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

Clinical trial: DNA Tests in Detecting Disseminated Disease in Tumor, Blood, and Bone Marrow Samples From Patients With Rhabdomyosarcoma

Summary: RATIONALE: DNA analysis of tumor, blood, and bone marrow may help doctors predict if the disease has been disseminated.
  PURPOSE: This research trial studies DNA tests in detecting disseminated disease in tumor, blood, and bone marrow samples from patients with rhabdomyosarcoma.

Detailed description: OBJECTIVES:
  -  To establish a panel of hypermethylation assays for minimal disseminated disease analysis in rhabdomyosarcoma (RMS).
  -  To apply the hypermethylation assays to a series of bone marrow specimens from RMS patients.
  OUTLINE: Archived tumor, bone marrow, and peripheral blood samples are analyzed for DNA hypermethylation by PCR-based assays and microarray assays. Results are then compared with each patient's clinical and pathological characteristics, and outcomes. Patterns of locus hypermethylation in tumor and paired bone marrow samples are also compared.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosed with rhabdomyosarcoma (RMS)
  -  Tumor, bone marrow, and peripheral blood samples from the Children's Oncology Group D9803 trial of intermediate-risk RMS
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

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

Clinical trial: Characterization of Pulmonary Artery Stenoses in Alagille Syndrome - a Medical Record Review

Summary: Patients who have Alagille Syndrome (AGS) also frequently have blockages (or "stenoses") of their pulmonary arteries. Little is known about the degree or variability of these stenoses, or the effect of this disease on the right ventricle (the chamber of the heart which pumps blood to the lungs). This study will first quantify and describe pulmonary artery stenosis in patients with Alagille Syndrome. The study will also assess the effect of these stenoses on the right ventricle. The investigators hope to learn the degree and characteristics of pulmonary artery stenosis in Alagille Syndrome. The investigators also hope to learn the effect of this pulmonary artery stenosis on the right ventricle in patients with Alagille Syndrome. This information is critical in the management of patients with Alagille syndrome, as there is currently no data to guide clinicians on the management of pulmonary artery stenosis. Furthermore, the information from this study may help physicians manage pulmonary artery stenosis in other patients as well.

Detailed description: The investigators hope to learn the degree and characteristics of pulmonary artery stenosis in Alagille Syndrome. We also hope to learn the effect of this pulmonary artery stenosis on the right ventricle in patients with Alagille Syndrome. This information is critical in the management of patients with Alagille syndrome, as there is currently no data to guide clinicians on the management of pulmonary artery stenosis. Furthermore, the information from this study may help physicians manage pulmonary artery stenosis in other patients as well. For the third aim, we hope to learn about the different blood vessel abnormalities in the brain, and which abnormalities are most likely to lead to stroke.

Eligibility: Inclusion Criteria:
  -  Diagnosis of Alagille 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: cKIT, BRAF/NRAS Mutations in Advanced Melanoma : Clinical Outcome in Response to Tyrosine-kinase Inhibitors - KitMel Project

Summary: Background: Metastatic melanoma has a devastating prognosis and is one of the top causes of cancer death in young patients. Until now, available therapies were few and unreliable, but recent understanding of melanomas' molecular pathways has improve their classification and new clinical strategies have been proposed.
  Initial studies showed that B-Raf/N-Ras mutations (respectively V600E and Q61) are the most frequent alteration being present in 70 to 80% of melanomas, characterizing non Chronic Sun-induced Damage skins (CSD). These include Superficial Spreading Melanomas (SSM) and Nodular Melanomas (NM). Other studies showed that c-Kit mutations are presently the predominant activating mutation (20 - 40 %) in Acro-Lentiginous Melanomas (ALM), Mucous Melanomas (MM) and in melanomas arising on CSD skin. c-Kit mutation pattern is more complex with four exons being affected leading to different mutations, which incidence and biological impact are less documented.
  BRAF/NRAS genetics alterations drive constantly cell growth, being thus attractive targets. Spectacular results have indeed been obtained with the BRAF inhibitor that targets the V600E BRAF-mutated form. Data from GIST disease revealed that the different c-Kit mutations modulate differently c-Kit function and the response to targeted therapies.
  Because c-Kit targeted therapy is a critical clinical issue, the investigators aimed to identify the most frequent mutations present in our population to propose appropriate screening test and adapt the therapy.
  Methods: 250 melanoma samples corresponding to an homogeneous white-Caucasian population (Brittany, France) will be screened. c-Kit exons 11, 13, 17 and 18 will be sequenced (direct sequencing and pyrosequencing when possible). c-Kit copy number will be quantified by q-PCR and level of c-Kit determined by immunohistochemistry (IHC, CD117). Samples will also be analyzed for B-Raf mutations in codon 464, 466, 469 and 600, and for N-Ras mutations in codon 12, 13 and 61 (Pyrosequencing).
  Expected Results:
  Taken together, the investigators anticipate that the present genetic analysis of the tumours from patients with advanced melanoma will first document the type and frequency of cKit mutations, will confirm or not that BRAF, NRAS and cKit mutations are mutually exclusive and document their repartition in the melanomas sub-types. Finally this study will clue researchers in to how well patients will respond to a therapy that targets the growth-promoting proteins BRAF/NRAS and cKIT.


Eligibility: Inclusion Criteria:
  -  melanoma
  -  white caucasian population

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

Clinical trial: Study of CMAB009 to Treat KRAS Wild Type Metastatic Colorectal Cancer

Summary: The primary purpose of this study is to evaluate the clinical response and safety of CMAB009 plus irinotecan versus irinotecan-only as second-line treatment after fluoropyrimidine and oxaliplatin failure in KRAS wild-type metastatic colorectal cancer patients

Detailed description: CMAB009 is a recombinant, human/mouse chimeric monoclonal antibody (mAb) that binds specifically to the extracellular domain of EGFR. It is composed of the Fv regions of a murine anti-EGFR antibody with human IgG1 heavy and k light chain constant regions and it is expressed by Chinese hamster ovary cells. It has the same amino acid sequence as cetuximab (C225, Erbitux®) , but it has slightly different abilities for glycosylation and other post-translational modifications, and it is developed by Shanghai Zhangjiang Biotechnology Limited Company and produced by Biomabs. Phase I study results suggest that CMAB009 showed well-tolerated safety profile and primary efficacy. This multicenter, open-label study was to determine whether adding CMAB009 to irinotecan increased the response rate and prolongs survival in patients with KRAS wild-type metastatic colorectal cancer (mCRC) previously treated with fluoropyrimidine and oxaliplatin.

Eligibility: Inclusion Criteria:
  -  histologically confirmed metastatic colorectal adenocarcinoma
  -  KRAS wild-type tumors, EGFR-expressing or EGFR-nonexpressing by immunohistochemistry;
  -  has measurable lesion, at least 1cm in diametre by CT or MRI, at least 2cm diametre by physical examination or other iconography
  -  ECOG performance status 0 to 1
  -  Failure (disease progression/discontinuation due to toxicity) of fluoropyrimidine and oxaliplatin treatment,stop at least one month thereafter, irinotecan-naïve
  Exclusion Criteria:
  -  Previous irinotecan or anti-EGFR therapies
  -  hematologic function: hemoglobin, less than 90g per liter; neutrophil count, less than 1500 per cubic millimeter; and platelet count, less than 100,000 per cubic millimeter
  -  liver function: bilirubin, more than 1.0 times the upper limit of normal; aspartate aminotransferase and alanine aminotransferase, more than 5.0 times and 2.5 times the upper limit of normal with hepatic metastasis or not
  -  Renal function: serum creatinine, more than 1.5 times the upper limit of normal
  -  Patients with symptomatic central nervous system metastases

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

Clinical trial: INSIGHT (Insight Into Nephrotic Syndrome)

Summary: INSIGHT is a longitudinal study of childhood nephrotic syndrome to determine genetic, serologic and environmental factors contributing to nephrotic syndrome and disease progression.

Detailed description: INSIGHT is a longitudinal observational study of childhood nephrotic syndrome to determine genetic, serologic and environmental factors contributing to nephrotic syndrome and disease progression. This is a large multiethnic cohort to test hypotheses of gene and environmental risk factors and disease progression. Participants are recruited from Toronto, Ontario and surrounding regions. Additional sites will be added on in the future.

Eligibility: Inclusion Criteria:
  1. diagnosis of nephrotic syndrome
  2. signed informed consent and assent appropriate for age
  3. ages 1-18 years old and
  4. ability to complete questionnaires
  Exclusion Criteria:
  1. congenital nephrotic syndrome (less than age 1)
  2. syndromic disease with multiple organ involvement
  3. inability to provide consent by primary care providers
  4. conditions such as systemic lupus erythematous.

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

Clinical trial: Factors of Steroid Dependency in Idiopathic Nephrotic Syndrome

Summary: The primary purpose of the study is to identify the factors of steroid dependency in childhood idiopathic nephrotic syndrome. The steroid dependency is defined by a relapse of nephrotic syndrome within the 3 weeks that follow the withdrawal of steroid therapy after the first manifestation. Different clinical and biological factors will be analyzed: age of first manifestation, delay of remission, ethnicity, and preceding viral infection, geolocalization in the Parisian area, genoprevalence of herpes viruses and polymorphisms in the genes involved in the response to steroid therapy.

Detailed description: Patients with a steroid dependent nephrotic syndrome will be compared to those with a non steroid dependent form of nephrotic syndrome at the end of the first manifestation. An additional blood volume will be sampled in patients and controls during a scheduled biological check-up for the initial disease. Genetics factors will be checked using a DNA chips devoted to the response to steroid therapy and viral genome of EBV, CMV, HHV7 will be searched for using PCR reaction in total blood DNA extract.

Eligibility: Inclusion Criteria:
  -  children below 16 years
  -  first manifestation of nephrotic syndrome
  -  steroid sensitivity according to the recommendations of the french "pediatric society nephrology"
  Exclusion Criteria:
  -  patients who don't stay in Paris during the study

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

Clinical trial: Infliximab IBD Influenza Vaccine Study

Summary: The investigators will compare the immunogenicity of influenza vaccine in adults and children with inflammatory bowel disease by timing of vaccine in relation to maintenance infliximab dosing. The primary objective is to compare the proportion of IBD patients on maintenance infliximab who mount serologic protection to each component of the influenza vaccination between patients vaccinated on day of infliximab infusion (Day 0 to 4) and patients vaccinated at the mid-point between infliximab infusions (Day 21 to 28). Serologic protection will be defined by a hemagglutination-inhibition titer ≥ 1:40. The secondary objective is to compare the proportion of IBD patients who mount an immunogenic response (≥ 4-fold increase from pre to post-vaccination titer) to each component of the influenza vaccination between patients vaccinated on day of infliximab infusion and those vaccinated at the mid-point.


Eligibility: Inclusion Criteria:
  -  Diagnosis of IBD established by accepted criteria
  -  On maintenance infliximab administered every 6 to 8 weeks (already received at least 6 weeks of infliximab)
  -  Between ages 9 and 60 years
  Exclusion Criteria:
  1. Pregnancy
  2. Hypersensitivity reaction to previous dose of influenza vaccine
  3. Known hypersensitivity to eggs or chicken or other components of influenza vaccine

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

Clinical trial: Haemolytic Uraemic Syndrome in Childhood: Clinical, Cognitive and Psychological Aspects

Summary: The purpose of this study is to investigate the clinical, cognitive outcome and psychosocial outcome of haemolytic uraemic syndrome in childhood.
  The haemolytic uraemic syndrome (HUS) is the leading cause of acute renal failure in childhood. The more common typical HUS is mostly caused by Shigatoxin-producing enterohaemorrhagic Escherichia coli (EHEC). The rarer atypical HUS is mainly caused by different genetic abnormalities in complement regulatory proteins.
  About 50 till 60 percent of all patients with HUS develop a severe acute renal failure and require dialysis. Resulting from new diagnostic and therapeutic approaches the survival rate increased during the last years. Despite this, there are only few data concerning long-term prognosis, cognitive and motoric development, as well as psychological coping and health-related quality of life of affected children and their parents.

Detailed description: The main purposes of this study are: the evaluation of the long-term renal function of pediatric HUS-patients; the evaluation of the dialysis method in the acute phase of the disease and its impact on the duration of the renal-placement-therapy, as well as the long-term renal function; the evaluation of the intellectual and motoric performance of affected children and the evaluation of the health-related quality of life and psychological processing of the patients themselves and their parents.
  All cases of HUS treated at the University Children`s Hospital Zurich between 1995 and 2012 will be analyzed retrospectively. In the course of a routine-follow-up-examination the clinical data of patients up to the age of 17 years will be actualized and completed. The results of clinical and paraclinical investigations related to renal function will be evaluated to describe the clinical features of haemolytic uraemic syndrome in childhood.
  Intellectual performance will be analyzed with the Wechsler-Intelligence Scale for Children-IV (WISC-IV) and motoric performance with the Zurich Neuromotor Assessment in children at the age from 6 to 16 years.
  The health-related quality-of-life of all parents and affected children from the age of 7 years will be assessed by different generic quality-of-life-instruments.

Eligibility: Inclusion Criteria:
  -  children and youth from 2 months to 17 years who had suffered from haemolytic uraemic syndrome
  -  willingness and ability to participate in the study
  -  freely signed informed consent
  Exclusion Criteria:
  -  missing written informed consent
  -  children who do not fulfil the age criterion

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

Clinical trial: Assess the Risk of Solid Organ Transplant Rejection Following Vaccination With Pandemrix™ in UK

Summary: This study aims to assess the risk of solid organ transplant (SOT) rejection following vaccination with Pandemrix™ and/ or seasonal influenza vaccination.

Detailed description: Data on the safety of pandemic H1N1 vaccination in transplanted patients is relatively limited; to date, although some studies showed transient increases in alloreactivity, there is no evidence that H1N1 vaccines caused clinical rejection or organ dysfunction. In addition, studies have shown that influenza infection is a known independent risk factors for rejection. Considering that transplant recipients are a target population for immunisation with future pandemic vaccines, it is important to investigate the risk of rejection following vaccination in this patient population.
  Using the self-controlled case series design that allows to control implicitly for potential confounding factors, this study aims at investigating the risk of solid organ transplant rejection (liver, kidney, lung, heart, pancreas) following vaccination with Pandemrix™ in the United Kingdom Clinical Practice Research Datalink GP Online Database (CPRD GOLD). Data from the Hospital Episodes Statistics database will also be used. The effect of seasonal influenza vaccination and of various infections including influenza H1N1 will also be explored.

Eligibility: Inclusion Criteria:
  -  Subject defined as acceptable in the CPRD GOLD.
  -  Subject with at least one solid organ transplant rejection reported in the CPRD GOLD and/or HES during the overall study periods (01 September 2006 to 31 October 2010).
  Exclusion Criteria:
  • Subject from HES matched to more than one subject in the CPRD GOLD.

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

Clinical trial: MEVALONATE KINASE GENE MUTATIONS AND THEIR CLINICAL CORRELATIONS IN BEHÇET'S DISEASE

Summary: Background: Genetics is suggested to play a critical role in the development of Behçet's disease (BD). Shared phenotypic features requires an approach to the differential diagnosis from periodic febrile syndromes particularly from mevalonate kinase deficiency related diseases. We planned to study for evaluating the frequency of mutations and their clinical significance in mevalonate kinase gene in Turkish patients with Behçet's disease.


Eligibility: Inclusion Criteria:
  -  Behçet patients
  Exclusion Criteria:
  -  Diagnosis of periodic fever syndromes

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

Clinical trial: Rare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford

Summary: CoRDS, or the Coordination of Rare Diseases at Sanford, is based at Sanford Research in Sioux Falls, South Dakota. It provides researchers with a centralized, international patient registry for all rare diseases. This program allows patients and researchers to connect as easily as possible to help advance treatments and cures for rare diseases. The CoRDS team works with patient advocacy groups, individuals and researchers to help in the advancement of research in over 7,000 rare diseases. The registry is free for patients to enroll and researchers to access. Visit sanfordresearch.org/CoRDS to enroll.

Detailed description: CoRDS collects contact, sociodemographic and health information about participants. This information is entered into CoRDS and linked to a unique coded identifier. Below are some examples of information requested on the Questionnaire that will be entered into CoRDS:
  -  Contact information: Name, Mailing Address, Phone Number, Email Address
  -  Sociodemographic information: Date of Birth, Place of Birth, Sex, Gender, Ethnicity
  -  Health information: Family History, Information related to Diagnosis
  De-identified information in CoRDS will be made available to researchers, if they have obtained approval for their research project from (1) the Institutional Review Board (IRB) at the researcher's institution and (2) a panel of experts.
  A subset of de-identified information collected from each profile may be shared with certain other databases. This is done in order to help improve understanding of rare diseases, to avoid the duplication of efforts and to collaborate with existing research efforts with organizations dedicated to rare diseases.
  Participants may elect to have their information shared with patient advocacy groups (PAGs) representing individuals with rare or uncommon diseases who have partnered with CoRDS. The PAG will sign an agreement stating that they will not use the information for Research purposes. CoRDS personnel will not be held responsible for the use of information by the PAG.
  The CoRDS Registry will not be paid by Researchers, Other Patient Registries or Patient Advocacy Groups (PAGs) for access to information in CoRDS.
  If a parent/LAR consents on behalf of a minor, CoRDS will contact the participant when he or she reaches the age of 18 in order to obtain consent. If this consent is not obtained in a timely manner, the participant will be withdrawn from CoRDS.
  CoRDS contacts participants annually to confirm continued interest in participation in CoRDS, and to request that participants update the information they have provided.

Eligibility: Inclusion Criteria:
  -  Diagnosis of a rare disease, a disease of unknown prevalence, undiagnosed or an unaffected carrier of a rare/uncommon disease
  Exclusion Criteria:
  -  Diagnosis of a disease which is not rare

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

Clinical trial: Haploidentical Stem Cell Transplantation and NK Cell Therapy in Patients With High-risk Solid Tumors

Summary: To evaluate feasibility and efficacy of haploidentical stem cell transplantation in patients with high-risk solid tumors who failed after tandem high-dose chemotherapy and autologous stem cell transplantation.
  To evaluate feasibility and efficacy of NK cell infusion after haploidentical stem cell transplantation in patients with high-risk solid tumors who failed after tandem high-dose chemotherapy and autologous stem cell transplantation.

Detailed description: HaploSCT following reduced-intensity conditioning (RIC) regimen will be performed in patients with high-risk solid tumors. Both parents will be evaluated for their KIR genotype and phenotype and the one with the greatest degree of KIR-L mismatch with the patient will be selected as the donor. In addition, ex-vivo expanded NK cells derived from the donor will then be administered after haploSCT to increase the GVT effect. Low-dose IL-2 will be given after expanded NK cell infusion to enhance NK cell alloreactivity.

Eligibility: Inclusion Criteria:
  -  age < 21 years old
  -  Patients with high-risk solid tumors who failed prior HDCT/autoSCT
  -  Patients with a suitable haploidentical donor
  -  High-risk solid tumors include high-risk neuroblastoma, metastatic or relapsed Ewing sarcoma, relapsed osteosarcoma, high-risk brain tumors, relapsed germ cell tumors, relapsed soft tissue sarcoma, relapsed rhabdomyosarcoma, and etc.
  -  stable disease with salvage chemotherapy after relapse
  Exclusion Criteria:
  -  organ dysfunction(NCI common toxicity criteria grade > 2)
  -  progression of disease despite salvage chemotherapy

Relevance to patient case: not relevant