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

Clinical trial: Use of Omega 3 Oil Emulsion for Parenteral Nutrition Associated Cholestasis

Summary: This is a clinical study designed to evaluate the safety and benefit of a fish oil based fat emulsion in the treatment of liver disease associated with prolonged use of intravenous nutrition.

Detailed description: Specific Aims of Study
  1. To determine the safety profile of an intravenous omega-3 fat emulsion (Omegaven™)
  2. To determine if established PN associated liver disease can be reversed or its progression halted by using a parenteral fat emulsion prepared from fish oil as measured by normalization of serum levels of hepatic enzymes and bilirubin.

Eligibility: Inclusion Criteria:
  1. Age < 18 years old
  2. Patients will be PN dependent (unable to meet nutritional needs solely by enteral nutrition) and are expected to require PN for at least another 30 days, may be inpatient or outpatient
  3. Patients considered eligible for study participation must have parenteral nutrition associated liver disease (PNALD) as defined as a direct bilirubin of 2 mg/dl or more. Other causes of liver disease should be excluded. A liver biopsy is not necessary for treatment
  4. Direct bilirubin > 2.0 mg/dl
  5. Signed patient informed consent
  6. The patient must have utilized standard therapies to prevent the progression of his/her liver disease including surgical treatment, cyclic PN, avoiding overfeeding, reduction/removal of copper and manganese from PN, advancement of enteral feeding, or the use of ursodiol (i.e., Actigall®)
  Exclusion Criteria:
  1. Pregnancy
  2. Other causes of chronic liver disease (Hepatitis C, Cystic fibrosis, biliary atresia, and alpha 1 anti-trypsin deficiency)
  3. Enrollment in any other clinical trial involving an investigational agent (unless approved by the designated physicians on the multidisciplinary team)
  4. The parent or guardian or child unwilling to provide consent or assent
  5. Patients known to be allergic to fish or egg protein and patients with the following contraindications to Omegaven™ use:
  -  Impaired lipid metabolism
  -  Severe hemorrhagic disorders
  -  Unstable diabetes mellitus
  -  Collapse and shock
  -  Stroke/embolism
  -  Recent cardiac infarction
  -  Undefined coma status

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

Clinical trial: DNA Methylation Biomarkers and Metastasis of Gastric Carcinoma

Summary: Gastric carcinoma (GC) is the second leading cause of cancer death throughout the world. In previous multi-center study, we have found that the prevalence of GDNF family receptor alpha 1(GFRA1), serum response factor (SRF), and ZNF382 methylation alterations were inversely and coordinately associated with GC metastasis and the patients' overall survival throughout discovery and testing cohorts in China, Japan and Korea. The present cohort study is to investigate whether methylation of those genes can predict the metastasis and prognosis of GC.

Detailed description: Background: Metastasis is the leading cause of death for gastric carcinoma (GC). Currently, GC prognosis is primarily determined based on the clinical data and pathological stages of patients at the time of diagnosis and treatment. However, successful management of GC patients is still hampered by lack of highly sensitive and specific biomarkers capable of predicting prognosis and likelihood of metastasis. GFRA1 hypomethylation along with SRF and ZNF382 hypermethylation were found to be potential synergistic biomarkers for the prediction of GC metastasis in our previous multi-center study. In addition, p16 and E-cadherin were also correlated with GC metastasis in Chinese cohort. To investigate the predictive value of those genes' methylation on metastasis potential in GC, we carried out the prospective cohort study.
  Methods: 198 early stage GC patients without lymph node or distal metastasis were included in the present study. Baseline information of E-cadherin, GFRA1, p16, SRF and ZNF382 methylation status of the GC from 191 cases was obtained by MethyLight. The follow-up examination was carried out in a double-blind study with a 6-month interval. The association between gene methylation and metastasis of GC was analyzed with SPSS16.0 software. All P-values were two-sided.

Eligibility: Inclusion Criteria:
  -  Histological diagnosis of gastric adenocarcinoma;
  -  Early stage GC without lymph node and distal metastasis;
  -  Availability of frozen, fresh GC and corresponding surgical margin samples;
  -  Available of methylation status of gene CpG island in the extracted DNA sample.
  Exclusion Criteria:
  -  GC with lymph node or distal metastasis;
  -  Quality of the prepared DNA is not good enough for detection of gene methylation;
  -  GC cases were subjected to the neoadjuvant chemotherapy.

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

Clinical trial: Genetic, Serological Fecal and Clinical Markers in Siblings of Children With Inflammatory Bowel Disease

Summary: Although the precise etiology of inflammatory bowel disease (IBD) is still unknown, over the last decade active research allowed to gain more precise insights in the pathophysiology of IBD indicating that the chronic inflammation of the intestinal mucosa is directed against the microbiota of the gut in particularly susceptible individuals. Genetic studies and more recently genome-wide association studies (GWAS) have allowed to identify over 70 susceptibility genes which confer an increased risk of developing IBD. In the last years the attention of researchers has shifted to the identification of the early immunological changes that occur already at a preclinical stage of the disease, trying also at identifying the disease before it shows itself. Recently, the ability of a combination of serological markers in predicting the development of IBD has been demonstrated in adults. However, there are no studies evaluating a cohort of children at high risk for the disease, in whom the first immunological changes underlying the development of IBD could be studied, including a combination of genetic, serological, fecal and clinical markers.
  The purpose of this study is to evaluate in a population genetically well-characterized, as siblings and twins of patients affected with IBD, early genetic, serologic, fecal and clinical markers of disease, which may be present even years before developing the disease. The identification of these markers in predisposed individuals could help to implement strategies for prevention or early treatment to modify the natural history of IBD.

Detailed description: This is a multicenter, prospective, study evaluating the role of serological, genetic, fecal and clinical markers in predicting the development of IBD in a high risk population. The study will be divided in two phases. In the first phase the prevalence of genetic, serologic, fecal, clinical risk factors in 100 siblings of children affected with IBD compared to 100 healthy children with no family history for IBD will be evaluated. The estimated duration of the first phase of the study is 12 months. In a second phase, a long-term follow-up (5 years) will be performed in order to evaluate the accidental cases of IBD in this population.

Eligibility: Inclusion Criteria:
  -  siblings of children affected with IBD
  -  children without a family history of IBD
  Exclusion Criteria:
  -  age > 18 years
  -  age < 6 years
  -  concomitant autoimmune disorders

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

Clinical trial: Comparison Between Base and Cover Slide From Endoscopic Ultrasound Guided Fine Needle Aspiration for Pancreatic Cancer

Summary: The purpose of this study is to determine whether there is a difference of diagnostic accuracy between cover slides and base slides from EUS-FNA cytopathologic sample in patients who were previously suspected of pancreatic cancer in radiologic test.

Detailed description: 1. background
  1. Pancreatic cancer is the challenging malignancy in diagnosis and treatment.
  2. Recently, EUS-FNA has played a important role in diagnosing pancreatic cancer.
  3. Samples from EUS-FNA are sent to following three types of preparations.
  -  cytologic smear (by pull apart method)
  -  cell block
  -  histologic biopsy
  4. In cytologic smear method, endoscopists tend to send as many as slides, while pathologists want minimal slides if they warrant diagnostic accuracy.
  5. Therefore we are going to find a point of contact between high diagnostic yield and minimal overloading of pathologist.
  2. Method
  1. We are going to enrolled the patients who were suspected of pancreatic cancer in previous radiologic test.
  2. One identical and skilled endoscopist performs EUS-FNA with multiple punctures.
  3. We get total 8 pairs of slides (= 8 covers + 8 bases).
  4. All the cover slides are collected to the bottle-A, all the base slide to the bottle-B.
  5. One identical and skilled pathologist inspects these slide in blind method. (She cannot show the label of bottle so that she does not know what bottle is A or B.)
  6. She record the positive or negative in each bottle. (If there is only one slide is positive in malignant cell, the bottle is positive.)
  7. In these manner, we collect the all subjects' cytopathologic results as a pair of outcome. All the possible combinations are following four examples:
  -  (cover/base) = (positive/positive) = (+/+)
  -  (cover/base) = (positive/negative) = (+/-)
  -  (cover/base) = (negative/positive) = (-/+)
  -  (cover/base) = (negative/negative) = (-/-)
  8. Then we are going to take a two-sided non-inferiority test of proportion using McNemar's test.

Eligibility: Inclusion Criteria:
  -  patients who were suspected of pancreatic cancer in previous radiologic test such as computed tomography, magnetic resonance imaging or Positron Emission Tomography.
  Exclusion Criteria:
  -  failed smear due to inexperienced assistant
  -  loss of slide
  -  patients who were diagnosed with other lesion far from pancreatic cancer in prospective confirmative tests.
  -  patients who refuse to participate in this study
  -  report of other pathologist who are not a previously-assigned pathologist

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

Clinical trial: Genetic Causes of FSGS, Nephrotic Syndrome, or Kidney Failure

Summary: The investigators are trying to learn more about the cause of kidney diseases such as Focal Segmental Glomerulosclerosis (FSGS) and Nephrotic syndrome by studying genetics. The investigators are interested in discovering which genes play a role in causing a predisposition to FSGS/NS. The investigators also want to learn why FSGS/NS can run in families. Participation in our study involves a saliva sample and a urine sample that you can give from home. There is no cost to participate. All information is kept private and confidential. The investigators also like to include healthy volunteers (parents, spouses) if interested/available but of course this is completely optional.

Detailed description: The investigators welcome anyone (with or without a family history) with unexplained, non syndromic FSGS, nephrotic syndrome, or proteinuria to join the study. Participation involves a saliva (or blood if it is preferable) sample and urine sample (if applicable). There is no cost to participate and the study can be done from home in most cases.

Eligibility: Inclusion Criteria:
  -  Subjects with FSGS (focal segmental glomerulosclerosis)
  -  Subjects with NS (nephrotic syndrome)
  -  Subjects with unexplained kidney failure (have had a transplant or on dialysis)
  -  Subjects with unexplained proteinuria
  -  Family members of a person with FSGS, NS, kidney failure, or unexplained protein in their urine
  -  Healthy volunteers
  Exclusion Criteria:
  -  Patients whose kidney disease is already explained by another syndrome such as (Branchio Oto Renal Syndrome or Alports syndrome)
  -  Patients who already know the genetic cause of their kidney disease

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

Clinical trial: Pancreatic Cancer Early Detection Program

Summary: Early detection testing is recommended for individuals at elevated risk for the development of Pancreatic Cancer. This Protocol will define sufficiently elevated risk as either equal to or greater than five times the general population risk, or five times the average risk (1.5%) of developing pancreatic cancer by age 70; that is a 7.5% lifetime risk. Our inclusion criteria has a strong focus on the risk for pancreatic cancer imparted by the presence of hereditary cancer genes, as well as by family history. Enrolled subjects will undergo Endoscopic Ultrasound (EUS) alternating with Magnetic Resonance Imaging (MRI), every six to 12 months, for up to 5 years.

Detailed description: Interested individuals can be referred by physicians, or by family or friends.
  Individuals are informed that the purpose of this study is to collect outcome data following early detection testing based upon our criteria for elevated risk.
  Consent is obtained by any of the co-investigators. Consent is obtained for the primary PCEDP, and also obtained to allow for data to be used by our Cancer Program.
  We have a weekly review of all calls made and of all enrollments.
  We have a monthly meeting to review all proceeding regarding the study.
  Our IRB routinely reviews the proceedings of the study
  Our institution has a monthly Clinical research Committee meeting.

Eligibility: Inclusion Criteria: Any of the following:
  1. Known carrier of either the BRCA2 or CDKN2A mutation;
  2. Known carrier of any of the following mutations (BRCA1, MLH1, MSH2, PMS2, MSH6, EPCAM , P53, PALB2, APC, or ATM) PLUS first or second degree relative affected with pancreatic cancer;
  3. Individual with Peutz-Jeghers Syndrome;
  4. Familial Pancreatic Cancer, defined as at least two affected relatives with Pancreatic Cancer, who are first degree relatives with each other, and at least one of those affected must be first degree relative to the study subject;
  5. Both parents affected, any age:
  6. Any first degree relative diagnosed with pancreatic cancer under age 50;
  7. Chronic Pancreatitis Syndrome, defined by either PRSS1 or SPINK1 mutations AND appropriate clinical and family history
  Exclusion Criteria:
  1. Any medical condition that contraindicates endoscopy or biopsy
  2. Any medical condition that contraindicates MRI
  3. Status post partial or complete resection of the pancreas
  4. History of pancreatic cancer, either endocrine or exocrine
  5. Clinical suspicion of pancreatic cancer, or any previous radiographic or histologic diagnosis of a pre-malignant finding, including IPMN (Intraductal papillary mucinous neoplasm) and PanIN (Pancreatic intraepithelial Neoplasm).
  6. diagnosis of dementia
  7. Uncontrolled, current illness
  8. Renal insufficiency with serum creatinine greater than 2.0 mg/dl

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

Clinical trial: Micro RNAs as a Marker of Aortic Aneurysm in Hereditary Aortopathy Syndromes

Summary: The primary objective of this study is to determine whether specific patterns of circulating micro-ribonucleic acids (miRNAs) are associated with aortic aneurysm and dissection in patients with hereditary aortopathy syndromes. The most common of these syndromes is Marfan Syndrome (MFS), but several other recognized aortopathy syndromes are well characterized. The investigators propose the use of a simple blood test, from which miRNA profiles can be measured in individuals with aortopathy syndromes to be compared with miRNAs observed in a control population that has no known predisposition for aortic disease. The investigators hypothesize that microRNA profiles in individuals with Marfan syndrome, and related disorders, will be distinct from those seen in a control group. The investigators predict that up- or down-regulation of certain miRNAs will correlate with the presence and severity of aortic aneurysm, responses to medical therapy, and ultimately could be used to determine when an individual may be at risk of dissection.


Eligibility: Inclusion Criteria: To be in the study, the participant must meet the following criteria
  1. Diagnosis of hereditary aortopathy based upon:
  -  Confirmation of a disease causing mutation in a known aortopathy disorder OR
  -  Confirmation of disease based on published clinical criteria
  2. Participants is male or female and greater than 30 days old
  3. Participants are able to undergo standard of care cardiac monitoring including an echocardiogram
  4. Willing and able to provide written informed consent by parent(s) or guardian(s) after the nature of the study has been explained and prior to any research related procedures
  5. Signed HIPPA compliant research authorization
  Exclusion Criteria: Participant will be excluded from the study for any of the following criteria
  1. Diagnosis of a hereditary aortopathy can not be confirmed
  2. Existence of an additional comorbid condition- including a co-existing genetic syndrome, heart failure, renal disease, rheumatologic disease, history of malignancy, thyroid disease, recent stroke, other life-limiting illness not related to cardiovascular disease.
  3. Extreme prematurity, <28 weeks gestational age

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

Clinical trial: Lapatinib Plus Trametinib in KRAS Mutant NSCLC

Summary: This is an open-label phase I/II multi-center study consisting of two parts. Part A of this study is designed to identify the recommended phase 2 dose (RP2D) of lapatinib combined with trametinib in patients with metastatic KRASm and PIK3CA wild-type (PIK3CAwt) non-small cell lung cancer (NSCLC). Part B is designed to perform a randomized comparison of the lapatinib-trametinib combination versus standard of care therapy in patients with metastatic KRASm/PIK3CAwt NSCLC.


Eligibility: Inclusion Criteria:
  -  Histological or cytological proof of metastatic NSCLC; for PART B: treated with first line therapy for metastatic disease only.
  -  Written documentation of a known pathogenic KRAS (exon 2, 3 or 4) mutation and PIK3CA wild-type (exon 9 and 20)
  -  Age ≥ 18 years
  -  Able and willing to give written informed consent
  -  WHO performance status of 0 or 1 (part A and B)
  Exclusion Criteria:
  -  Any treatment with investigational drugs within 30 days prior to receiving the first dose of investigational treatment.
  -  History of another primary malignancy
  -  Symptomatic or untreated leptomeningeal disease
  -  Symptomatic brain metastasis
  -  History of interstitial lung disease or pneumonitis
  -  Uncontrolled infectious disease or known Human Immunodeficiency Virus HIV-1 or HIV-2 type patients
  -  Retinal degenerative disease (hereditary retinal degeneration or age-related macular degeneration), or a history of uveitis, retinal vein occlusion, central serous retinopathy, or retinal detachment
  -  Patients with left ventricular ejection fraction (LVEF) < 50%

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

Clinical trial: PREPL in Health and Disease

Summary: Evaluation of PREPL activity in healthy controls and known or possible PREPL deficient patients

Detailed description: PREPL is defective in hypotonia cystinuria syndrome and in isolated PREPL deficiency. The investigators have constructed a blood test to evaluate PREPL activity in patients with possible PREPL deficiency.
  The study will determine normal values for age (0-18) for PREPL activity in blood.
  Also, patients with a clinical phenotype that overlaps with PREPL deficiency (including patients with known primary PREPL deficiency and Prader-Willi syndrome) will be evaluated for PREPL activity in blood.
  A last part of the study will involve muscle biopsies during elective anesthesia/surgery for other reasons. There will be 2 groups: patients without signs of PREPL deficiency undergoing surgery (controls) and patients with Prader-Willi syndrome undergoing anesthesia or surgery (patients). The control group will be age-matched to the hypotonia group. In the muscle biopsies, PREPL activity and expression will be evaluated.

Eligibility: Inclusion Criteria:
  -  According to group
  -  Control group: children seen at a postinfectious consultation
  Exclusion Criteria:
  -  Control group: symptoms overlapping with PREPL deficiency, genetic or syndromic disease, atypically developing children
  -  other groups: contraindication for blood draw
  -  group with muscle biopsy: contra-indication for muscle biopsy

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

Clinical trial: Triple Negative Breast Cancer and Germline Hereditary Breast and Ovarian Cancer Mutation Carrier Registry

Summary: PROGECT is a registry for patients with Triple Negative breast cancer (TNBC) or patients who have an identified germline mutations (such as a mutation on the BRCA1 or BRCA2 genes).

Detailed description: This study is being done to collect cancer-related information from patients with triple negative breast cancer and patients with hereditary genetic mutations. This information will help us better understand the link between genetic changes and cancer outcome in patients with triple negative breast cancer.

Eligibility: Inclusion criteria include:
  Triple Negative Breast Cancer
  -  ER/PR <10% and HER negative per current ASCO/CAP guidelines
  -  Stages I-IV
  -  Any age at diagnosis
  -  Patient must be within 5 years of diagnosis
  -  Eligible regardless of genetic testing status
  -  Genetic testing recommended for patients meeting NCCN and Medicare guidelines
  AND/OR
  Germline mutation Carriers
  -  Patients with deleterious or uncertain mutations in HBOC genes (BRCA, PTEN, P53, -PALB2 etc) are eligible regardless of type/site of cancer
  -  Healthy patients harboring mutations also eligible
  -  There is no time limit from the time of diagnosis of cancer and enrollment.
  -  Eligible regardless of personal history of cancer
  Exclusion Criteria include:
  Triple Negative Breast Cancer -Patient is not within five years of diagnosis
  Germline mutation Carriers:
  -Patient only carries a HBOC mutation that is classified as "polymorphism" of "favor polymorphism"

Relevance to patient case: not relevant