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

Clinical trial: Pegteograstim in Children With Solid Tumors

Summary: To evaluate the efficacy and safety of pegteograstim on chemotherapy-induced neutropenia in children with solid tumors

Detailed description: Children with solid tumor experience neutropenia after cytotoxic chemotherapy, and they usually receive granulocyte colony-stimulating factor (G-CSF) to stimulate neutrophil recovery. However it needs daily injection of G-CSF. Pegteograstim is a new formulation of PEGylated recombinant human G-CSF analogue pegfilgrastim. In this study, investigators aimed to evaluate the efficacy and safety of pegteograstim on chemotherapy-induced neutropenia in children with solid tumors.

Eligibility: Inclusion Criteria:
  -  Patients with solid tumor who undergo chemotherapy with carboplatin, etoposide, doxorubicin, cyclophosphamide (CEDC) and ifosfamide, carboplatin, etoposide (ICE) regimen
  Exclusion Criteria:
  -  Patients with organ dysfunction (creatinine > 2mg/dL, ejection fraction <40% or severe arrhythmia/conduction disorder, other severe organ dysfunction)
  -  Hypersensitivity to pegteograstim, protein originated from E-coli, pegfilgrastim, filgrastim or latex.
  -  Patients with bleeding tendency to whom subcutaneous injection should be avoided.
  -  Active infection or infectious fever during the screening period.
  -  Genetic problem to fructose tolerance.
  -  Patients who participated in other clinical trial within 4 weeks before enrollment.
  -  Pregnant and nursing women

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

Clinical trial: Utilizing a Multi-gene Testing Approach to Identify Hereditary Pancreatic Cancer

Summary: The primary objective of the study will be to estimate the prevalence of germline mutations in patients who present consecutively within 12 weeks of a confirmed diagnosis of pancreatic ductal adenocarcinoma.

Detailed description: The proposed research is a multi-site prospective and observational plan to investigate the prevalence of germline mutations in patients diagnosed with pancreatic cancer. Thirty two genes will be analyzed, all of which have been associated with an increased risk for cancer. The genes are included on CancerNextTM a multi-gene next generation sequencing and array CGH test. The 32 genes include: APC, ATM, BARD1, BRCA1, BRCA2, BRIP1, BMPR1A, CDH1, CDK4, CDKN2A, CHEK2, EPCAM, GREM1, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, NF1, PALB2, PMS2, POLD1, POLE, PTEN, RAD50, RAD51C, RAD51D, SMAD4, SMARCA4, STK11, and TP53 .

Eligibility: Inclusion Criteria:
  -  Male and female patients between the ages of 18 and 89 years of age.
  -  Diagnosed within the previous 12 weeks with histologically or cytologically confirmed PDAC Stage I to IV.
  -  Ability of participant to understand and the willingness to sign a written informed consent document.
  -  Participant must agree to sample collection and genetic testing using the 32 gene test, CancerNextTM and allow the test result to be part of their medical record.
  Exclusion Criteria:
  -  Diagnosed with intraductal papillary mucinous neoplasms, mucinous cystic neoplasms, pancreatic neuroendocrine tumors or dysplasia without PDAC.
  -  Diagnosed with PDAC more than 12 weeks before presenting to the clinical site.
  -  Patients meeting the above enrollment criteria who have had CancerNext performed previously.

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

Clinical trial: Rescue Treatment Pattern, Drug Resistance Recurrence, and Direct Medical Costs Associated With Chinese Patients With Chronic Hepatitis B and Drug Resistance to Nucleot(s)Ide Analogue Therapy

Summary: The purpose of this study is to describe current rescue treatment pattern for nucleot(s)ide analogue (NA) resistance and assess the real-world treatment outcomes and health resources utilization of rescue treatments for drug resistance in a clinical cohort of Chinese patients with chronic hepatitis B (CHB).


Eligibility: Inclusion Criteria:
  -  CHB patient with drug resistance confirmed by hepatitis B virus (HBV) gene mutation and virological breakthrough
  -  Patient receiving rescue treatments for drug resistance to previous NA therapy for CHB
  -  Patient who was regularly followed at least every 6 months for drug resistance at the tertiary liver clinic of SXH
  Exclusion Criteria:
  -  Patient with a diagnosis of hepatocellular carcinoma, decompensated cirrhosis, and/or liver transplantation prior to the development of drug resistance to NA therapy for CHB
  -  Patient with co-infection with hepatitis C virus, hepatitis D virus, and/or human immunodeficiency virus
  -  Patient with life expectancy less than 6 months after the date of the first laboratory test indicating drug resistance
  Other protocol defined inclusion/exclusion criteria could apply

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

Clinical trial: SCHEDULE Follow Up Visit 5-7 yr

Summary: This protocol is written to describe the procedures for a single 5, 6 or 7 year follow-up control visit of patients who participated in the 12-month SCHEDULE-study and the following 3-year follow-up examination/visit. The aim of this 5 to 7-year follow-up visit is to examine the effect of long term treatment, i.e. 5, 6 or 7 years, with early initiation of everolimus (Certican®) and early elimination of cyclosporine (CsA), compared to standard immunosuppressive regimen including CsA, on renal and heart function. During the time period of this follow-up examinations, this visit will be performed as part of a routine annual visit 5, 6 or 7 years since transplantation (and inclusion in the original SCHEDULE study).


Eligibility: Inclusion Criteria:
  -  Patients who participated in the SCHEDULE 12-month main study, and who completed the 3 year follow-up visit
  -  Patients who are coming for a regular annual clinic visit 5 to 7 years after randomization in the main study
  -  Obtaining of a separate signed patient informed consent will be required for participation in this follow-up examination.
  Exclusion Criteria:
  -  Patients with a retransplanted heart since the original SCHEDULE study

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

Clinical trial: Molecular Genetic Study of Mayer-Rokitansky-Kuster-Hauser Syndrome

Summary: In order to understand the molecular mechanisms leading to Mayer-Rokitansky-Kuster-Hauser syndrome (MRKH), the research team has to identify molecular bases of this anomaly.
  Toward this goal, the research team would like to include in the study patients with MRKH syndrome, as well as their healthy relatives, in order to perform genetic analyses, especially whole exome sequencing.
  This study has been set up in order to collect biological samples from patients with MRKH and their relatives.

Detailed description: The MRKH is a congenital and rare malformation characterised by the absence of the uterus and of 2/3 of the vagina. The incidence is 1 in 4500 female children (46,XX) and a genetic component has been identified.
  In order to understand the molecular mechanisms leading to this disease, the research team has to identify the genetic abnormalities.
  This study will be led by the research team of the Imagine Institute and the clinical teams associated with the Reference Center for Rare Diseases PGR (Rare Gynecologic Diseases). Both groups are based on the Necker Hospital campus, and already closely collaborate on research into MRKH syndrome.
  This collaboration will allow to :
  i) collect biological samples from the propositus and their relatives,
  ii) have a medical expertise.
  The clinicians involved in the study will recruit patients, whose participation will involve providing a biological sample, ie, a blood sample and/or uterine tissue collected during surgical ablation, in the event that surgery is performed during clinical follow-up of the patients. No specific intervention will be planned for the purposes of this study.
  In order to perform genetic analysis on trios, the healthy relatives of the patients (parents, brothers, sisters) will also be included. Blood samples will be taken once for healthy relatives.
  Genetic analysis, especially whole exome sequencing, will be performed on blood samples by the research team of Imagine Institute.

Eligibility: Inclusion Criteria:
  -  Patient with MRKH syndrome OR healthy relative of patient included
  -  Having signed the Informed consent form (or parents in case of patient under 18 years)
  Exclusion Criteria:
  -  Refusal to participate in genetic analyses
  -  Participation in a therapeutical clinical study in the 30 days prior to inclusion in the present study.

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

Clinical trial: EGFRdelEx19 and KRAS Exon 2 Mutation Detection in EBUS-TBNA

Summary: First-line treatment with afatinib prolongs overall survival in patients with metastatic non-small-cell lung cancer (NSCLC) harboring EGFR exon 19 deletion mutations. Conversely, somatic KRAS mutations are negative predictors for benefit from EGFR-targeting agents. In this study we want to compare a new highly sensitive method for the detection of EGFRdelEx19 and KRAS Exon 2 with targeted-resequencing multiplex-PCR (NGS).

Detailed description: First-line treatment with afatinib prolongs overall survival in patients with metastatic non-small-cell lung cancer (NSCLC) harboring EGFR exon 19 deletion mutations. Conversely, somatic KRAS mutations are negative predictors for benefit from EGFR-targeting agents. Rapid availability of these biomarker results is mandatory to prevent delayed or inferior treatments.
  Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is well-established for lung cancer diagnosis and staging. Next generation sequencing (NGS) via targeted resequencing allows simultaneous interrogation for multiple mutations, but has its limitations based on the amount of tumor tissue required and assay times. RT-PCR using Light-Cycler technology (LC-RTPCR) is a rapid and sensitive assay to detect somatic mutations in various tissues from NSCLC patients. The study's aim was to analyze if LC-RTPCR is feasible for rapid EGFRdelEx19 and KRAS Exon 2 mutation detection in EBUS-TBNA samples and to compare results with results obtained via standard NGS mutation analyses.

Eligibility: Inclusion Criteria:
  -  lung adenocarcinoma positive EBUS-TBNA specimen
  Exclusion Criteria:
  -  other diagnosis

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

Clinical trial: Expanded Access to Provide Larotrectinib for the Treatment of Cancers With a NTRK Gene Fusion

Summary: Larotrectinib expanded access is for patients with cancer with a NTRK1, NTRK2, or NTRK3 gene fusion, who are ineligible for an ongoing larotrectinib clinical trial or have other considerations that prevent access to larotrectinib through an existing clinical trial. Gene fusion occurs when a gene is made by joining parts of two different genes. NTRK gene fusion can lead to the development of solid tumors in a variety of tissue types. The study drug larotrectinib blocks the action of the NTRK gene fusion.
  Expanded access is intended to treat individual patients with different types of cancers with a NTRK gene fusion who are unresponsive to current standard treatment for their condition and also are unable to participate in ongoing clinical trials.


Eligibility: Inclusion Criteria:
  -  Diagnosis of cancer with a NTRK1, NTRK2, or NTRK3 gene fusion
  -  Subjects are unable to participate in an ongoing larotrectinib clinical trial
  -  Medically suitable for treatment with larotrectinib
  Exclusion Criteria:
  -  Currently enrolled in an ongoing clinical study of larotrectinib or another TRK inhibitor

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

Clinical trial: Safety and Efficacy of Combination Acthar Gel and Tacrolimus in the Treatment of Steroid Resistant Nephrotic Syndrome

Summary: The management of steroid-resistant nephrotic syndrome (SRNS) remains a persistent problem for investigators in part because of the wide array of pathogenic mechanisms that contribute to these disorders as well as the lack of adequately powered, controlled trials. While glucocorticoids remain the primary therapy for many forms of protein uric glomerular diseases, prolonged use is associated with significant morbidities including steroid induced diabetes, metabolic bone disease, and excessive weight gain.

Detailed description: Multiple agents have been investigated in the treatment of patients with SRNS, but there is no consensus on what constitutes optimal therapy. Previous studies have examined the efficacy of combining intravenous cyclophosphamide with corticosteroids and have shown complete and partial response rates between 40% and 60%. More recently, calcineurin inhibitors (CNI) have become an effective second line therapy with similar response rates between 50%-70%. However, both treatment regiments are limited by the risk for infection as well as the development of CNI-induced nephrotoxicity and progressive renal disease. Acthar gel is a porcine pituitary preparation composed of ACTH and other proopiomelanocortin peptides and is currently approved for treatment of idiopathic nephrotic syndrome. Previous studies, as well as more current studies, have shown that ACTHar gel can effectively reduce proteinuria in idiopathic membranous glomerulonephritis and other forms of glomerulopathy including focal segmental glomerulosclerosis (FSGS) and advanced diabetic nephropathy. While the mechanism is unknown, previous studies have shown that melanocortin 1-receptors are expressed in glomerular podocytes and that activation of this receptor pathway could be involved in the protein lowering effects of ACTHar gel. Incubation of cultured podocytes with ACTH leads to activation of MCR-1 receptors and the subsequent stimulation of protein kinase A (PKA) through a G-protein-dependent pathway. The downstream phosphorylation and stabilization of Rho GTPases, synaptopodin and other cell-cytoskeletal associated proteins may stabilize podocyte function and density.

Eligibility: Inclusion Criteria:
  -  refractory nephrotic syndrome secondary, defined as subjects having a urine protein/Cr ratio over 3.0 while actively receiving ACE inhibitors and hyperglycemic therapy (i.e., insulin or oral hyperglycemic agents).
  -  Type I or Type II diabetes
  -  receiving combination therapy with an ACE inhibitor and a second protein lowering agent (e.g., ARB, non dihydropyridine CCB, or spironolactone).
  Exclusion Criteria:
  -  known primary or secondary membranous glomerulonephritis (GN)
  -  primary or secondary focal segmental glomerulosclerosis
  -  other nondiabetic forms of glomerulopathy

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

Clinical trial: Prevalence of BRCA1 and BRCA2 Mutations in Ovarian Cancer Patients in the Gulf Region

Summary: A prospective, multi-centre, epidemiological observational study designed to evaluate the prevalence of BRCA1 and BRCA2 (BReast CAncer gene) mutations in current and newly diagnosed ovarian cancer patients across different countries in the Gulf region. This study will also describe the epidemiological features for the disease for the enrolled patients.


Eligibility: Inclusion Criteria:
  1. Subjects willing to sign the informed consent form (ICF)
  2. Female subjects 18 years of age or older
  3. Have histologically confirmed diagnosis of Federation of Gynecology and Obstetrics (FIGO) ovarian epithelial, primary peritoneal cancer made by one or more of the following:
  1. Standard staging laparotomy including bilateral salpingo-oophorectomy,omentectomy, and lymph node sampling and debulking and/or
  2. Surgical resection and radiographic evidence consistent with ovarian cancer
  3. Paracentesis or biopsy with radiographic evidence consistent with ovarian cancer(normal appearing pancreas, liver, and gastrointestinal tract).
  4. Have availability of paraffin-embedded archived tumor tissue block (preferred) or, if a block is not possible, a minimum of twenty 10-um sections.
  Exclusion Criteria:
  Patients who meet any of the following criteria are ineligible to participate in the study and hence will not be consented:
  1. The diagnosis is not of a primary ovarian cancer; thus, patients will be excluded if a previous cancer has metastasized to the ovary, or if there is a secondary malignancy that is associated with the ovarian cancer.
  2. Is not able or willing to provide written informed consent.
  3. Have a diagnosis of other severe acute or chronic medical or psychiatric conditions that may increase the risk associated with study participation or may interfere with the interpretation of the study.
  4. Be a patient who, in the judgment of the Investigator, would be inappropriate for enrollment in this study.
  A rationale will be documented for all patients who are screened and ultimately excluded from the study as a result of meeting any of the aforementioned exclusion criteria

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

Clinical trial: The Leigh Syndrome Registry

Summary: The purpose of this study is to develop a database containing clinical and laboratory information for patients with Leigh syndrome. The goal is to provide a greater understanding of Leigh syndrome allowing further characterization of this disease.

Detailed description: Leigh syndrome, also known as juvenile sub-acute necrotizing encephalopathy, is a progressive neurodegenerative disorder associated with dysfunction of mitochondrial oxidative phosphorylation (OXPHOS). First described in 1951 by British neuropsychiatrist Archibald Denis Leigh, the condition has evolved from a post mortem diagnosis to a clinical entity with characteristic radiologic and laboratory findings.
  Leigh syndrome is a rare and heterogeneous disease, finding a substantial number of patients to study is difficult. The lack of natural history data in Leigh syndrome and the small number of patients included in clinical reports thus far has limited the ability to fully comprehend the progression of this disease and assess prognostic factors. A Leigh syndrome database will help improve our understanding of this rare disease leading to an improved ability to predict outcomes and/or improve treatment paradigms. Collecting natural history data on Leigh syndrome and integrating this information into a database will be useful in understanding the course of the disease and identifying trends.

Eligibility: Inclusion Criteria:
  -  All participants with a diagnosis of Leigh syndrome will be invited to participate
  Exclusion Criteria:
  -  People without Leigh syndrome

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

Clinical trial: PRKAA2 Genetic Polymorphisms and Its Susceptibility to Chinese Type 2 Diabetes Mellitus and Diabetic Nephropathy

Summary: Metformin is a classical oral antidiabetic drug, often recommended to be the first-choice treatment of type 2 diabetes mellitus (T2DM). Based on the previous research on PRKAA2, STK11 and diabetes, this study aimed to investigate the distributive characteristic of PRKAA2 and STK11 polymorphisms and the potential influence of STK11polymorphisms on metformin efficacy among Chinese T2DM patients, discuss the association of PRKAA2 polymorphisms between T2DM patients and healthy subjects.


Eligibility: Inclusion Criteria:
  -  diagnosed with T2DM in keeping with the WHO criteria in 1999 [14], with fasting blood glucose (FBG) ≥ 7.0mmol ⁄ L and ⁄ or postprandial blood glucose (PBG) ≥ 11.1mmol ⁄ L; not using other antidiabetic drugs within the experimental period.
  Exclusion Criteria:
  -  other significant illness such as cancer, myocardial infarction, stroke, severe liver, and kidney disease

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

Clinical trial: Frequency of EGFR and KRAS Mutations and Clinical-prognostic Correlation in Brazilian Lung Cancer Patients

Summary: The assessment of the type and frequency of EGFR and KRAS mutations in lung cancer patients, as well as clinical-prognostic correlation, are crucial in the era of targeted therapies. EGFR-activating mutations predict responsiveness to EGFR tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC) patients and KRAS analysis will be useful in a near future for newest target drugs. In Brazil, few data about the prevalence of EGFR and KRAS mutations is available and their knowledge would allow optimize personalized medicine.

Detailed description: Assessment of the types and frequency of EGFR and KRAS mutations in NSCLC, as well clinical-prognostic correlations has been extensively studied in many populations. Few Brazilian studies evaluating mutational status in NSCLC has been done so far, none of then explored the regional background nor have considered the quantitative analysis of mutant cell in each sample. Quantitative analysis of the tumor maybe relevant for treatment design for positive samples, p.e a tumor with 90% of mutant clones versus a 15% of mutant clones, which can be obtained currently by the method of pyrosequencing. In this study, investigators will assess EGFR and KRAS status through the pyrosequencing quantitative technique, and will also correlate these with clinical-pathological variables among both adenocarcinoma and squamous cell histological subtypes. So far, no study that have made this correlation is available.

Eligibility: Inclusion Criteria:
  -  Brazilian patients with metastatic non-small cell lung cancer.
  Exclusion Criteria:
  -  Small cell lung cancer and non-metastatic patients.

Relevance to patient case: not relevant