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

Clinical trial: Study of Accurate Diagnosis and Treatment of Peutz-Jeghers Syndrome

Summary: The mutation of STK11 has been regcognized to be the major cause of Peutz-Jeghers syndrome (PJS).The aim of this study was to confirm the mutation rate of gene associated with gastrointestinal malignancies,including STK11, APC,PMS1,et al. Furtherly, the investigators analyze the association of STK11 with gut microbiota.

Detailed description: All patients diagnosed as PJS were enrolled and accepted second generation gene sequencing with their blood specimens. Then all patients allocated into gene mutation group and no gene mutation group according to if the cases accompany with gene mutation of STK11.Also, health persons were enrolled and a case controlled study will be carried out.All patients and health persons accepted 16s rRNA sequencing with their feces specimens.

Eligibility: Inclusion Criteria:
  1. Subject with ages from 18-70 years old.
  2. Subject diagnosed with Peutz-Jeughers syndrome.
  3. Subject without hypertension, diabetes and other gastrointestinal diseases.
  4. The consent form has been signed.
  Exclusion Criteria:
  1. Subject is younger than 18 years or older than 70 years.
  2. Subject with hypertension,diabetes and other gastrointestinal diseases.
  3. Subject taken or adminstered medicine associated with digestive function during latest 1 month.
  4. Pregnant women.

Relevance to patient case: definitely relevant
Patient case: 11-year-old male with Peutz-Jeghers syndrome; genetic feature: STK11

Clinical trial: Blood and Stool Sample Collection in Subjects Participating in Colorectal Cancer Screening: Act Bold

Summary: The primary objective of this study is to collect de-identified, clinically-characterized stool and whole blood specimens for use in developing and evaluating the performance of new biomarker assays for detection of colorectal cancer (CRC).

Detailed description: Subjects will be men and women, 40 years of age or older who are scheduled for a colonoscopy. Approximately 3,000 subjects will be enrolled.

Eligibility: Inclusion Criteria:
  -  Subject is male or female, 40 years of age or older.
  -  Subject is at average or increased risk for development of CRC.
  -  Subject presents for screening or surveillance colonoscopy.
  -  Subject has no symptoms that require immediate, or near term, referral for diagnostic or therapeutic colonoscopy.
  -  Subject understands the study procedures and is able to provide informed consent to participate in the study and authorization for release of relevant protected health information to the study Investigator.
  Exclusion Criteria:
  -  Any previous cancer diagnosis (with the exceptions of basal cell or squamous cell skin cancers) and/or cancer related treatment (e.g. chemotherapy, immunotherapy, radiation, and/or surgery) within the past 5 years.
  -  Subject has a diagnosis or personal history of any of the following conditions, including:
  1. Familial adenomatous polyposis (also referred to as "FAP", including attenuated FAP and Gardner's syndrome).
  2. Hereditary non-polyposis CRC syndrome (also referred to as "HNPCC" or "Lynch Syndrome").
  3. Other hereditary cancer syndromes including but are not limited to Peutz-Jeghers Syndrome, MYH-Associated Polyposis (MAP), Turcot's (or Crail's) Syndrome, Cowden's Syndrome, Juvenile Polyposis, Neurofibromatosis and Familial Hyperplastic Polyposis.
  -  Subject has a family history of:
  1. Familial adenomatous polyposis (also referred to as "FAP").
  2. Hereditary non-polyposis CRC syndrome (also referred to as "HNPCC" or "Lynch Syndrome").
  -  Subjects with Cronkhite-Canada Syndrome.
  -  IV contrast (e.g. CT and MRI) within 1 day [or 24 hours] of blood collection.
  -  Subject has any condition that in the opinion of the Investigator should preclude participation in the study

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

Clinical trial: Efficiency of Everolimus for the Treatment of Kidney Transplanted Patients Presenting a Missing Self-induced NK-mediated Rejection

Summary: Background:
  Long-term success of organ transplantation is limited by the inexorable loss of graft function due to rejection. Prevalent dogma defends that allograft rejection is exclusively mediated by the adaptive immune system: T cells are responsible for cellular rejections and B cells producing donor specific antibodies (DSA) are responsible for humoral rejection. Recently, we demonstrated that innate NK cells could be implicated in the generation of chronic vascular rejections lesions by sensing the absence of expression of self Major Histocompatibility Complex (MHC) class I molecules ("missing self") on graft endothelial cells with their Killer cell immunoglobulin-like (KIR) receptors. Using human in vitro and murine in vivo models, we also showed that Mammalian Target Of Rapamycin (mTOR) inhibitors could efficiently prevent this new kind of rejection.
  Objective:
  The aim of our project is therefore to test in a cohort of kidney transplanted patients the efficiency of mTOR inhibitors to treat this new kind of rejection
  Methods:
  A cohort of 20 kidney transplant patients with a missing self on their graft responsible for a NK-mediated rejection will be established prospectively. An mTOR inhibitor will be introduced in these patients for 6 months in association with a calcineurin inhibitor and corticosteroids. Graft function, histological lesions and NK activability will be monitored following this modification of treatment.


Eligibility: Inclusion Criteria:
  -  Patient aged > 18 years
  -  Kidney transplanted patient
  -  Having microvascular inflammation lesion on his graft biopsy associated to mild chronic lesions
  -  In absence of donor specific antibodies
  -  In presence of a missing self
  Exclusion Criteria:
  -  Proteinuria/creatininuria > 100 mg/mmol
  -  Antecedent of poor tolerance or hypersensibility to everolimus or sirolimus
  -  Severe chronic lesions
  -  Presence of donor specific antibodies

Relevance to patient case: not relevant
Patient case: 19-year-old female with long QT syndrome; genetic feature: KCNH2

Clinical trial: Epidemiology of Long QTand Asian Sudden Death in Sleep

Summary: To conduct a cross-sectional epidemiologic study of the determinants of prolonged heart rate corrected QT interval (QTc) among 300 men and 300 woman in the population with the highest known risk of SUDS: Southeast Asian refugees in Thailand. .

Detailed description: BACKGROUND:
  Sudden and unexplained death in sleep (SUDS) is a leading cause of death of young men in several Asian populations. The immediate cause is ventricular fibrillation in the absence of known disease. A strong environmental component may be inferred from the regional nature of SUDS in groups that are culturally and genetically distinct and the rapid decline in rates of SUDS after migration of Southeast (SE) Asian refugees to the United States. Risk of SUDS rises sharply to a peak among men aged 35 years of age, then declines with increasing age. In a pilot studies of SE Asian refugee men in Thailand with the highest known risk of SUDS, the investigators documented high-prevalences of prolonged heart rate corrected QT interval (QTc), thiamine deficiency, hypokalemia, and a positive association between poor thiamine status, measured by erythrocyte transketolase activity (ETK), and QTc. These limited studies were unable to precisely quantify the relationship between QTc and thiamine status, lacked sufficient power to examine the relationship between QTc and hypokalemia, did not include other electrolytes, and did not address the striking differences in risk of SUDS by sex and age.
  DESIGN NARRATIVE:
  The study was cross-sectional in design. During a 14-month period, informed consent was obtained from subjects selected in an age-stratified random sample of refugees scheduled for routine medical screening. Blood samples, 12-lead and 24-hour ECGs, and interview data were collected to test the following hypotheses: (1) mean QTc was greater in men than women, (2) mean QTc was greater in men aged 30-39 years than in men younger or older; no similar relationship was expected among women, (3) QTc was positively correlated with poor thiamine status, measured by erythrocyte transketolase activity, (4-6) QTc was negatively correlated with serum levels of potassium, magnesium, and total calcium, and (7) QTc was associated with abnormalities of autonomic control of the heart, as indicated by power spectral analysis of heart rate variability. Secondary aims included studying interactions of thiamine status and electrolytes in the prolongation of QTc, dynamic analysis of QT variation by heart rate level in 24-hr ECGs, and collection of blood specimens for later genetic studies

Eligibility: No eligibility criteria

Relevance to patient case: not relevant
Patient case: 19-year-old female with long QT syndrome; genetic feature: KCNH2

Clinical trial: A Study of the Efficacy and Safety of ICA-17043 (With or Without Hydroxyurea) in Patients With Sickle Cell Anemia.

Summary: ICA-17043 is being developed for the chronic treatment of patients with sickle cell disease (SCD) in both adults and children. ICA-17043 is a potent and specific inhibitor of a channel in human red blood cells (RBCs) that blocks RBC dehydration. ICA-17043 is expected to inhibit RBC dehydration and thus should prevent or delay the sickling process. By reducing sickled cells, an improvement in anemia, a reduction in painful crises, and ultimately, less end-organ disease is anticipated.


Eligibility: Inclusion Criteria:
  -  Homozygous (HbSS) Sickle Cell Anemia
  -  Otherwise healthy (based on medical history, physical examination, 12-lead ECG, and clinical laboratory tests)
  -  Patients may be receiving hydroxyurea, but must have been dose stabilized for at least 3 months
  -  Patient has a history of at least one acute vaso-occlusive event requiring hospitalization
  Exclusion Criteria:
  -  Patient participating in a chronic transfusion program
  -  Patient having a total hemoglobin of < 4.0 g/dL or > 10.0 g/dL
  -  Patient having a HbA > 10%
  -  Patient considering undergoing an elective surgery
  -  Patient taking prohibited medications such as Epoetin, Warfarin, etc.
  -  Patient who has had previous gastrointestinal surgery, except cholecystectomy or appendectomy
  -  Patient with significant active cardiovascular, neurologic, endocrine, hepatic, or renal disorders unrelated to sickle cell anemia

Relevance to patient case: not relevant
Patient case: 19-year-old female with long QT syndrome; genetic feature: KCNH2

Clinical trial: Genetic Determinants of Sudden Cardiac Death

Summary: To evaluate whether genetic variation in selected candidate genes is associated with risk of sudden cardiac death in the general population.

Detailed description: BACKGROUND Sudden cardiac death (SCD) affects 400,000 individuals each year in the U.S. alone. Over half have no evidence of heart disease prior to death, and our ability to identify those at risk and, therefore prevent SCD, is poor. Mutations in cardiac ion channel genes including SCN5A, KCNQ1, KCNH2, KCNE1, KCNE2 and RyR2 have been implicated in monogenic traits with high risk of SCD, such as the long-QT, Brugada, sudden infant death syndrome (SIDS), and catecholaminergic polymorphic ventricular tachycardia. Alterations in ion channel function can result in life-threatening ventricular arrhythmias in diverse disease states. Therefore, sequence variants in these genes that alter function or transcription of these ion channels may confer a predisposition to ventricular arrhythmia and SCD in broader populations.
  DESIGN NARRATIVE This research program proposes to determine if sequence variants in the above and other candidate genes are associated with an increased risk of SCD in apparently-healthy populations. Cases of SCD will be assembled from 5 NIH-funded prospective cohorts with a total of 106,314 individuals with existent blood samples. All cohorts are exceptionally well-characterized with respect to environmental exposures and have collected medical records on cardiovascular endpoints. We will characterize all coding sequence variation and selected non-coding sequence variation among 100 cases and controls from these cohorts for the 6 genes. We will then employ a nested case-control design and conditional logistic regression to test for associations between haplotypes (haplotype tag SNPs) in both coding and non-coding regions of candidate genes and SCD risk. We will also test directly for associations between single loci that may have functional significance and SCD risk. An estimated 600 cases of well-documented SCD will be confirmed over the first 3 years of the grant period, and these cases will be matched on age, sex, ethnicity, and geographic location to two control subjects from the same cohort. In addition, based upon known sex difference in the phenotypic expression of the candidate genes in the primary arrhythmic disorders, we will specifically examine sex difference in the risk of SCD associated with sequence variation in these genes. The findings generated will have substantial implications for our understanding of the SCD syndrome and risk stratification in the general population.

Eligibility: No eligibility criteria.

Relevance to patient case: not relevant
Patient case: 19-year-old female with long QT syndrome; genetic feature: KCNH2

Clinical trial: Cohorts and Collections: Clinical and Genetic Study of Parkinson's Disease and Epilepsies

Summary: The DNA and Cell Bank of Instituts Federatifs de Recherche (IFR) of Neurosciences has been running for the last 15 years at the Institut National de la Santé Et de la Recherche Médicale (INSERM) Unit 679 (former unit 289). Since its creation, this structure has been the support of research projects in genetics for neurological and psychiatric disorders. The cohorts established have led to discoveries in monogenic disorders, such as cerebellar ataxias, spastic paraplegias, frontotemporal dementias, epilepsies, Parkinson’s and Alzheimer’s disease, Charcot-Marie-Tooth disease and related entities. The research projects based on the study of the genetic bases in Parkinson’s disease and epilepsies are especially developed for this grant.
  Concerning Parkinson’s disease, the project is based on the extension of the existing cohort throughout the French Parkinson’s Disease Study Group network. Concerning epilepsies, this project is the occasion to build this network with the constitution of a new cohort.
  The specific aims of the scientific projects are the following for Parkinson’s disease:
  -  to evaluate the frequency, the nature and the phenotype associated with parkin mutations in familial or sporadic forms of the disease, according to the age at onset, and
  -  to identify the genetic susceptibility factors in Parkinson’s disease with the study of affected sibpairs and with case/controls association studies.
  For epilepsies, the aims are:
  -  to evaluate the frequency, the nature and the phenotype associated with SCN1A, SCNab and GABR2 gene mutations in familial or sporadic forms of the affection associated with febrile seizures, and
  -  to search for an intervention SCN1A, SCN1B and GABRG2 as susceptible genes in these forms of epilepsies.


Eligibility: Inclusion Criteria:
  -  Patients presenting with Parkinson's disease, with a family history or not,
  -  Minors presenting clinical signs of the disease,
  -  Controls (without signs of the disease), matched by sex and age with the patients,
  -  Relatives for the familial cases,
  -  Patients presenting with an epilepsy episode (myoclonic epilepsy of the newborn, with febrile seizures, of the frontal lobe)
  Exclusion Criteria:
  -  Lack of signed informed consent

Relevance to patient case: not relevant
Patient case: 19-year-old female with long QT syndrome; genetic feature: KCNH2

Clinical trial: WT1 for the Detection of Minimal Residual Disease

Summary: The purpose of this study is to determine if WT1 is an adequate measurement of minimal residual disease in leukemic patients.

Detailed description: Patients with acute Leukemia may have a large number of leukemic cells at the time that leukemia is evident clinically. At the time that we determine that a patient is in complete remission (CR) the patient may still have leukemic cells present in smaller quantities. One of the most important factors in the successful treatment of patients with leukemia is the ability to determine if the eradication of leukemia has been achieved. The determination of Minimal Residual Disease may be important in the determination of the therapy that a given patient will receive as determined by the level of residual disease.
  WT1 gene function and expression. The WT1 gene is a candidate gene for Wilms tumor, which is thought to arise as a result from inactivation of both alleles of the WT1 gene located at chromosome 11p13. The WT1 gene has been considered a tumor suppressor gene because intragenic deletions or mutations are found in tumors, germline mutations have been found in-patients with leukemia, and mediates growth suppression of Wilms tumor cells expressing a WT1 splicing variant.

Eligibility: Inclusion Criteria:
  -  Age less than 21 years of age.
  -  Patients with the following diseases: Acute lymphoblastic Leukemia (ALL) at the time of diagnoses or relapse, Acute non-lymphoblastic leukemia (ANLL) at diagnosis or after relapse and Chronic Myelogenous leukemia in chronic or accelerated phase.
  -  Patients will be eligible for any of the available treatment protocols or protocols for stem cell transplantation, regardless of the source of stem cells.
  -  Patients or legal guardians will sign an Institutional Review Board (IRB) approved informed consent.
  -  Patients will have venous access or peripheral vein for sampling.

Relevance to patient case: not relevant
Patient case: 19-year-old female with long QT syndrome; genetic feature: KCNH2

Clinical trial: Long-Term, Open Label Atomoxetine Study

Summary: To learn about the safety and any side effects of atomoxetine when given to children and adolescents for about 5 years (long-term) and to learn whether atomoxetine can help children and adolescents with attention-deficit/hyperactivity disorder (ADHD) who take the drug for about 5 years (long-term).
  Study participants can be atomoxetine naive, atomoxetine experienced whose therapy has been interrupted or, atomoxetine experienced on a known stable dose.


Eligibility: Inclusion Criteria:
  -  Must be at least 6 years old but less than 18 years old when enrolled in first atomoxetine study
  -  Must meet the study criteria for ADHD
  -  Must be willing to have blood drawn and to complete other test required for this study
  Exclusion Criteria:
  -  allergic to more than 1 kind of medicine or have had multiple bad reactions to any drug
  -  taking certain medicines that could interact with atomoxetine
  -  plan to move too far away from a doctor participating in this study in the next 5 years
  -  current or past history of any of the following: alcohol or drug abuse within the past 3 months, bipolar I or II disorder, high blood pressure, organic brain disease or seizures, psychosis, other disorders or conditions diagnosed by a doctor that might make you unsuitable to participate in this study

Relevance to patient case: not relevant
Patient case: 19-year-old female with long QT syndrome; genetic feature: KCNH2

Clinical trial: Molecular Genetic Screening and Identification of Congenital Arrhythmogenic Diseases

Summary: The aim of this study is the identification of familial congenital arrhythmogenic disorders and their clinical follow-up.

Detailed description: Molecular genetic screening in patients with:
  -  supraventricular
  -  ventricular arrhythmia
  -  syncopes of unknown origin and/or suspicion of an arrhythmogenic origin
  -  family members of patients with sudden cardiac death and aborted sudden cardiac death
  Examination of patients includes routine testing like electrocardiogram (ECG), sequential ECGs, exercise testing, invasive electrophysiological stimulation, cardiac magnetic resonance imaging, intravenous drug challenge for identification/exclusion of eg Brugada syndrome. Examples are patients with Long QT Syndrome, Short QT Syndrome, Brugada Syndrome, familial atrial fibrillation, WPW-syndrome, arrhythmias due to familial hypertrophic cardiomyopathy or arrhythmogenic right ventricular dysplasia. Blood samples are taken for further molecular genetic screening.

Eligibility: Inclusion Criteria:
  -  Patients with a history of syncope, abnormal ECG and suspicion of an arrhythmogenic disease
  -  Patients with long QT syndrome
  -  Patients with short QT syndrome, shortened QT intervals, borderline shortened QT intervals
  -  Patients with Brugada syndrome
  -  Patients with hypertrophic cardiomyopathy
  -  Patients with arrhythmogenic right ventricular dysplasia
  Exclusion Criteria:
  -  Inability to understand study protocol

Relevance to patient case: not relevant
Patient case: 19-year-old female with long QT syndrome; genetic feature: KCNH2

Clinical trial: Effect of Domperidone on QT Interval in Premature Infants

Summary: 30 premature infants treated by domperidone upon decision of the attending neonatologist will have a daily recording of electrocardiogram for the first 7 seven days of treatment, and pharmacokinetics dosages at Day 7. Their ECG will be compared to 30 non treated premature infants, matched for gestational age, postnatal age and sex.


Eligibility: Inclusion Criteria:
  Gestational age less than 36 weeksPostnatal age greater than 10 days Treated / not treated by domperidone (case/control)Signed parental informed consent
  Exclusion Criteria:
  Severe cardiac arrhythmia Congenital heart disease (persistent ductus arteriosus excluded)Familial history of congenital long QT syndrome

Relevance to patient case: not relevant
Patient case: 19-year-old female with long QT syndrome; genetic feature: KCNH2

Clinical trial: Fosamprenavir Expanded Access

Summary: This open-label study will enable HIV-infected adults with limited treatment options to receive fosamprenavir until commercial supplies are available in Switzerland.


Eligibility: Inclusion Criteria:
  -  HIV-1 infected subjects.
  -  Subjects must belong to one of the following populations:
  1. Subjects with limited treatment options due to viral resistance, interactions, or tolerability issues with other antiretroviral drugs.
  2. Subjects who already receive amprenavir (Agenerase®)
  3. Subjects for whom once daily dosing of antiretroviral therapy is indicated, including, once daily dosing with fosamprenavir/ritonavir.

Relevance to patient case: not relevant