immune are the main causes. The acquired idiopathic nephrotic syndrome presents histologically minimal glomerular lesions, sometimes associated with segmental and focal hyalinosis. The idiopathic nephrotic syndrome (INS) represents 85% of children's glomerular nephropathy and 25-30% of adult's.
  Relapses are frequents, and can be pejorative up to 10% and lead to end-stage kidney failure.
  Another immune cause is the extramembranous glomerulonephritis mediated by molecular targets specific autoantibodies expressed at the podocytes surface.
  Other immune causes include lupus nephropathy, ANCA vascularitis, Goodpasture disease, Berger disease.
  Easy diagnosis between these causes can be made with the renal biopsy.
  Miss-1, a new protein activated during a inflammatory event, could be an actor in nephrotic syndromes by modifying the podocyte's adhesion on the glomerular basal membrane. This would modulate the structure and function of the slit diaphragm, as well as junctions between the podocyte and the glomerular basal membrane, regulating podocytes' apoptosis.

Detailed description: This project is meant to propose and validate specific and non-invasive diagnostic and prognostic tests for the acquired idiopathic nephrotic syndrome.
  These tests rely on the measure of Miss-1 expression in circulating blood cells on flow cytometry and its plasmatic concentration.
  To date, no equivalent tests exist to diagnose idiopathic nephrotic syndrome (INS) from other causes.
  These simple tests would allow a quick diagnosis of acquired INS by avoiding an invasive renal biopsy. It would also help anticipate the relapses of the disease and guide the treatment modalities as do nowadays the PLA2R antibodies in idiopathic membranous nephropathy.
  We will propose the tests to every consent patient, hospitalized in the participating centers (Néphrologie pédiatrique of Robert Debré hospital, Néphrologie adulte of Tenon hospital) with a nephrotic syndrome.

Eligibility: Inclusion Criteria:
  -  All new hospitalized patient
  -  Presenting a nephrotic syndrome according to its definition
  -  For which an anatomopathological diagnostic and its evolution can be or will be carried
  -  Children of any age can be included if they present a nephrotic syndrome
  Exclusion Criteria:
  - Patients already treated with glucocorticoids and/or immunosuppressor

Relevance to patient case: not relevant
Patient case: 11-year-old male with Peutz-Jeghers syndrome; genetic feature: STK11

Clinical trial: Prospective Pilot Study Identifying Clinically Relevant Biological Targets for Medical Therapy

Summary: New data suggests that the current treatment for pediatric adamantinomatous craniopharyngioma (CPA) may not be as effective as it could be.

Detailed description: Current treatment regimens for pediatric CPA are limited to surgery and radiation therapy. This pilot study seeks to identify biologically rational therapeutics for the medical treatment of adamantinomatous CPA by confirming the overexpression of specific molecules.

Eligibility: Inclusion Criteria:
  1. Patients between 0-21 years of age.
  2. Patients with the diagnosis or clinical suspicion of craniopharyngioma in whom planned clinical management will include tissue sampling.
  Exclusion Criteria:
  1. Patients in whom final pathology does not demonstrate adamantinomatous craniopharyngioma
  2. Patients in whom tissue specimen is not obtained/available
  3. Patients over 21 years of age.
  4. Patients who choose not to participate

Relevance to patient case: not relevant
Patient case: 11-year-old male with Peutz-Jeghers syndrome; genetic feature: STK11

Clinical trial: Genomic and Proteomic Study of Richter Syndrome (CGPSR)

Summary: Biological study on Richter Syndrome (RS), an agressive lymphoma that arises from Chronic Lymphocytice Leukemia (CLL). RS presents with the same histological aspect as primitive Diffuse Large B-Cell Lymphoma (DLBCL), but is associated with a poor prognosis, due to chemorefractoriness.
  This study aims at understanding the biological determinants of chemotherapy resistance in Richter Syndrome.

Detailed description: With the help of the French National Research Group on CLL (FILO / French Innovative Leukemia Organization), the investigators are currently gathering fresh frozen cell pellets at CLL stage, and lymph node biopsies at Richter stage. The investigators also gathered lymph node biopsies from DLBCL, as a reference group.
  The investigators will perform genomic and proteomic comparative studies between CLL and Richter, as well as between Richter and primitive DLBCL, to understand the biological determinants of clonal evolution and chemorefractoriness of Richter Syndrom.

Eligibility: Inclusion Criteria:
  -  Diagnosis of a Diffuse Large B-Cell Lymphoma arising in the context of a Chronic Lymphocytic Leukemia (group 1) or diagnosis of a primitive Diffuse Large B-Cell Lymphoma (group 2), or diagnosis of a Diffuse Large B-Cell Lymphoma arising in a context of small cells lymphoma, excluding CLL (group 3), or benefit from a diagnostic lymph node biopsy that did not reveal any tumor involvment (primitive or metastatic) (group 4).
  -  Patients must benefit from a lymph node biopsy at diagnosis.
  -  Patients must be followed by a FILO (French Innovative Leukemia Organization) member
  -  Histology of Diffuse Large B-Cell Lymphoma or Hodgkin histology.
  -  Suitable clinical data available.
  -  Samples must meet the following requirement :RIN (RNA Integrity Number) > 5 et DIN (DNA Integrity Number) > 6.5.
  Exclusion Criteria:
  • Samples that do not meet the inclusion criteria (insufficient clinical data, analysis impossible due to insufficient sample quality).

Relevance to patient case: not relevant
Patient case: 11-year-old male with Peutz-Jeghers syndrome; genetic feature: STK11

Clinical trial: Angelman Syndrome Italian Registry

Summary: The Italian Angelman Registry is a national registry for patients with Angelman Syndrome. No experimental intervention is involved in participation. The data provided are stored in the registry according the EU General Data Protection Regulation (GDPR, enforced on 25 May 2018), unless participants wish to withdraw their child/ adult's information from the registry.

Detailed description: Parents/caregivers of a child or an adult with Angelman Syndrome living in Italy are eligible to insert data in this registry. The individuals must have a diagnosis of Angelman Syndrome confirmed by genetic testing results. The registry has been launched in February 2018 in coincidence with the International Angelman Day and the recruitment will be open until February 2021.

Eligibility: Inclusion Criteria:
  -  Molecular diagnosis of Angelman syndrome
  Exclusion Criteria:
  -  Does not meet diagnostic criteria for Angelman Syndrome Other medical or genetic disorders (except autism)

Relevance to patient case: not relevant
Patient case: 11-year-old male with Peutz-Jeghers syndrome; genetic feature: STK11

Clinical trial: Registry of Acute Coronary Syndrome From University Hospital of Vigo

Summary: CardoCHUVI registry was aim to study ischemic and bleeding complication after an acute coronary syndrome (ACS), both in-hospital and follow-up events.

Detailed description: CardioCHUVI is a retrospective study aim to analyze all consecutively patients admitted by acute coronary syndrome to University Hospital Alvaro Cunqueiro of Vigo, between January 2010 to January 2018
  The objective of the project was to study cardiac and bleeding complications, such as reinfarction, heart failure, atrial fibrillation, stroke, and bleeding events, together with all-cause and cardiac mortality

Eligibility: Inclusion Criteria:
  -  Any patient admitted to University Hospital Alvaro Cunqueiro of Vigo for acute coronary syndrome.
  Exclusion Criteria:
  -  Secondary acute coronary syndromes during a hospital admission for another cause (i.e. acute myocardial infarction in the context of a sepsis)

Relevance to patient case: not relevant
Patient case: 11-year-old male with Peutz-Jeghers syndrome; genetic feature: STK11

Clinical trial: BLI, NBI or White Light Colonoscopy for Proximal Colonic Adenoma

Summary: This is a prospective randomised trial comparing the proximal adenoma detection rate and miss rate by blue laser imaging (BLI), narrow band imaging or white light colonoscopy.

Detailed description: Study population:
  Consecutive adult patients, age 40 or above, undergoing outpatient colonoscopy in the Queen Mary Hospital are invited to participate in this prospective randomized study. Patients are excluded if they are unable to provide informed consent or have undergone previous colorectal resection, or have personal history of colorectal cancer, inflammatory bowel disease, familial adenomatous polyposis, Peutz-Jeghers syndrome, or other polyposis syndromes. Patients who are considered to be unsafe for polypectomy including patients with bleeding tendency and those with severe comorbid illnesses will be excluded. In addition, patients are excluded post-randomization if either the cecum could not be intubated for various reasons or Boston Bowel Preparation Scale (BBPS) score is <2.
  Study design and randomization:
  This is a prospective randomized crossover trial comparing the proximal adenoma detection rate and miss rate of BLI (ELUXEO endoscopic system) vs NBI (290 video system) vs WLI which is conducted in the Endoscopy Center of the Queen Mary Hospital of Hong Kong. Eligible patients are randomly allocated to four groups in a 1:1:1 ratio to undergo tandem colonoscopy of the proximal colon, defined as cecum to splenic flexure. The three groups are: (1) NBI follow by WLI; (2) BLI follow up WLI; (3) WLI follow by WLI. Randomization will be carried out by computer generated random sequences and stratified according to endoscopist's experiences (experienced versus fellows) and indications of colonoscopy (symptomatic vs screening/surveillance). All procedures are performed with high-definition endoscopes. The patients are blinded to the group assignment.

Eligibility: Inclusion Criteria:
  -  Age 40 or above
  -  scheduled for colonoscopy
  Exclusion Criteria:
  -  unable to provide informed consent
  -  have undergone previous colorectal resection,
  -  personal history of colorectal cancer, inflammatory bowel disease, familial adenomatous polyposis, Peutz-Jeghers syndrome, or other polyposis syndromes.
  -  Patients who are considered to be unsafe for polypectomy including patients with bleeding tendency and those with severe comorbid illnesses
  -  poor bowel preparation

Relevance to patient case: not relevant
Patient case: 11-year-old male with Peutz-Jeghers syndrome; genetic feature: STK11

Clinical trial: Angelman & Rett Syndrome: Interaction and Communication

Summary: We aim to describe the communicative and sensory profile of children with Angelman syndrome or Rett syndrome and their use of augmentative and alternative communication. In addition, parents are surveyed regarding parent-child interaction and access to communication support.


Eligibility: Inclusion Criteria:
  -  Angelman or Rett syndrome
  Exclusion Criteria:
  -  none

Relevance to patient case: not relevant
Patient case: 11-year-old male with Peutz-Jeghers syndrome; genetic feature: STK11

Clinical trial: Metformin in Children and Adults With Fragile X Syndrome

Summary: Fragile X Syndrome (FXS) is caused by loss of FMR1 expression on the X chromosome that leads to increased mRNA translation, which results in hyperactivation of ERK (extracellular signal-regulated kinase) and mTORC1 (mechanistic target of rafampicin complex 1) signaling and consequently in synaptic dysfunction and neurological development. There is presently no cure for FXS. Recent studies suggest that metformin (a widely prescribed drug for type II diabetes in children and adults) which crosses the blood-brain barrier, corrects various neurological and behavioral FXS phenotypes by normalizing ERK signaling, EIF4E phosphorylation and lowering expression of MMP9 to normal. Since this drug has not been previously used specifically for treatment of FXS (only few cases reported), the investigators propose an open-label trial of metformin in children and adults with FXS to better understand the safety and efficacy in both behavior and cognition.


Eligibility: Inclusion Criteria:
  -  Aged between 10 et 40 years old
  -  BMI > 18.3
  -  Molecular diagnosis of FXS
  -  Accompanied by his legal tutor
  -  IQ < 70
  Exclusion Criteria:
  -  Pregnancy/Breastfeeding
  -  Intolerance to metformin
  -  History of lactic acidosis
  -  Gastric/renal/hepatic pathology
  -  Acute medical condition
  -  Concomitant use of ACE inhibitors
  -  Taking more than 3 antipsychotic drugs
  -  Modification of antipsychotic treatments in the last 6 weeks

Relevance to patient case: not relevant
Patient case: 11-year-old male with Peutz-Jeghers syndrome; genetic feature: STK11

Clinical trial: Biomarkers for Prediction of Tumor Response to Radiotherapy

Summary: This study aims to explore potential biomarkers for prediction of therapeutic outcomes in patients with solid tumors after radiotherapy

Detailed description: Patients pathologically confirmed with solid tumor that requires radiotherapy will be recruited to this study. All enrolled will have tumor biopsy at primary site and peripheral blood collection during the course of radiotherapy and when the disease progresses. These biological specimens will be used for exploration of potential biomarkers that could predict the tumor response and long-term outcome of patients.

Eligibility: Inclusion Criteria:
  -  Pathological proven diagnosis of solid tumors
  -  Tumor accessible for biopsy during the course of radiotherapy
  -  Patient must provide study-specific informed consent prior to study entry
  Exclusion Criteria:
  -  History of autoimmune diseases
  -  History of immunotherapy
  -  Prior radiation therapy that would result in overlap of planned radiation therapy fields
  -  Will receive immunotherapy during the course of radiotherapy
  -  Contraindications for biopsy, such as high bleeding risk

Relevance to patient case: not relevant
Patient case: 11-year-old male with Peutz-Jeghers syndrome; genetic feature: STK11

Clinical trial: Evaluation of Ocular Lens Proteins in Cataract From Individuals With Down Syndrome

Summary: This study involves the collection ocular lens tissue from individuals with Down syndrome and age-matched controls at the time of cataract surgery.

Detailed description: Individuals with Down syndrome have an increased rate of cataract. The reason for this increase is unclear. Normally, once cataracts become a significant impairment, an ophthalmologist will determine when cataract surgery should be performed. When this surgery is performed, cataractous tissues are cut out and discarded with medical waste. In this study, these tissue will be collected and protein analysis performed to determine what changes in different proteins are found in Down syndrome lenses as compared to normal cataractous lenses.

Eligibility: Inclusion Criteria:
  -  Undergoing cataract surgery for lens extraction.
  Exclusion Criteria:
  -  Known genetic cause other than Down syndrome causing cataract.

Relevance to patient case: not relevant
Patient case: 11-year-old male with Peutz-Jeghers syndrome; genetic feature: STK11

Clinical trial: Efficacy of Rapamycin (Sirolimus) in the Treatment of Peutz-Jeghers Syndrome

Summary: A prospective non-randomized open label single arm clinical trial to examine the efficacy and safety of sirolimus in patients with Peutz-Jeghers Syndrome.

Detailed description: PJS (Peutz-Jeghers Syndrome) is mostly caused by mutations in Lkb1 gene, which leads to an increased activity of mTOR pathway, thus making mTOR inhibitor (sirolimus) a promising candidate in treatment and prevention of PJS. The efficacy of sirolimus (rapamycin) on PJS has been demonstrated in mouse model, but no clinical trials have been reported. Our study was designed as a prospective non-randomized open label single arm clinical trial to examine its efficacy and safety.

Eligibility: Inclusion Criteria:
  -  Patients are diagnosed with PJS.
  -  Patients have gastrointestinal polyps related syndromes, including abdominal pain, abdominal distension, gastrointestinal bleeding, etc, with imageological examination suggesting intestinal obstruction or intussusception; or whose symptoms recur after previous digestive endoscopic treatment and surgery; or who are inappropriate or unwilling to accept the above treatment again and wish to receive pharmacotherapy.
  -  Conventional treatment didn't work well in patients combined with PJS-related tumors.
  -  Physical condition (ECGO): 0~3
  -  Organ function is good and biochemical indices meet the following conditions:
  -  AST≤2.5×upper limit of normal value (ULN),
  -  ALT≤2.5×upper limit of normal value (ULN),
  -  Serum total bilirubin (TSB)≤1.5×upper limit of normal value (ULN),
  -  Creatinine≤1.5×upper limit of normal value (ULN).
  -  No other medications have been received for intestinal polyps within 3 months prior to the clinical trial.
  -  Patients participate in the trial voluntarily and have signed the informed consent by the participant or his/her legal guardian.
  Exclusion Criteria:
  -  Patients underwent a surgery within 2 weeks.
  -  Patients may need emergency surgery in the near future.
  -  Patients are allergic to any ingredient of rapamycin.
  -  Patients suffer from a disease requiring immediate blood transfusion.
  -  Patients suffer from any disease or condition that may impact implementation of the study or interpretation of the results. This type of diseases includes:
  -  Known severe blood coagulation disorders
  -  Known anemia that is not caused by intestinal polyps
  -  Known hemoglobinopathy
  -  Other gastrointestinal infectious diseases
  -  Serious heart, liver, kidney and other concomitant diseases that may endanger lives
  -  Patients are in pregnancy and lactation.
  -  Alcohol or drug (such as aperient) abuse
  -  Patients took part in another clinical trial that may influence this study.
  -  The researchers believe that there are other unfavorable reasons for the patient to become a subject.

Relevance to patient case: not relevant