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

Clinical trial: The COLON Study: Colorectal Cancer Cohort

Summary: The main aim of this observational, prospective cohort study is to assess associations of diet and other lifestyle factors with colorectal cancer recurrence, survival and quality of life.

Detailed description: The COLON study is a multi-centre prospective cohort study among incident colorectal cancer patients recruited from 12 hospitals in the Netherlands. Patients with colorectal cancer are invited upon diagnosis. Upon recruitment, after 6 months, 2 years and 5 years, patients fill out food-frequency questionnaires; questionnaires about dietary supplement use, physical activity, weight, height, and quality of life; and donate blood samples. Diagnostic CT-scans are collected to assess cross-sectional areas of skeletal muscle, subcutaneous fat, visceral fat and intermuscular fat, and to assess muscle attenuation. Blood samples are biobanked to facilitate future analyse of biomarkers, nutrients, DNA etc. Analysis of serum 25-hydroxy vitamin D levels, B-vitamins and metabolomic profiles are scheduled. A subgroup of patients with colon cancer is asked to provide faecal samples before and at several time points after colon resection to study changes in gut microbiota during treatment. For all patients, information on vital status is retrieved by linkage with national registries. Information on clinical characteristics, including treatment-related toxicity and co-morbidity data, is gathered from linkage with the Netherlands Cancer Registry and with hospital databases or medical records. Hazard ratios will be calculated for dietary and lifestyle factors at diagnosis in relation to recurrence and survival. Repeated measures analyses will be performed to assess changes over time in dietary and other factors in relation to recurrence and survival.
  The aim is to recruit at least 2000 patients with available data and blood samples.

Eligibility: Inclusion Criteria:
  - Patients newly diagnosed with colorectal cancer in one of the participating hospitals
  Exclusion Criteria:
  -  Non-Dutch speaking
  -  A history of colorectal cancer or (partial) bowel resection
  -  Chronic inflammatory bowel disease
  -  Hereditary colorectal cancer syndromes (Lynch syndrome, FAP, Peutz-Jegher)
  -  Dementia or another mental condition that makes it impossible to fill out questionnaires

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

Clinical trial: Biomarker for Hyaline Fibromatosis Syndrome (BioHFS)

Summary: Development of a new MS-based biomarker for the early and sensitive diagnosis of Hyaline fibromatosis syndrome from the blood

Detailed description: Hyaline fibromatosis syndrome (HFS) is rare autosomal recessive disease characterized by the deposition of amorphous hyaline material in skin and visceral organs. It represents a disease spectrum with infantile systemic hyalinosis (ISH) being the severe form and juvenile hyaline fibromatosis (JHF) being the mild form. Dermatologic manifestations include thickened skin, perianal nodules, and facial papules, gingival hyperplasia, large subcutaneous tumors on the scalp, hyperpigmented plaques over the metacarpophalangeal joints and malleoli, and joint contractures. ISH shows a severe visceral involvement, recurrent infections, and early death.
  The lesions appear as pearly papules or fleshy nodules. The severity is variable. Some individuals present in infancy and have additional visceral or systemic involvement, which can lead to early death. These patients may show intractable diarrhea and increased susceptibility to infection. Other patients have later onset of a milder disorder affecting only the face and digits. Additional features include gingival hypertrophy, progressive joint contractures resulting in severe limitation of mobility, osteopenia, and osteoporosis. Histologic analysis of skin lesions shows proliferation of spindle-shaped cells forming strands in a homogeneous and hyaline eosinophilic extracellular material in the dermis.
  New methods, like mass-spectrometry give a good chance to characterize specific metabolic alterations in the blood of affected patients that allow diagnosing in the future the disease earlier, with a higher sensitivity and specificity.
  Therefore it is the goal of the study to identify and validate a new biochemical marker from the blood of the affected patients helping to benefit other patients by an early diagnose and thereby with an earlier treatment.

Eligibility: Inclusion Criteria:
  -  Informed consent will be obtained from the parents before any study related procedures.
  -  Patients of both gender older than 2 months
  -  The patient has a diagnosis of Hyaline fibromatosis syndrome or a high-grade suspicion for Hyaline fibromatosis syndrome
  High-grade suspicion present, if one or more inclusion criteria are valid:
  -  Positive family anamnesis for Hyaline fibromatosis syndrome
  -  Coarse facies
  -  Subcutaneous nodule
  -  Gingival fibromatosis
  -  Skeletal muscle atrophy
  -  Progressive flexion contractures
  Exclusion Criteria:
  -  No Informed consent from the parents before any study related procedures.
  -  Patients of both gender younger than 2 months
  -  No diagnosis of Hyaline fibromatosis syndrome or no valid criteria for profound suspicion of Hyaline fibromatosis syndrome

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

Clinical trial: INF-α Innate Immune Response to Gliadin

Summary: Background & Aims The enteropathy in Celiac Disease (CD) is due the adaptive and to the innate immune response to gliadin peptides. Gliadin peptide P31-43 activates innate immune response and interferes with vesicular trafficking. Type 1 interferons (INFs) and viral infections play a role in CD pathogenesis. In this paper investigators investigated the role of P31-43 in the activation of the INF-α pathway.
  Methods Small intestinal biopsies of CD patients both with active disease on gluten containing diet (GCD) and in remission phase of the disease on a gluten free diet (GFD) and controls were analyzed before and after culture with P31-43. The levels of toll like receptor 7 (TLR7), myeloid differentiation primary response 88 (MyD88), myxovirus resistance protein 1 (MxA) and nuclear factor-κB (NF-κB) proteins and INF-α mRNA was analyzed in intestinal biopsies.

Detailed description: Intestinal biopsies from CD patients and controls were obtained after EGDS performed during routine analysis. The biopsies were immediately immersed in culture medium (Dulbecco's modified medium, DMEM) in a falcon tube and kept for 16h at 37 C before cultivation. Biopsies were cultivated as described in Barone MV1, Caputo I, Ribecco MT, Maglio M, Marzari R, Sblattero D, Troncone R, Auricchio S, Esposito C. Humoral immune response to tissue transglutaminase is related to epithelial cell proliferation in celiac disease. Gastroenterology. 2007,132(4):1245-53.

Eligibility: Inclusion Criteria:
  biopsy fragments from duodenum were obtained from CD patients with villous atrophy on GCD, controls, affected by gastroesophageal reflux, and CD patients on GFD.
  Exclusion Criteria:
  other inflammatory intestinal diseases

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

Clinical trial: High Definition Endoscopy and Virtual Chromoendoscopy Versus Standard Resolution Endoscopy in Detection of Colon Polyps

Summary: Over the last years a number of new endoscopic imaging modalities have been introduced (high-definition and virtual chromoendoscopy). Given the theoretical advantage of these new imaging techniques, the investigators aimed to investigate their use for the detection of polyps during colonoscopy.


Eligibility: Inclusion Criteria:
  -  referred for colonoscopy
  -  signed informed consent
  Exclusion Criteria:
  -  subtotal colectomy
  -  known colorectal tumor or polyp prior to colonoscopy
  -  genetic predisposition to colon cancer namely FAP, HNPCC, Hyperplastic polyposis syndrome, juvenile polyposis, Peutz-Jeghers syndrome
  -  inflammatory bowel disease
  -  primary sclerosering cholangitis

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

Clinical trial: sPLA2 in EBC During Acute Chest Syndrome

Summary: Secretory phosholipases A2 (sPLA2) are significantly elevated in the plasma of sickle cell disease patients with acute chest syndrome (ACS), and similar enzymes have been measured in exhaled breath condensate (EBC), which is collected easily and non-invasively. The investigators hypothesize that sPLA2 will be measurable in EBC samples from sickle cell patients with acute chest syndrome.

Detailed description: The purpose of this research study is to test the ease and effectiveness of collecting exhaled breath condensate (liquid) to measure levels of a biomarker, secretory phospholipases A2 (sPLA2) in people with sickle cell disease during an attack of acute chest syndrome. sPLA2 levels have been reported to be much higher in persons with acute chest syndrome and might be useful to diagnose and to evaluate the effects of therapy.
  Serial monitoring of plasma sPLA2 levels might lead to earlier or more accurate detection of acute chest syndrome and monitoring of its progression or improvement in patients with sickle cell disease. However, there is a significant inherent risk of frequent blood collection further dropping the blood (hemoglobin) levels of an already anemic patient. If sPLA2 can be measured in exhaled breath condensate, this non-invasive and well-tolerated sample collection might allow for serial monitoring of the enzyme without depleting the patient's already diminished blood supply.

Eligibility: Inclusion Criteria:
  1. Diagnosis of sickle cell anemia (the most severe types of sickle cell disease) as demonstrated by one of the following genotypes: HbSS, HbSβ0
  2. Age ≥ 7 and < 40 years
  3. Diagnosis of ACS as defined below
  4. EBC collection able to be initiated within 48 hours of diagnosis of ACS
  Definition of acute chest syndrome to be used: New radiographic pulmonary infiltrate of at least one complete lung segment in addition to 2 or more of the following symptoms: fever, chest pain, dyspnea, tachypnea, hypoxia. Given the small number of subjects in this feasibility study, we are using the more conservative definition in order to ensure samples are from patients with true ACS. This will increase the likelihood that sPLA2 levels will be high enough for measurement.
  Exclusion Criteria:
  1. Blood product transfusion in the previous 3 months (due to potential alterations in biomarkers, including sPLA2)
  2. Chronic inflammatory conditions other than sickle cell (due to elevation from baseline of sPLA2 in inflammatory conditions)
  3. Physical inability to correctly breathe into the mouthpiece for the required amount of time without compromising respiratory status
  4. Intubated patients (though EBC can be measured in intubated patients, we will not include this subpopulation for the purpose of this study)
  5. Pregnancy (due to the hematologic and respiratory changes that physiologically occur during gestation)

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

Clinical trial: New Genes in the Carcinogenesis of Colorectal Cancer

Summary: Colo rectal cancer is one of the greatest ,mutual malignancies worldwide ,accounting for an estimated 1.3 million new cases and >500,000 mortality ⁄ year . is the fourth leading cause of cancer-associated mortality worldwide with speedily ,cumulative ,occurrence rate in the worldwide

Detailed description: colo rectal cancer represents a global and local problem, as it is one of the commonest types of cancer all over the world. Globally, Colo rectal cancer in women (9.2% of diagnoses) it is the second most common cause of cancer . it is the third most common in men (10.0%). After lung, stomach, and liver cancer it is the fourth most common cause of cancer death.
  Cancer is a multistep procedure resulting from an ongoing accretion of genetic and epigenetic fluctuations to the genome.
  Spartin is a protein that in humans is encoded by the SPG20 gene. This protein may be involved in endosomal trafficking, microtubule dynamics, or both functions. Aberrant promoter methylation of genes is a common epigenetic alteration in colo rectal cancer .
  This has stimulated the prospect to implement a dependable, reasonable and simple approach for Colo rectal detection . The SPG20 gene is situated in chromosome band 13q13.3; the SPG20 gene converts the spartin protein, which is a multi functional protein that has formerly been recognized to be complicated in intra cellular epidermal growth factor receptor trading , The serine-threonine kinase 31 (STK31) gene was initially identified through cDNA subtraction as a testis-specific protein kinase gene expressed in mouse spermatogonia . Recently, STK31 has been described as a novel cancer testis (CT) antigen, highly expressed in Gastrointestinal cancer cells (colo rectal, gastric and esophageal cancer), while restricted to testis and fetal brain in normal tissues .
  It was found that SPG20 is mutated in Troy er syndrome, an hereditary spastic paraplegia

Eligibility: Inclusion Criteria:
  -  age between 35-65
  -  patient with colorectal cancer (at any stage)
  -  both sex included
  Exclusion Criteria:
  -  pediatric patients
  -  patient with insufficient data
  -  cardiac patient
  -  pregnant women

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

Clinical trial: Study of Universal Screening for Lynch Syndrome in Chinese Patients of Endometrial Cancer

Summary: In patients diagnosed as endometrial cancer by thorough pathologic examinations, Lynch syndromes are screened by (1)immunohistochemical staining (for MLH1, MSH2, MSH6 and PMS2), (2) tests of microsatellite instability and (3) clinical criteria (Amsterdam I or II criteria and Bethesda criteria). For patients with any suspicious discoveries of Lynch syndromes from aforementioned screening methods, a molecular diagnosis with next-generation sequencing for mismatch repair genes (MLH1, MSH2, MSH6, PMS2, and EPCAM) is given to confirm Lynch syndromes. For patients of Lynch syndromes and endometrial cancer, relatives of blood lineage are tested by Sanger method or qPCR to find out carriers of mutation genes of Lynch syndromes.


Eligibility: Inclusion Criteria:
  -  Survivals of endometrial cancer
  Exclusion Criteria:
  -  Metatatic malignacies to uterine
  -  Leiomyosarcoma of uterus

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

Clinical trial: Risk-Reducing Surgeries for Hereditary Ovarian Cancer

Summary: Based on studies of "Inherited Susceptible Genes Among Epithelial Ovarian Cancer" (NCT03015376, clinicaltrials.gov) and "Cohort Study of Universal Screening for Lynch Syndrome in Chinese Patients of Endometrial Cancer" (NCT03291106, clinicaltrials.gov), we provide risk-reducing surgeries of salpingo-oophorectomy with/without hysterectomy for healthy carriers with mutation genes of hereditary ovarian cancer, which is defined ovarian cancer with relevant pathogenic mutations.


Eligibility: Inclusion Criteria:
  -  Carriers with known and definite mutation genes of hereditary ovarian cancer.
  -  With children and without further requirement of pregnancy.
  -  No less than 35 years for carriers with mutation gene of BRCA1.
  -  No less than 40 years for carriers with mutation gene of BRCA2.
  -  No less than 45 years for carriers with mutation genes of BRIP1, RAD51C, RAD51D and RAD51.
  -  No less than 50 years for carriers with mutation genes of ATM, MSH2, MLH1, SH6, PMS2, EPCAM and STK11.
  Exclusion Criteria:
  -  Without children.
  -  Not reaching appreciate ages.
  -  With contraindications of laparoscopy.
  -  Refusal of risk-reducing surgeries.

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

Clinical trial: Rifampin in CYP24A1-related Hypercalcemia and Hypercalciuria

Summary: This study evaluates the efficacy of rifampin in the treatment of hypercalcemia and/or hypercalciuria in participants with biallelic inactivating mutations of the CYP24A1 gene. Eligible subjects will receive rifampin for a total of 16 weeks during this study.

Detailed description: Idiopathic infantile hypercalcemia (IIH; omim 143880) is a genetic disorder of mineral metabolism characterized by severe hypercalcemia and/or hypercalciuria, suppressed serum levels of parathyroid hormone (PTH) and elevated levels of the active vitamin D metabolite, 1,25(OH)2D. Biallelic inactivating mutations of CYP24A1, the gene encoding the 24-hydroxylase enzyme that represents the principal pathway for inactivation of vitamin D metabolites, cause the most common and severe form of IIH.
  Investigators have preliminary data supporting a novel therapeutic approach to repurpose rifampin as an agent to induce over-expression of CYP3A4, an enzyme that is expressed in the liver and intestine. When CYP3A4 is induced, the increased enzyme activity provides an alternative catabolic pathway for inactivation of vitamin D metabolites. The purpose of this study is to obtain support for an open label, escalating dose study to assess the effect, safety, and tolerability of once daily oral rifampin in participants with IIH due to inactivating mutations in CYP24A1.
  In this study, Investigators will recruit 18 patients with biallelic inactivating mutations of CYP24A1. Participants will be observed for 8-weeks before a 16-week treatment phase of rifampin and 8 further weeks of observation. In addition to following the effect of treatment on calcium homeostasis, Investigators will also study the pharmacokinetics of rifampin in this condition and the effect on intestinal calcium absorption.

Eligibility: Inclusion Criteria:
  -  Males or females age 6 months to 50 years.
  -  Biallelic mutations of CYP24A1
  -  Serum and/or urinary calcium above the normal reference range for age
  -  Serum PTH concentration <20 pg/ml
  -  Elevated or normal serum concentration of 1,25-dihydroxyvitamin D3.
  Exclusion Criteria:
  -  Parents/guardians or subjects who, in the opinion of the Investigator, may be non-compliant with study schedules or procedures.
  -  Allergy to rifampin or related medications
  -  Current therapies with medications or foods that are considered by the research team to potentially affect mineral metabolism, alter clearance of rifampin, or inhibit CYP3A4.
  -  Pregnancy or breastfeeding
  -  Laboratory abnormalities that indicate clinically significant hepatic, or renal disease:
  AST/SGOT > 2.0 times the upper limit of normal ALT/SGPT > 2.0 times the upper limit of normal Total bilirubin > 2.0 times the upper limit of normal Creatinine > 2.0 times the upper limit of normal

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

Clinical trial: Comparing the Impact of Cancer on Quality of Life Between Survivors of Childhood Solid Tumors and Leukemia

Summary: The aim of the study is to examine the impact of cancer and treatment-related effects on the physical and psychosocial well-being and quality of life among Hong Kong Chinese survivors of childhood solid tumors.

Detailed description: In general, cancer can be divided into two main categories: blood cancer and solid tumors. Leukemia refer to the cancers in blood while solid tumors refer to the cancers which involve the formation of an abnormal mass without any liquid or cysts. Patients suffer from leukemia are usually have better prognosis which result in better psychological well-being when compared with those suffer from solid tumors (Rodin et al., 2010). The development of solid tumors in children is different from that in adult. Some of the solid tumors such as osteosarcoma, neuroblastoma, rhabdomyosarcoma, Wilms' tumor and retinoblastoma are exclusively found in children. Other types of solid tumors such as brain tumor can also be found in children.
  Yet, most of recent studies in Hong Kong have focused in general childhood cancer survivors or their family members but no study has been conducted to focus on the physical and psychological well-being of survivors of childhood solid tumors (Li, Lopez, Chung, Ho, & Chiu, 2013; Wills, 2009). Therefore, the quality of life and psychological well-being of solid tumors survivors are always be overestimated. The actual psychological needs of solid tumors survivors may be overlooked. There is thus an imperative need to investigate the impact of cancer and treatment-related effects on the physical and psychosocial well-being and quality of life among Hong Kong Chinese survivors of childhood solid tumors.

Eligibility: Inclusion Criteria:
  -  (1) Hong Kong Chinese under the age of 30 years at the time of study participation;
  -  (2) diagnosed with solid tumors or hematological malignancies under the age of 19 years;
  -  (3) completed the entire course of treatment for at least 6 months;
  -  (4) able to speak fluent Cantonese and read Chinese.
  Exclusion Criteria:
  -  Survivors with secondary malignancy, organic cause psychosis, cognitive or learning problems, or under active cancer treatment will be excluded from this study.

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

Clinical trial: An Observational Study to Evaluate AZD9291 Treatment in Patients With T790M Positive Non-small Cell Lung Cancer

Summary: AZD9291 Early Access Program (EAP) was available in Taiwan during October 2015 to September 2016, a time period before the approval of AZD9291, to supply the unlicensed AZD9291 for the NSCLC patients who received at least one prior EGFR TKI therapy. At the end of September 2016, more than 450 patients have been under AZD9291 treatment through the EAP. This observational study aims to evaluate the clinical benefit of AZD9291 treatment for these patients who were in the EAP

Detailed description: AZD9291 Early Access Program (EAP) was available in Taiwan during October 2015 to September 2016, a time period before the approval of AZD9291, to supply the unlicensed AZD9291 for the NSCLC patients who received at least one prior EGFR TKI therapy. At the end of September 2016, more than 450 patients have been under AZD9291 treatment through the EAP. This observational study aims to evaluate the clinical benefit of AZD9291 treatment for these patients who were in the EAP

Eligibility: Inclusion Criteria:
  -  At least 20 years of age
  -  Patients who were in the AZD9291 Early Access Program
  -  Received at least one dose of AZD9291 treatment as mono-therapy, supported by available source documents
  -  Patient who discontinued the single use of AZD9291, had disease progression, or died under AZD9291 treatment, whichever comes last, during the period from October 01, 2015 to December 31, 2018
  -  Patients agree to provide the written informed consent or the informed consent is waived by IRB.
  Exclusion Criteria:
  • Patients who did not receive at least one dose of EGFR TKI for the treatment of EGFR mutation (+) NSCLC

Relevance to patient case: not relevant