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

Clinical trial: Pancreatic Cancer Screening of High-Risk Individuals in Arkansas

Summary: 100 subjects who have a family history of pancreatic cancer (PC), or known genetic syndromes associated with increased risk of pancreatic cancer, will be followed for five years. This data will be used to determine the pancreatic cancer and precancerous lesion detection rate in High Risk Individuals (HRIs). Subjects may agree to annual imaging and annual biomarkers or to biomarkers only.


Eligibility: Inclusion Criteria:
  -  Have a family history of PC as listed below or who have one of the following syndromes: Peutz-Jeghers syndrome - STK11; BRCA 1 and 2; PALB2; ATM; FAMMM / P16; HNPCC (Lynch) / MMR genes; Hereditary pancreatitis - PRSS1
  -  Individuals with three or more affected blood relatives (1st, 2nd or 3rd degree)
  -  Individuals with two or more affected blood relatives with PC, with at least one affected FDR, should be considered for screening.
  -  Patients with a history of Peutz-Jeghers syndrome should be screened, regardless of family history of PC.
  -  Patients with a known p16 (FAMMM syndrome) with one affected 1st or 2nd degree relative will be considered for screening.
  -  Patients with a known BRCA1 or BRCA2 mutation with one affected 1st or 2nd degree relative should be considered for screening.
  -  Patients with a known PALB2 mutation with one affected family member should be considered for screening.
  -  Patients with a known Mismatch-repair gene-mutation carriers (Lynch syndrome) with one affected family member should be considered for screening.
  Exclusion Criteria:
  -  Not candidates for surgery

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

Clinical trial: The Role of Small Bowel Ultrasound in Initiation of Infliximab in Crohn's Disease Patients

Summary: Goal is to prospectively determine if stool calprotectin and change in bowel wall thickness and hyperemia, as seen on small bowel ultrasound, at week 0, 14, and 54 can be used to predict response at week 54 to infliximab in pediatric patients with small bowel Crohn's Disease.

Detailed description: We will examine whether non-invasive disease monitoring tools such as bowel wall thickness as measured by small bowel ultrasound (SBUS) and mucosal inflammation as measured by fecal calprotectin, are independently associated with infliximab durability.

Eligibility: Inclusion Criteria:
  -  Age 6-23 years
  -  Initiating Infliximab therapy
  -  Crohns disease involving the distal small bowel +/- proximal colon
  -  Willingness to undergo SBUS and fecal calprotectin collection prior to starting infliximab and again at week 14 and week 54
  -  Able to give consent by patient and/or legal guardian
  Exclusion Criteria:
  -  Ulcerative colitis or non-Crohn's Disease patients
  -  Lack of small bowel disease
  -  Patients started on alternative therapy
  -  Unable or unwilling to provide consent

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

Clinical trial: Expanded Access Protocol Using CD3+/CD19+ Depleted PBSC

Summary: The goal of this protocol is to expand access for patients who lack a fully HLA (Human leukocyte antigen) matched sibling donor and who are candidates for allogeneic hematopoietic stem cell transplant (HSCT). These patients have a serious or immediately life-threatening disease for which HSCT is indicated. These patients are not eligible for other Children's Hospital of Philadelphia IRB approved protocols that utilize CliniMACs technology for T depletion.

Detailed description: Only 25-30% of patients who may benefit from HSCT have a matched related donor. There is a higher rate of complications using cells from an unrelated or partially matched related donor. T cells within the donor cells may cause a complication called graft vs. host disease (GVHD). The goal of this study is to use the CliniMACs device to remove the T cells that cause GVHD, called T cell depletion.

Eligibility: Inclusion Criteria:
  1. Patients who lack a fully HLA matched sibling and who are candidates for allogeneic hematopoietic stem cell transplant (HSCT) but do not meet criteria for current open institutional protocols using ClinMACs device for CD3+/CD19+ depletion.
  2. Patients with the following transplantable diseases:
  Non-malignant diseases:
  Metabolic storage diseases correctable by HSCT
  Bone marrow failure syndromes
  Immunodeficiencies/immune dysregulation syndromes
  Malignant diseases:
  Acute leukemias
  Chronic leukemias
  Lymphomas
  Myelodyplastic syndrome
  3. Organ function criteria:
  Lansky or Karnofsky performance ≥60
  Serum creatinine ≤3xupper limit of normal for age
  Hepatic: Transaminases ≤10xnormal
  Cardiac shortening fraction ≥27%
  Bilirubin <2.5x normal (unless elevation due to Gilberts disease)
  4. No active untreated infection
  5. Signed informed consent
  6. No fully HLA matched sibling donor available
  7. Females of childbearing potential must have negative pregnancy test
  Exclusion Criteria:
  1. Uncontrolled bacterial, viral or fungal infections
  2. Fully HLA matched sibling donor
  3. Donor unable to donate peripheral stem cells
  4. Pregnant Females

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

Clinical trial: Metagenomic Evaluation of the Gut Microbiome in Patients With Lynch Syndrome and Other Hereditary Colonic Polyposis Syndromes

Summary: The purpose of this study is to understand the role bacteria that normally live in the colon may play in colorectal cancer risk, in addition to the hereditary risk to colorectal cancer. The investigators will collect stool specimens as well as additional colon biopsy specimens during the patient's scheduled colonoscopy procedure. The investigators will also collect a questionnaire about diet and lifestyle. The samples will be used to study the impact of diet on naturally-occurring oral and gut bacteria and their influences on human health including risk of cancer.


Eligibility: Inclusion Criteria:
  -  Male or Female age 18 or older
  -  Hereditary colorectal cancer syndrome with one of the following:
  -  Lynch syndrome, as defined by the presence of a deleterious germline mutation in the MLH1, MSH2, MSH6, PMS2 or EPCAM genes
  -  Other hereditary colonic polyposis syndromes, as defined by the presence of a deleterious germline mutation in any one of the following polyposis genes (APC, biallelic MYH, STK11, SMAD4, BMPR1A, or other CRC-risk associated genes at discretion of PI)
  Exclusion Criteria:
  -  Unable to provide informed consent for testing
  -  Unable to complete English language questionnaire
  -  Receiving active chemotherapy
  -  Having completed active chemotherapy less then 12 months prior to day of scheduled lower endoscopy
  -  No infectious or drug induced colitis less then 12 months prior to day of scheduled lower endoscopy
  -  No history of inflammatory colitis (Crohn's disease or ulcerative colitis)

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

Clinical trial: To Evaluate Plasmajet in Achieving Complete Cytoreduction of Advanced EOC- Initial Feasibility Study

Summary: Surgery for ovarian cancer involves a big cut on your tummy (abdomen) followed by removal of pelvic organs (womb, tubes and ovaries), abdominal organs (fat tissue {omentum}, appendix) and any other tissues involved with cancer. Several studies worldwide have reported that women survive longer and enjoy a longer disease free interval before their disease returns if all visible disease is removed at the time of their surgery. Achieving this is not easy and often there is widespread disease and the surgeons are unable to remove every tumour nodule present as it is attached to the surface of the bowel, diaphragm and other important Extensive surgery with prolonged operating is associated with higher risks. Plasma energy is commonly referred to as the 4th state of matter after solid, liquid and gas. When a gas is heated, it partially or wholly ionizes resulting in high energy particles like ions, electrons and atoms referred to as 'plasma'. PlasmaJet® (PJ) is a new device which uses fine jet of neutral argon plasma from the handpiece that has been shown to have the ability to vaporise nodules close to sensitive organs like the bowel. It may offer the potential to treat the tumour nodules close to sensitive areas like the bowel. There have been no studies exploring its role in vaporising tumour nodules and its impact on survival. The PJ may be used by the surgeon to seal bleeding tissues (coagulate) or to burn away thin layers of tissue (ablate) by vaporization. It is licensed for use to achieve effects of coagulation and ablation. It is similar to conventional surgical devices that are routinely used (called diathermy) to achieve these effects. The PJ however is slightly different in that it may also be used on tissue to vaporise tumour nodules in women with ovarian cancer during surgery though the full extent of this role remains unclear.


Eligibility: Inclusion Criteria:
  -  Imaging+/- Clinical +/- laparoscopic e/o pelvic mass and metastatic disease (FIGO III/IV disease) at presentation.
  -  Confirmation of malignancy on histological/cytological criteria.
  -  All women aged 18 or over with newly diagnosed FIGO stage III to Stage IV EOC undergoing surgical treatment.
  -  All women fit to undergo treatment.
  -  No synchronous malignancy likely to interfere with comparisons.
  -  Written and informed patient consent
  Exclusion Criteria:
  -  Patient choice
  -  Patient unfit for any treatment modality
  -  Patients who are medically unfit for surgery and would only be suitable for chemotherapy.
  WITHDRAWAL CRITERIA
  -  Unforeseen complications in the individual patient will be recorded and then analysed.
  -  Life threatening situation to the patient, due to any other unrelated complication.
  -  Patients are free to withdraw from the study at any time with no impact on their care whatsoever.

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

Clinical trial: A Trial of Trametinib and Panitumumab in RAS/RAF Wild Type Advanced Colorectal Cancer

Summary: This is a phase 2 study (the second phase in testing a new drug or drug combination) to see how useful the combination of two drugs, panitumumab and trametinib, are in patients with advanced colorectal cancer with KRAS, NRAS, or BRAF wild type (genes that are not mutated).
  Panitumumab is a drug that is approved by Health Canada for the treatment of advanced colorectal cancer with KRAS wild type. Panitumumab works by binding to and blocking the protein, epidermal growth factor receptor (EGFR) from working.
  Trametinib is a drug that is approved by Health Canada for the treatment of melanoma with a mutation in the BRAF gene. Trametinib works by binding to and blocking mitogen-activated protein kinase kinase (MEK) 1 and MEK2 from working.
  Previous studies have shown that the combination of panitumumab and trametinib may be more useful in KRAS, NRAS, or BRAF wild type colorectal cancer.


Eligibility: Inclusion Criteria:
  -  18 years of age or older
  -  KRAS/NRAS/BRAF wild type colorectal cancer, not responsive to standard therapies, no approved or curative therapy, refuse standard therapy
  -  Prior 5-FU, oxaliplatin and irinotecan
  -  ECOG Performance Status of 0 or 1
  -  Able to swallow/retain oral drugs
  -  Able and agree to have provide tumor tissue/have biopsies
  -  Agree to use contraception
  -  Not pregnant
  -  Adequate organ system function
  Exclusion Criteria:
  -  Chemotherapy, radiotherapy, immunotherapy, or other anti-cancer therapies <28 days or 5 half lives
  -  Prior EGFR, MEK, or RAF inhibitor or regorafenib
  -  Current use of prohibited medications
  -  Unresolved side effects
  -  GI disease or other condition affecting GI absorption
  -  Mucosal or internal bleeding
  -  Any major surgery <four weeks
  -  HIV, HBV, or HCV positive
  -  Active infection
  -  Leptomeningeal disease
  -  Brain metastases
  -  Unacceptable QTcF interval
  -  Significant uncontrolled arrhythmias
  -  Acute coronary syndromes, myocardial infarction, coronary angioplasty, or stenting or bypass grafting < 6 mos.
  -  Class II, III, or IV heart failure
  -  Other clinically significant ECGs
  -  Intra - cardiac defibrillators
  -  Cardiac metastases
  -  Condition that may interfere with patient safety
  -  Hypersensitivity to study drugs
  -  Severe or uncontrolled systemic diseases
  -  Pregnant or lactating
  -  Retinal vein occlusion
  -  Interstitial lung disease or pneumonitis
  -  Active liver or biliary disease

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

Clinical trial: Screening Protein Markers in Patients With Rheumatoid Arthritis and Hot-dampness and Blood Stasis Syndrome

Summary: The purpose of this study is to explore the protein markers and to applicate those protein markers in syndrome diagnosis of hot-dampness and blood stasis syndrome in patients with RA.

Detailed description: RA is one of the main disabling diseases in nowadays, which is an autoimmune disease with complex networks mechanism involving multiple signaling pathways and existing cross path. The investigators consider that the "heat-dampness and blood stasis" syndrome is the main syndrome and major pathogenesis for active RA, which on the base of the theory of traditional Chinese medicine and a large quantity of clinical practice, and also examined by mechanism experiments. But the material basis of this syndrome is remained unclear, lack of high specific objective basis to ensure the syndrome differentiation consistency accurately in clinical practice. Proteomic techniques study cells or the body by all the protein expression and function, thus has the potential efficient for decoding syndrome biological basis. Proteomic techniques are the most effective way to reveal the essence of TCM syndrome. The investigators will use proteomic technology to explore the protein markers and to applicate those protein markers in syndrome diagnosis of hot-dampness and blood stasis syndrome in patients with RA. With strong clinical applicability, this will reveal the scientific connotation of this syndrome, preliminarily guide the syndrome differentiation.

Eligibility: Inclusion Criteria:
  -  Subjects are made or confirmed diagnosis according to the American College of Rheumatology criterion and "heat-dampness and blood stasis" syndrome according to Traditional Chinese Medicine.
  Exclusion Criteria:
  1. Subjects have other serious diseases, such as liver and kidney disease, cerebral-cardio vascular diseases.
  2. Subjects, who belong to "non-heat-dampness and blood stasis" syndrome, have double syndrome of heat or dampness.

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

Clinical trial: A Study of Cologuard™ in an Average Risk Population Assessing a Three Year Test Interval

Summary: This is a prospective longitudinal study to assess the impact of repeat Cologuard testing at 3 years in average risk patients.

Detailed description: This is a prospective longitudinal study to assess the impact of repeat Cologuard testing at 3 years in average risk patients. Enrolled subjects will be prescribed Cologuard per approved labeling at baseline. Subjects with positive results will be referred to colonoscopy and study participation completed. Subjects with negative Cologuard results will be seen annually for 3 years. At year 3, subjects will repeat Cologuard, followed by colonoscopy, regardless of the Cologuard test outcome. Subjects who have a colonoscopy at any time during the study will be discontinued following collection of the colonoscopy and associated histopathology results.

Eligibility: Inclusion Criteria:
  1. Subject has been prescribed Cologuard for colorectal cancer screening
  2. Subject is at average risk for development of colorectal cancer
  3. Subject is 50 years or older
  4. Subject willing and able to sign informed consent.
  Exclusion Criteria:
  1. Subject had a colonoscopy in the previous 9 years
  2. Subject has undergone any double-contrast barium enema, virtual (CT-based) colonoscopy, or flexible sigmoidoscopy within the previous five (5) years.
  3. Subject has had a positive fecal occult blood test or FIT within the previous six (6) months.
  4. Subject has any condition that in the opinion of the investigator should preclude participation in the study (e.g., subject not eligible for a diagnostic colonoscopy).
  5. Subject has a history of colorectal cancer or advanced adenoma.
  6. Subject has a history of aerodigestive tract cancer
  7. Subject has had a prior colorectal resection for any reason other than sigmoid diverticular disease
  8. Subject has had overt rectal bleeding, e.g. hematochezia or melena, within the previous 30 days. (Blood on toilet paper, after wiping, does not constitute rectal bleeding)
  9. Subject has a diagnosis or personal history of any of the following high-risk conditions for colorectal cancer:
  -  Inflammatory bowel disease (IBD) including chronic ulcerative colitis (CUC) and Crohn's disease.
  -  2 first-degree relatives who have been diagnosed with colon cancer. (Note: first-degree relatives include parents, siblings and offspring).
  -  One first-degree relative with CRC diagnosed before the age of 60.
  10. Subject has a family history of:
  -  Familial adenomatous polyposis (also referred to as "FAP", including attenuated FAP).
  -  Hereditary non-polyposis colorectal cancer syndrome (also referred to as "HNPCC" or "Lynch Syndrome").
  -  Other hereditary cancer syndromes including but are not limited to Peutz-Jeghers Syndrome, MYH-Associated Polyposis (MAP), Gardner's Syndrome, Turcot's (or Crail's) Syndrome, Cowden's Syndrome, Juvenile Polyposis, Cronkhite-Canada Syndrome, Neurofibromatosis and Familial Hyperplastic Polyposis.

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

Clinical trial: Study to Evaluate the Safety and Efficacy of Everolimus, in Subjects With PIK3CA Amplification, PTEN Loss and PIK3CA Mutation Refractory Solid Tumors

Summary: This study is a single-arm, phase II study of everolimus in patients with PTEN loss ,PIK3CA mutation and PIK3CA amplification Refractory Solid Tumors .
  Everolimus 10 mg will be administered orally qd daily.
  To investigate the efficacy and safety of everolimus in patients with PTEN loss ,PIK3CA mutantion and PIK3CA amplification Refractory Solid Tumors.


Eligibility: Inclusion Criteria:
  1. Provision of fully informed consent prior to any study specific procedures.
  2. Patients must be ≥20 years of age.
  3. PIK3CA amplification, PTEN loss and PIK3CA mutation Refractory Solid Tumors that has recurred or progressed following standard therapy, or that has not responded to standard therapy, or for which there is no standard therapy.
  4. ECOG performance status 0-2.
  5. Have measurable or evaluated disease based on RECIST1.1. as determined by investigator.
  6. Adequate Organ Function Laboratory Values
  -  Absolute neutrophil count ≥ 1.5 x 109/L, Hemoglobin ≥ 9g/dL, Platelets ≥ 75 x 109/L
  -  bilirubin ≤ 1.5 x upper limit of normal AST/ALT ≤ 2.5 x upper limit of normal (5.0 X upper limit of normal , for subjects with liver metastases)
  -  creatinine ≤1.5 x UNL
  7. Patients of child-bearing potential should be using adequate contraceptive measures (two forms of highly reliable methods) should not be breast feeding and must have a negative pregnancy test prior to start of dosing.
  8. Adequate heart function.
  Exclusion Criteria:
  1. Patients with second primary cancer, except: adequately treated non-melanoma skin cancer, curatively treated in-situ cancer of the cervix, or other solid tumours curatively treated with no evidence of disease for ≤5 years.
  2. Has known active central nervous system (CNS) metastases.
  3. Has an active infection requiring systemic therapy.
  4. Pregnancy or breast feeding
  5. Patients with cardiac problem.
  6. KRAS mutation (codon 12 or 13) or BRAF mutation (V600)
  7. Any previous treatment with everolimus

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

Clinical trial: The Pilot Study Evaluate the Safety and Efficacy of Sirolimus in Patients With PIK3CA Mutation and/or PIK3CA Amplification Refractory Solid Tumors

Summary: This study is a single-arm, phase II study of sirolimus in patient with PIK3CA mutation and PIK3CA amplication Refractory solid tumors.
  sirolimus 1mg will be administered orally qd daily.
  To investigate the efficacy of sirolimus in patients with PIK3CA mutation and PIK3CA amplication Refractory solid tumors.


Eligibility: Inclusion Criteria:
  1. Provision of fully informed consent prior to any study specific procedures.
  2. Patients must be ≥20 years of age.
  3. PIK3CA amplification and/or PIK3CA mutation Refractory Solid Tumors.
  4. ECOG performance status 0-2.
  5. Have measurable or evaluated disease based on RECIST1.1. as determined by investigator.
  6. Adequate Organ Function Laboratory Values
  -  Absolute neutrophil count ≥ 1.5 x 109/L, Hemoglobin ≥ 9g/dL, Platelets ≥ 100 x 109/L
  -  bilirubin ≤ 1.5 x upper limit of normal AST/ALT ≤ 2.5 x upper limit of normal (5.0 X upper limit of normal , for subjects with liver metastases)
  -  creatinine ≤1.5 x UNL
  7. Patients of child-bearing potential should be using adequate contraceptive measures (two forms of highly reliable methods) should not be breast feeding and must have a negative pregnancy test prior to start of dosing.
  8. Adequate heart function.
  Exclusion Criteria:
  1. Patients with second primary cancer, except: adequately treated non-melanoma skin cancer, curatively treated in-situ cancer of the cervix, or other solid tumours curatively treated with no evidence of disease for ≤5 years.
  2. Has known active central nervous system (CNS) metastases.
  3. Has an active infection requiring systemic therapy.
  4. Pregnancy or breast feeding
  5. Patients with cardiac problem.

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

Clinical trial: Resolution of Primary Immune Defect in 22q11.2 Deletion Syndrome

Summary: -  Evaluate about age of resolution in immune defect in 22q11.2 Deletion Syndrome
  -  Incidence of immunodeficiencies in 22q11.2 Deletion Syndrome

Detailed description: 22q11.2 Deletion Syndrome is the most common for microdeletion syndrome. The incidence is about 1:4000 of live birth. Clinical features in this syndrome are vary which consist of conotruncal cardiac anomalies, developmental disabilities, palatal anomalies, speech delay, hypocalcemia, characteristic facial features and immunodeficiencies. The most common type of immunodeficiencies is T cell defect that associated with thymic hypoplasia. In the present time, the investigators don't know about the resolution of immune defect in this syndrome.

Eligibility: Inclusion Criteria:
  -  22q11.2 deletion syndrome patients in allergy and immunology clinic, genetic clinic, cardio clinic, genetic clinic and development clinic
  Exclusion Criteria:
  -  loss follow up in 22q11.2 deletion syndrome patients or incomplete medical record

Relevance to patient case: not relevant