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

Clinical trial: Chronic Graft-Versus-Host Disease in Patients Who Have Undergone Donor Stem Cell Transplant

Summary: RATIONALE: Studying samples of tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to chronic graft-versus-host disease in patients who have undergone donor stem cell transplant.
  PURPOSE: This phase I trial is studying chronic graft-versus-host disease in patients who have undergone donor stem cell transplant.

Detailed description: OBJECTIVES:
  -  To determine and define the biological basis of different subtypes of chronic graft-vs-host disease using a targeted single nucleotide polymorphisms approach in patients who have undergone allogeneic stem cell transplantation.
  OUTLINE: Two important aspects of the methodologies that will be employed for the analysis of SNPs associated with GVHD are throughput efficiency to be able to perform the assays on a reasonable number of samples as well as having the ability to add or remove SNPs to the assay panel. While a genome-wide association study to identify variants associated with GVHD would offer an unbiased approach, our patient cohort size would not allow significant statistical power in the study. Therefore, a more targeted approach using two established technologies is proposed.
  The Sequenome assay uses the unique combination of a single-base primer extension assay incorporating one of four modified nucleotides. The four modified nucleotides each have a unique mass that allows them to be distinguished from one another using mass spectrometry. Each SNP is determined analyzing the primer extension product from a PCR amplicon that surrounds the SNP of interest. The development of each assay involves designing flanking PCR primers and an internal extension assay using web-based software provided by Sequenome. The assays can be designed to analyze up to 30 SNPs in a single reaction, providing a customizable, efficient and high-throughput assay for SNPs of interest.

Eligibility: DISEASE CHARACTERISTICS:
  -  Underwent prior matched related or unrelated allogeneic stem cell transplantation (SCT)
  -  Presence OR absence of chronic graft-vs-host disease after day 100 and alive after day 180 post-transplantation
  -  No T-cell depleted SCT, cord blood transplantation, mismatched allogeneic transplantation, or autologous transplantation
  -  Available recipient and donor DNA (samples collected from the Vanderbilt University or the Fred Hutchinson Cancer Center tissue bank)
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

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

Clinical trial: Pilot Study of the Effects of the Desipramine on the Neurovegetative Parameters of the Child With Rett Syndrome

Summary: Rett syndrome is a neurodevelopmental disorder characterized by cognitive impairment, communication dysfunction, stereotypic movement disorder, and growth failure. Rett syndrome is caused by mutations in the Methyl CpG-Binding Protein-2 (MECP2) gene and has no treatment.
  A mouse experimental model of Rett syndrome created by genetic invalidation of the MECP2 gene is available. It had been then observed that adult MECP2-deficient mice show respiratory alterations and found that endogenous noradrenaline helps to maintain a normal respiratory rhythm. Desipramine, a selective inhibitor of norepinephrine reuptake, seems to be efficient to reduce the respiratory alteration occuring in MECP2-deficient mice (Insem patent 2005, Villard and Roux 2006).
  The aim of the study is to evaluate these obtained results in MECP2-deficient mice on patients with Rett syndrome.

Detailed description: Rett syndrome is a neurodevelopmental disorder characterized by cognitive impairment, communication dysfunction, stereotypic movement disorder, and growth failure. The diagnosis of Rett syndrome is based on consensus clinical criteria. Rett syndrome is caused by mutations in the Methyl CpG-Binding Protein-2 (MECP2) gene and has no treatment.
  Only a few improved cases have been reported concerning buspirone (Andaku, 2005, 1 patient), topiramate (Goyal, 2004, 8 patients), diazepam (Kurihara, 2001, 1 patient) and carnitin (Plochl, 2004, 1 patient).
  Only one randomized study versus placebo has been published about a treatment by naltrexone including 25 patients. A light improvement of respiratory parameters was then observed with a deterioration of the cognitive function (Percy, 2004).
  A mouse experimental model of Rett syndrome created by genetic invalidation of the MECP2 gene is available. It had been then observed that adult MECP2-deficient mice show respiratory alterations and found that endogenous noradrenaline helps to maintain a normal respiratory rhythm. Desipramine, a selective inhibitor of norepinephrine reuptake, seems to be efficient to reduce the respiratory alteration occuring in MECP2-deficient mice (Insem patent 2005, Villard and Roux 2006).
  The aim of the study is to evaluate these obtained results in MECP2-deficient mice on patients with Rett syndrome.

Eligibility: Inclusion Criteria:
  -  Rett syndrome;
  -  Girls weighing less than 60 kg;
  -  Respiratory alteration;
  -  Diagnosis of Rett syndrome confirmed by MECP2 genotyping (Xq28).
  Exclusion Criteria:
  -  Boys;
  -  Pregnancy and breath feeding;
  -  Case history of status epilepticus;
  -  Patient treated by IMAO or sultopride;
  -  Hepatic or renal failure.

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

Clinical trial: Study of Biomarkers in DNA Samples From Patients With Acute Lymphoblastic Leukemia or Acute Myeloid Leukemia

Summary: RATIONALE: Studying samples of DNA from patients with cancer in the laboratory may help doctors identify and learn more about biomarkers related to cancer.
  PURPOSE: This research study is looking at biomarkers in DNA samples from patients with acute lymphoblastic leukemia or acute myeloid leukemia.

Detailed description: OBJECTIVES:
  -  Collect DNA samples from patients with cytogenetically, well characterized, and uniformly treated acute lymphoblastic leukemia or acute myeloid leukemia for use in analysis of a wide range of host factors influencing etiology and outcome of the disease.
  -  Identify host factors that can be determined at onset of treatment to predict outcome of chemotherapy, and thus modify the therapy administered.
  OUTLINE: Previously collected DNA samples are analyzed for polymorphisms at a variety of loci. Gene expression and expression profiles are correlated with genotype and therapy outcomes.

Eligibility: DISEASE CHARACTERISTICS:
  -  DNA samples available from patients meeting the following criteria:
  -  Infants with acute lymphoblastic leukemia (ALL) or acute myeloid leukemia (AML)
  -  Patients with pre-B ALL, including responders vs non-responders in selected genotypes [hyperdiploid, hypodiploid, t(12;21), t(9;22), t(1;19), and t(4;11)] and responders and non-responders regardless of genotype
  -  Pediatric patients with AML registered on POG-9421
  -  Adult patients with ALL, including t(8.21), inv(16), t(15;17), complex cytogenetics, and secondary AML
  -  Pediatric patients with relapsed ALL enrolled on COG-AALL01P2
  -  Pediatric patients enrolled on COG-9900 and other CCG or POG trials
  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: Activated Protein C in Severe Acute Pancreatitis

Summary: Activated protein C (APC)has been shown to reduce mortality in severe sepsis(Bernard et al. 2001b). The clinical picture of severe acute pancreatitis (AP) is similar to that of sepsis. The investigators conducted a randomised double-blinded placebo-controlled pilot study in AP patients (16+16) with the same dose of APC that has been proven to be efficacious and safe in septic patients.
  The aim of the study is to investigate whether the APC replacement therapy diminishes the occurrence and severity of organ dysfunction in patients with severe AP. The effect of APC on inflammatory and hemostatic parameters is also assessed.

Detailed description: The study started in 2003 and was finished in 2007. The study was registered in The Helsinki University Central Hospital study register in 2003.

Eligibility: Inclusion Criteria:
  -  Admitted to hospital within 72 h of the onset of pain.
  -  Plasma amylase concentration more than three times the upper limit of the normal range and/or CT findings compatible with AP.
  -  Organ failure and <48h of the onset of the first organ failure
  Exclusion Criteria:
  -  HIV / B- or C hepatitis infection
  -  Pregnancy or breast feeding
  -  Active bleeding
  -  Increased risk of bleeding (thrombocytes <30x10E9/L or INR>3.0
  -  Gastrointestinal bleeding within 6 weeks or intracranial stroke within 3 months before the study
  -  Intravenous contrast extravasation or other signs (fresh hematoma) suggesting active hemorrhage within the pancreas or in the peripancreatic area on admission CT scan
  -  Use of antithrombin III within 12 h
  -  Use of acetylsalicylic acid or glycoprotein IIB/IA antagonist within 7 days / Thrombolytic therapy within 3 days
  -  Surgery requiring general or spinal anaesthesia within 12 h
  -  Previous pancreatic surgery
  -  Application of an epidural catheter within 48 h

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

Clinical trial: Phase III Trial to Evaluate the Elortinib vs Gefitinib in Advanced NSCLC With EGFR Exon 19 or 21 Mutations

Summary: This is a randomized controlled trial to compare efficacy and safety between erlotinib and gefitinib in advanced NSCLC harboring EGFR exon 19 or 21 mutations.Eligible patients were randomized to receive erlotinib or gefitinib in any line settings.The primary endpoint was progression-free survival (PFS).

Detailed description: Patients with stage IV NSCLC who have EGFR exon 19 or 21 mutations will randomized to received oral erlotinib 150mg or gefitinib 250mg once daily until disease progression or unacceptable toxicity. Method of direct DNA sequencing of tumor tissue is used to analysis EGFR mutation status of exons 18-21. The response will be evaluated by RECIST criteria first month,second month and then repeat every 3 months after the beginning of the treatment weeks.

Eligibility: Inclusion Criteria:
  -  Histologically or cytologically confirmed stage IIIB (wet) or IV NSCLC.
  -  Patients with positive EGFR exon19 or exon21 mutation as confirmed by direct sequencing histologically.
  -  Signing the informed consent form.
  -  The vital organ functions are tolerant to therapy.
  -  Have recovered to CTCAE2 grade below from toxicity of previous chemotherapy and radiotherapy
  -  PS 0-2 scores.
  -  Functional reserve of bone marrow is adequate, e.g. white blood cell count ≥3.0×109/L, planet count ≥90×109/L, and HB≥80×109/L.
  -  Serum bilirubin is 2 times less than the upper limit of normal (ULN), ALT and AST are 3 times less than ULN; for liver metastases, ALT and AST need to be 5 times less than ULN; creatinine should be 2 times less than ULN.
  Exclusion Criteria:
  -  Informed consent is not provided.
  -  Women of pregnancy or breastfeeding.
  -  Have difficulty in swallowing.

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

Clinical trial: Correlations Phenotype / Genotype in Down Syndrome

Summary: The purpose of this study is to correlate phenotype and genotype of Down syndrome patients in order to identify the biochemical reactions involved in their mental retardation and their other phenotypic characteristics.


Eligibility: Inclusion Criteria:
  -  Down syndrome patients
  -  age: 8years and older
  -  assessment by the psychometric tests
  -  possible blood tests
  Exclusion Criteria:
  -  no exclusion criteria

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

Clinical trial: Studying DNA in Tumor Tissue Samples From Patients With Localized or Metastatic Osteosarcoma

Summary: RATIONALE: Studying samples of tumor tissue and blood from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer.
  PURPOSE: This research study is looking at DNA in tumor tissue samples from patients with localized or metastatic osteosarcoma.

Detailed description: OBJECTIVES:
  -  Determine the genomic expression profile in tumor tissue samples from patients with localized or metastatic osteosarcoma using transcriptome sequencing.
  -  Identify activating and loss of function mutations and gene rearrangement in these tumor tissue samples using transcriptome sequencing.
  -  Identify candidate genes that are important in osteosarcoma and tumorigenesis using genome partition strategies for genomic DNA sequencing.
  -  Identify which mutations are associated with outcome.
  -  Establish which mutations are also found in germ line DNA that predispose the patient to osteosarcoma.
  OUTLINE: DNA and RNA from banked tumor tissue samples and DNA from paired blood samples are analyzed in sequencing studies using next-generation sequencing technology. The sequencing data from these tumor samples are matched to the Human RefSeq (for transcriptome sequencing) and normal human genome in the public databases and to the patient's germ line sequence to identify constitutional and somatic mutations.
  Clinical information that is associated with each sample (i.e., age, tumor site, size, primary metastases, response to chemotherapy, surgical remission, follow-up time, and treatment protocol) is also collected, if available.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of localized or metastatic osteosarcoma
  -  Banked snap-frozen tumor tissue samples and paired blood DNA samples available
  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: Defining Normal Citrulline Levels as a Diagnostic Tool for Screening of Gastrointestinal Disease in Premature Infants

Summary: Since the first description of citrulline as a potential marker for intestinal function in 1998, its use has been investigated in a variety of disease processes including Short Bowel Syndrome, Celiac disease, chemotherapy and radiation induced intestinal injury, infections producing intestinal cytopathic effects like Adenovirus, and predicting rejection in intestinal transplantation. The use of citrulline levels as a diagnostic tool to predict gastrointestinal disease in the premature population has not been properly addressed.
  The introduction of enteral nutrition in the premature infant is a process of trial and error, knowing that the immaturity of the gastrointestinal system may lead to frequent episodes of feeding intolerance. This is augmented by the fear of the development of necrotizing enterocolitis (NEC) once feeds are commenced. NEC is a condition characterized by disruption of the intestinal epithelial barrier, a pathogenic process shared with some of the conditions mentioned above for which citrulline has proven clinically useful.
  A normal pattern of citrulline production has not been established in the premature population. Previous studies have shown decreased levels of glutamine and arginine in premature infants up to 10 days prior to the development of necrotizing enterocolitis. Glutamine and arginine are two amino acids closely involved in the synthesis and catabolism of citrulline.
  The investigators therefore hypothesize that defining a normal pattern of citrulline production in the premature population may prove to be a clinically useful diagnostic tool to screen for gastrointestinal disease.

Detailed description: The use of citrulline levels as a diagnostic tool to predict gastrointestinal disease in the premature population has not been properly addressed.

Eligibility: Inclusion Criteria:
  1. Premature infants with gestational age between <32 weeks regardless of birth weight
  Exclusion Criteria:
  1. Inborn errors of metabolism
  2. Need for exchange transfusion
  3. Multiple congenital anomalies
  4. Renal failure (defined as urine output <1ml/k/h >24h, creatinine >1.8, or diagnosis of "non-oliguric renal failure" as determined by Pediatric nephrology)

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

Clinical trial: Vessel Wall Response of the Bio-Active-stent and Everolimus-Eluting Stent Assessed By Optical Coherence Tomography

Summary: The purpose of the trial is to evaluate the completeness of struts coverage and vessel wall response (strut malapposition, neoin-timal formation) to the bio-active-stent (BAS) versus ever-olimus-eluting stent (EES) implanted for the treatment of the culprit lesion in acute coronary syndrome.

Detailed description: A prospective, randomized and controlled study comparing the coverage of the BAS and EES implanted in acute coronary syndrome.
  Clinical follow-up at 1, 6, 12 and 18 months. OCT analysis at the time of the 6 to 8 months follow-up.

Eligibility: Inclusion Criteria:
  -  Patient is ≥ 18 years old;
  -  The patient is presenting with acute coronary syndrome, and according to hospital routine practice, eligible for percutaneous coronary intervention;
  -  Patient or the patient's legal representative has been informed of the nature of the study and has provided written informed consent as approved by the Institutional Ethics Committee of the respective clinical site.
  Exclusion Criteria:
  -  Lesions in coronary artery bypass grafts
  -  Left main disease
  -  Killip class III-IV
  -  Allergy to aspirin / thienopyridine
  -  Patient in anticoagulation therapy
  -  No suitable anatomy for OCT scan
  -  Ostial lesion
  -  Tortuosity anatomy
  -  Very distal lesion
  -  Vessel size > 3.75 mm

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

Clinical trial: Coronary Flow Reserve in Patients With Bio-active Stent or Everolimus-eluting Stent Implanted in Acute Coronary Syndrome

Summary: The aim of the trial is to assess coronary artery reactivity using adenosine-induced coronary flow reserve (CFR) by transthoracic echocardiography in patients with Bio-active stent (BAS) and Everolimus-eluting stent (EES) distal to the original culprit lesion at 6-8 months.

Detailed description: Objective: The aim of the trial is to assess coronary artery reactivity using adenosine-induced coronary flow reserve (CFR) by transthoracic echocardiography in patients with Bio-active stent (BAS) and Everolimus-eluting stent (EES) distal to the original culprit lesion at 6-8 months.
  Design: BASE-CFR is a substudy of the larger randomized multicenter BASE-ACS trial comparing bio-active Titan stent to everolimus-eluting stent in patients with acute coronary syndrome. CFR assessment will be performed at 6-8 months after stent implantation at the same time with OCT assessment. In-stent restenosis will be ruled out using OCT.
  Primary endpoint: CFR at 6-8 months after stent implantation.
  Secondary endpoint: Coronary flow velocity at baseline and during adenosine-induced hyperemia 6-8 months after stent implantation..
  Association of CFR to unendotheliazed stent struts and stent malapposition.
  Enrollment: 40 patients (20 receiving BAS and 20 receiving EES).
  Clinical site: Satakunta Central Hospital, Finland Turku University Hospital, Finland

Eligibility: Inclusion Criteria:
  -  The patient is enrolled to the BASE-ACS trial. Treated culprit lesion is in the proximal or middle LAD
  -  Patient or the patient's legal representative has been informed of the nature of the study and has provided written informed consent as approved by the Institutional Ethics Committee of the respective clinical site
  Exclusion Criteria:
  -  Diabetes mellitus
  -  Treated stent position other than LAD proximal or middle.
  -  EF<30%
  -  Bifurcation lesions
  -  Renal impairment (creatinine >120 mmol/L)
  -  No suitable anatomy for OCT scan or CFR measurement

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

Clinical trial: A Retrospective Study of Biomarkers in Non-Small Cell Lung Cancer

Summary: The purpose of this study is:
  1. To characterize the types and frequency of molecular alterations to the epidermal growth factor receptor (EGFR) pathway, FGFR4 and EML-ALK in Asian patients with non-small cell lung cancer
  2. To identify candidate biomarkers of importance in the EGFR and estrogen pathways
  Most, if not all, human malignancies including lung cancer are caused by somatic alterations of the genome, leading to activation of oncogenes or inactivation of tumor suppressor genes and their resultant oncogenic effects. In addition to mutations, increased chromosomal copy number (by amplification or polysomy) and DNA methylation are other mechanisms of oncogene activation and tumour suppressor gene inactivation respectively.
  Little is known about the relationship between these oncogenes of the EGFR family and the recently described oncogenes FGFR4 and fusion gene EML4-ALK. Recent data suggests molecularly defined subgroups of non-small cell lung cancer (NSCLC) exist and can be used to predict for sensitivity to targeted agents (erlotinib or gefitinib) or cytotoxic chemotherapy (pemetrexate, gemcitabine, platinum agents). The findings that estrogen receptors are present in lung tumours and that estrogen can stimulate growth and proliferation of lung cancers in vitro and in vivo are provocative. Further studies to evaluate the role of estrogens and other sex hormones in lung cancer are warranted.
  A further understanding of the molecular indicators of lung cancer prognosis and treatment prediction would improve drug development and patient treatment selection.
  Archived paraffin-embedded and fresh frozen NSCLC tumor tissue will be obtained via the Department of Pathology and the National University Tissue Repository respectively. Clinico-pathological characteristics will be obtained from the case records, Pathology and Tissue Repository. DNA will be isolated using standard techniques. Sequencing of genes in the EGFR signaling pathway: EGFR, KRAS, ErbB2, ErbB3, MET, PI3K, and BRAF as well as FGFR4. Unstained slides from the paraffin-embedded tissue will be obtained and subjected to fluoresce in vitro hybridization (FISH) for breakpoints in the EML4 and ALK genes as previously described. For cases that have been snap-frozen, RNA will be extracted and EML4-ALK fusions will be confirmed using RT-PCR and pre-specified primers. To analyse the expression of proteins of putative relevance to EGFR function (such as EGFR, ErbB2, ErbB3, AKT, MET, STAT, ERK, MAPK, cyclin D1, C/EBPa), downstream effects of EGFR: cell proliferation (Ki-67), angiogenesis (CD34, VEGF-A), apoptosis (bcl-2), metastasis, and hormonal influence (oestrogen and progesterone receptors, aromatase), TMA technology will be utilised. The status of the tumor suppressor genes PTEN and C/EBPa will be analysed.


Eligibility: Inclusion Criteria:
  -  Nil
  Exclusion Criteria:
  -  Nil

Relevance to patient case: not relevant