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

Clinical trial: Genetics of EGFR (Epidermal Growth Factor Receptor) Mutation Study

Summary: The investigators wish to document the distribution of EGFR somatic mutations, and assess the relationship between specific genotype, clinical demographic, therapy, and survival, in a large cohort of EGFR mutant NSCLC.
  The investigators also wish to comprehensively investigate the relationship between germline DNA and risk of EGFR mutant NSCLC developing, through a GWAS (Genome-Wide Association Studies) and candidate gene approach, and explore the relationship between germline DNA and clinical outcome, in order to potentially identify germline genetic modifiers of EGFR TKI (Tyrosine Kinase Inhibitor) outcome.

Detailed description: Objective 1: To identify germline allelic DNA variation associated with somatic EGFR mutation in NSCLC, Objective 2: Correlation between germline allelic variants and survival in EGFR somatic mutant NSCLC.
  Objective 3: Study germline allelic DNA variation associated with never /ex light smoking NSCLC.
  Objective 4: Catalogue distribution of somatic EGFR mutant genotypes in 1,000 EGFR mutant NSCLC cases and describe their relationship to clinical outcome.

Eligibility: -  Histologically or cytologically diagnosed NSCLC, all histologies are acceptable.
  -  Patients can be included in the study with any disease stage and at any time during the disease course.
  -  Any type (surgery, RadioTherapy, chemotherapy, targeted agents) of previous treatment and any line of treatment are eligible.
  -  Age ≥18 years.
  Absence of any psychological, familial, sociological or geographical condition potentially hampering compliance with the study protocol; those conditions should be discussed with the patient before registration in the trial.
  Before patient registration, written informed consent must be given according to ICH/GCP (International Conference on Harmonisation/Good Clinical Practice), and national/local regulations.

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

Clinical trial: Isolated Roux Loop Pancreaticojejunostomy Versus Pancreaticogastrostomy After Pancreaticoduodenectomy

Summary: Pancreaticoduodenectomy (PD)is the treatment of choice for patients with periampullary tumour (benign or malignant). In the recent years, the mortality rate of PD has decreased to 5% in many centers. However, pancreatic fistula (POPF) still occurs in 5 % to 40% of patients after PD. The hypothesis that isolated Roux loop PJ with isolated pancreatic drainage decrease the incidence of PF and severity with preservation of pancreatic function.
  So the investigators compare isolated Roux Loop Pancreaticojejunostomy (PJ) Versus Pancreaticogastrostomy (PG) as regards incidence of POPF, severity of POPF and functional outcome.

Detailed description: The hypothesis that isolated Roux loop PJ decrease the incidence of PF and severity with preservation of pancreatic function (exocrine and endocrine functions).
  Preoperative evaluation included abdominal CT, liver function, tumor marker CEA, CA19-9, preoperative ERCP were optional in selected cases (patients with high bilirubin with high enzymes. Patients with distant metastasis or locally advanced were excluded.
  Informed consent was obtained from all patients entered in the study Randomization: enrolled patients were randomized intraoperatively after PD resection to either isolated Roux PJ with isolated pancreatic drainage group or PG group by closed envelope which withdrawn by the nurse.
  Operative technique. Standard PD with regional lymphadenectomy was performed. PG was done between pancreatic stump and posterior surface of the stomach with 2 layer interrupted anastomosis,and duct to mucosa.
  Isolated Roux PJ group, reconstruction was begun using the transected jejunum and, which was anastomosed in end to side fashion. A separate Roux loop was performed for HJ, by dividing the jejunum about 40 cm beyond the pancreatic anastomosis and GJ was done in this loop (30 cm caudally from HJ). The PJ loop was anastomosed to the main loop (20 cm caudal to GJ).
  One intrabdominal drains in morrison space. Intraoperative data and postoperative data were collected. Pancreatic function assessment.
  The primary outcome was assessment the incidence of POPF after isolated Roux PJ and PG. The secondary outcomes were intraoperative blood loss, drain amount,day to resume oral intake hospital stay, operative duration, pancreatic function, postoperative complications delayed gastric emptying,

Eligibility: Inclusion Criteria:
  -  All periampullary tumour either benign or resectable malignant tumour
  Exclusion Criteria:
  -  locally advanced tumour infiltrating SMA
  -  Metastasis
  -  unfit

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

Clinical trial: The ImageKids Study: Developing the pMEDIC and the PICMI

Summary: The overall objectives of this study are to develop two indices capable of measuring intestinal damage, and, separately, inflammatory disease activity in Pediatric Crohn's disease by means of Magnetic Resonance Imaging with Enterography protocol (MRE) and pelvic MRI.

Detailed description: The PICMI Score and the pMEDIC are aimed to be discriminative (at one point in time), evaluative (measuring damage progression over time) and predictive. The indices will be used as endpoint measures in clinical research and also in clinical practice to identify those who are at risk for rapid disease progression and surgery.

Eligibility: Inclusion Criteria:
  1. Children (under 18 years of age) with established diagnosis of CD involving any location by the presence of accepted clinical, radiologic, endoscopic and histologic criteria (33, 34).
  2. Enrolment at the time of performing ileocolonoscopy and esophageal-gastroduodenoscopy (EGD) as part of clinical care for any reason.
  3. Children will be enrolled at any phase of the disease (at diagnosis and thereafter as required clinically). In order to ensure enough subjects with intestinal damage and since damage is progressing over time, enrolment will be stratified based on disease duration. Enrolment for each stratum of disease duration will be closed after reaching the expected sample size.
  -  20% of enrolled children will be within 3 months of diagnosis.
  -  20% of children will be between 3 months and 2 years.
  -  20% will be 2.01 to 3 years
  -  40% will have disease duration over 3-years.
  4. Children may be enrolled in any disease activity state (PCDAI 0-100).
  Exclusion Criteria:
  1. Young children requiring anesthesia for lack of cooperation will be excluded (since the enteric contrast cannot be administered during the 2 hours before anesthesia and it is crucial that the contrast be given just prior the test).
  2. For the first 120 children only, subjects not expected to be available for 18 month follow-up, will be excluded (the last 120 subjects may be enrolled as they are not followed longitudinally).

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

Clinical trial: Impact of Methylation Alterations in Colon Cancer: Epidemiology and Prognosis

Summary: We conducted a preliminary study in 2010 using the innovative Illumina GoldenGate (methylation assay) which has enabled us to characterize the level of methylation of 807 potential markers on a series of 200 adenocarcinomas of the colon (C18) and rectosigmoid junction (C19) resected between 1998 and 2001. The results, validated by pyrosequencing, allowed us to establish a panel of 12 markers to assess the level of methylation. The aim of this project is to validate the prognostic value of this panel in a second cohort of patients with adenocarcinomas (stage I to IV) resected between 2002 and 2006 in public and private hospitals (n=685).
  This study relies on an original collection of surgical specimens of colorectal cancers resected in public and private hospitals among patients resident in the département of Côte-d'Or and followed by the cancer registry of Burgundy. Samples obtained from each cancer and from adjacent normal mucosa are stored in liquid nitrogen in the Ferdinand Cabane Biological Resources Centre(certified S 96900). Annotations are collected by the cancer registry staff from multiple sources (pathologists, gastroenterologists, oncologists and radiotherapists).
  Pyrosequencing will be used to quantify the level of methylation. The percentage of methylated allele for each marker on cancerous DNA and the ratio of methylated markers to the number of markers analyzed will be determined. The molecular status of MSI, BRAF, KRAS, and PI3K will be taken into consideration.
  To study the prognosis, relative and relapse free-survival will be calculated. A multivariate relative survival analysis will be performed to determine independent prognostic factors taking into account the characteristics of patients and tumours and epigenetic and molecular alterations. Epigenetic alterations will be described according to age group, sex and subsite. The epigenetic phenotypes will be evaluated according to already known molecular status using logistic regression models.


Eligibility: Inclusion Criteria:
  -  Adenocarcinomas of the colon (C18) and rectosigmoid junction (C19)
  -  Resident in Côte-d'Or
  -  Treated by surgical resection
  Exclusion Criteria:
  -  Rectal cancer
  -  Cancer on Crohn's disease and ulcerate colitis
  -  Hereditary colon cancer (HNPCC, familial polyposis)

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

Clinical trial: Screening an Orthopedic Population for Mildly-affected Individuals With Morquio Syndrome A and Maroteaux-Lamy Syndrome

Summary: The purpose of this study is to identify patients with Morquio syndrome type A (MPS IVA) and Maroteaux-Lamy syndrome (MPS VI) who may have been missed or misdiagnosed due to atypical clinical features, a milder course, and/or negative urine screening. We will recruit participants who have certain hip and/or joint problems that could potentially be caused by one of these two genetic conditions through a chart review process conducted at Shriners Hospital for Children in Greenville, SC. Diagnostic testing will be performed for each participant to determine if he or she is affected by one of these two conditions. Results will be disclosed to all participants and their legal guardians, and appropriate follow up will be recommended for those who are found to have abnormal results.


Eligibility: Inclusion Criteria:
  -  Eligible participants must currently receive care in the Shriners Hospitals for Children system, and therefore, will be under 19 years of age.
  -  Eligible participants must have one of the following diagnoses: bilateral Legg-Calve-Perthes disease, bilateral hip dysplasia, multiple joint pain, unidentified skeletal dysplasia
  -  Eligible participants (or legal guardian) must be able and willing to sign informed consent/assent in English or Spanish.
  Exclusion Criteria:
  -  Participants with one or more or the above inclusion diagnoses who have a specific etiologic diagnosis will not be eligible to participate in this study.
  -  If we are unable to obtain the necessary specimens, the participant will be removed from the study.

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

Clinical trial: French Digestive Polyposis Cohorte Family Adenomatous Polyposis With APC and MYH Gene Mutations , Cowden's Disease With PTEN Gene Mutation, Peutz Jeghers Disease With STK 11 Gene Mutation ,juvénil Polyposis With SMAD 4 Gene Mutation , Serrated and Hyperplastic Polyposis

Summary: French cohorte about polyposis digestive diseases

Detailed description: Family Adenomatous Polyposis APC and MYH Genes Peutz Jeghers Disease Cowden Disease Festooned polyposis Juvenile polyposis Hyperplastic polyposis

Eligibility: Inclusion Criteria:
  -  APC Gene mutation
  -  MYH Homozygote mutation
  -  COWDEN Disease with PTEN gene mutation
  -  Peutz Jeghers Disease with STK 11 gene mutation
  -  Juvenile polyposis with SMAD 4 gene mutation
  Exclusion Criteria:
  -  heterozygote MYH Gene Mutation

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

Clinical trial: Carfilzomib for the Prevention of Graft Versus Host Disease

Summary: The aim of this study is to evaluate the safety and efficacy of Carfilzumib, which is a novel biological agent used in the treatment of multiple myeloma in preventing graft-versus-host disease, after stem cells transplantation from unrelated donors.


Eligibility: Inclusion Criteria:
  1. Patients with MDS/AML
  2. 18 years or older and willing and able to comply with the protocol requirements.
  3. LVEF ≥ 40%. 2-D transthoracic echocardiogram (ECHO) is the preferred method of evaluation. Multigated Acquisition Scan (MUGA) is acceptable if ECHO is not available.
  4. Patients undergoing 8-10/10 HLA matched unrelated and unmanipulated PBSC transplantation
  5. Patients conditioned with reduced intensity or reduced toxicity conditioning i.e. Fludarabine combine with Treosulfan or 2-4 days of I.V Busulfan.
  6. Patients must sign written informed consent.
  7. Adequate birth control in fertile patients.
  Exclusion Criteria:
  1. Patients undergoing other type of transplantation or with other type of basic disease other than AML or MDS.
  2. Patients with respiratory failure (DLCO < 30%).
  3. Active congestive heart failure (New York Heart Association [NYHA] Class III to IV), symptomatic ischemia, or conduction abnormalities uncontrolled by conventional intervention.
  4. Patients with > grade II liver renal toxicity.
  5. Psychiatric conditions/disease that impair the ability to give informed consent or to adequately co-operate
  6. Bilirubin > 3.0 mg/dl, transaminases > 3 times upper normal limit
  7. Creatinine > 2.0 mg/dl
  8. ECOG-Performance status > 2
  9. Uncontrolled infection
  10. Pregnancy or lactation
  11. CNS disease involvement
  12. Pleural effusion or ascites > 1 liter.

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

Clinical trial: The Cancer of the Pancreas Screening-5 CAPS5)Study

Summary: Johns Hopkins clinical research office quality assurance group will monitor and audit this study at Johns Hopkins. The Sub Investigator at each site will be responsible for internal monitoring at their site.

Detailed description: The Sub Investigator at each site will be responsible for internal monitoring at their site. The site sub Investigator and study team will report any serious adverse events to Principal Investigator and annually report adverse events.

Eligibility: Inclusion Criteria:
  -  Hereditary Pancreatitis or
  -  Peutz-Jeghers Syndrome or
  -  Strong family history of pancreas cancer on one side of the family tree or
  -  Confirmed germline mutation carrier (BRCA2, FAMMM, PALB2, BRCA1, HNPCC, PRSS1/2, or CTRC
  -  Endoscopic evaluation of pancreas scheduled
  Exclusion Criteria:
  -  Medical comorbidities or coagulopathy that contraindicate endoscopy
  -  Prior surgery that prevent optimal endoscopic ultrasound such as partial or complete gastrectomy with Bilroth or Roux-en-Y anastomosis
  -  Stricture or obstruction in the upper GI tract that does not allow passage of the echoendoscope
  -  Poor performance status
  -  Inability to provide informed consent
  -  Pregnancy.

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

Clinical trial: Evaluation of a "Flash-free" Adhesive Resin for Orthodontic Bracket Bonding

Summary: The purpose of this study is to compare bonding time, bond survival, amount of adhesive remaining on the tooth surface after bracket debonding, and time required for adhesive remnant cleanup between a new "flash-free" and a conventional adhesive resin for orthodontic bracket bonding.

Detailed description: Patients presenting for comprehensive orthodontic treatment with fixed appliances at the University of Minnesota, who are willing to participate, will be included in the initial study. Selection criteria will include full permanent dentition through the first molars, teeth with sound, non-carious buccal enamel and no pretreatment with chemical agents such as hydrogen peroxide, and no previous orthodontic treatment with fixed appliances. The patients will have their maxillary incisors, canines, and premolars bonded with ceramic orthodontic brackets pre-coated with a "flash-free" adhesive resin (Clarity Advanced Brackets APC flash-free, 3M Unitek, Monrovia, CA, USA) on one side and a conventional adhesive resin (Clarity Advanced Brackets APC II, 3M Unitek) on the other side. The side allocation and order of bonding will be randomized for each patient.

Eligibility: Inclusion Criteria:
  -  Full permanent dentition including incisors, canines, premolars, and first molars
  -  Teeth with sound, non-carious buccal enamel and no pretreatment with chemical agents such as hydrogen peroxide
  -  No previous orthodontic treatment with fixed appliances
  Exclusion Criteria:
  -  Mental/emotional/developmental disability
  -  Cleft lip and/or palate, craniofacial anomaly, or syndrome
  -  Obvious oral hygiene issues such as excessive plaque accumulation, gingivitis, and/or pre-existing white spot lesions
  -  Prosthodontic or restored substrate extending on the labial surface of maxillary teeth
  -  Known allergies to any acrylates contained in the study materials

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

Clinical trial: Continuous And Pulsed Ultrasound Treatments On Carpal Tunnel Syndrome

Summary: The aim of this placebo-controlled study was to evaluate the effects of pulsed and continuous ultrasound treatments combined with splint therapy on patients with mild and moderate idiopathic carpal tunnel syndrome

Detailed description: The study included 36 carpal tunnel syndrome patients who were randomly divided into 3 groups.The first group received 0 W/cm2 placebo ultrasound treatment. second group received 1.0 W/cm2 continuous ultrasound treatment and the third group received 1.0 W/cm2 1:4 pulsed ultrasound treatment 5 days a week for a total of 15 sessions. All patients were also treated with night splints during the treatment. Pretreatment and posttreatment Visual Analogue Scale scores, Symptom Severity Scale scores, Functional Status Scale scores, median nerve motor conduction velocity. and distal latency and sensory conduction velocity of median nerve in the 2nd finger and palm were compared.

Eligibility: Inclusion Criteria:
  -  Mild or moderate idiopathic carpal tunnel syndrome (without thenar atrophy or spontaneous activity on electrophysiological examination of the abductor pollicis brevis (APB) muscle)
  Exclusion Criteria:
  -  Secondary entrapment neuropathies
  -  Cervical radiculopathy
  -  Systemic diseases with increased risk of the carpal tunnel syndrome
  -  Gained surgical relief of the syndrome
  -  Treated with ultrasound for the syndrome
  -  A history of steroid injections into the carpal tunnel and of physical therapy within the last 3 months
  -  Patients with either thenar atrophy or spontaneous activity (fibrillation potentials and positive sharp waves) on electrophysiological examination

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

Clinical trial: Natural History and Biological Study of Netherton Syndrome

Summary: This study aims at studying the natural history of Netherton syndrome (NS), to identify the consequences of LEKTI deficiency on the immune system and to characterize new molecular mechanisms involved in the disease.


Eligibility: Inclusion Criteria:
  -  Adult or child (no age limit)
  -  Confirmed diagnosis of Netherton syndrome
  -  Signed informed consent form for the patient or his legal representative
  Exclusion Criteria:
  -  Bleeding disorder precluding skin biopsy

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

Clinical trial: Comparative Study Between Duct to Mucosa and Invagination Pancreaticojejunostomy After Pancreaticoduodenectomy:

Summary: Postoperative pancreatic fistula (POPF) remains a challenge even at specialized centers, and also affect significantly the surgical outcomes . The incidence of POPF after pancreaticoduodenectomy among different studies, ranging from 5 to 30%.Morbidity and mortality after pancreaticoduodenectomy are usually related to surgical management of the pancreatic stump. The safe pancreatic reconstruction after pancreaticoduodenectomy continues to be a challenge at high volume centers. The variety of reconstruction is a reflection of the lack of ideal one.Duct to mucosa and invagination are two classic PJ techniques. Many studies compared both techniques, but their surgical outcomes still unclear.The aim of the study was to assess the effectiveness and surgical outcomes of both techniques of PJ after pancreaticoduodenectomy.

Detailed description: Consecutive patients who were treated by pancreaticoduodenectomy at Gastroenterology Surgical Center, Mansoura, Egypt Exclusion criteria included any patients with locally advanced periampullary tumour, metastases, patients received neoadjuvant chemoradiotherapy, patients underwent pancreaticogastrostomy (PG), patients with advanced liver cirrhosis (Child B or C), malnutrition, or coagulopathy.
  All patients were subjected to careful history taking, clinical examination, routine laboratory investigation abdominal ultrasound, magnetic resonance cholangiopancreatography , and abdominal computerized tomography .
  The patients were randomized into two groups: Group I: patients underwent duct to mucosa PJ. Group II: patients underwent invagination PJ.
  The primary outcome was POPF rate.Secondary outcomes were operative time, operative time needed for reconstruction, length of postoperative hospital stay, postoperative morbidities

Eligibility: Inclusion Criteria:
  -Consecutive patients who were treated by pancreaticoduodenectomy
  Exclusion Criteria:
  -  Any patients with locally advanced periampullary tumour, metastases
  -  Patients received neoadjuvant chemoradiotherapy
  -  Patients underwent pancreaticogastrostomy (PG)
  -  Patients with advanced liver cirrhosis (Child B or C)
  -  Malnutrition
  -  Coagulopathy

Relevance to patient case: not relevant