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

Clinical trial: Curcumin in Pediatric Inflammatory Bowel Disease

Summary: This is a single center, open label forced dose titration study designed to determine the tolerability of curcumin in pediatric patients with inflammatory bowel disease (IBD). This study will provide initial tolerability and safety data in pediatric patients with IBD. Twenty patients with IBD in remission or with mild disease (score <34 on PUCAI or score <30 on the PCDAI) on sulfasalazine or mesalamine aged 8 to 18 years will be enrolled into this study. Each patient will participate in the study for nine weeks. From this study an appropriate dosage will be determined to proceed with a double blinded placebo controlled study.


Eligibility: Inclusion Criteria:
  -  Children and adolescents eight to eighteen years old
  -  Diagnosis of inflammatory bowel disease (IBD) made by a pediatric gastroenterologist based upon history, physical examination, laboratory/radiological studies and gastrointestinal histology
  -  Mild disease or in clinical remission based upon PUCAI or PCDAI score (score <34 on the PUCAI or score <30 on the PCDAI)
  -  Parent/guardian and participant must be able to attend study visits at screening, baseline, and weeks three, six, and nine
  -  Patient must be on a stable dose of IBD medications for at least 3 months
  -  Patient must be able to swallow study medication
  Exclusion Criteria:
  -  Abnormal laboratory values as defined in the protocol
  -  History of increased gastrointestinal symptoms ("flare") in the last 3 months
  -  Current use (past use of these medications is not an exclusion) of medications such as azathioprine, methotrexate or 6-mercaptopurine used to treat IBD
  -  Current use (past use of these medications is not an exclusion) of medications or over-the-counter treatments including but not limited to aspirin, NSAID, botanical treatments (ginger, feverfew, yellow clover, Salix species, Populus species, Betula species, and Gaultheria species), essential fatty acids (flax oil and fish oil). Allowed supplementation includes multivitamin, vitamin D & calcium, folate and vitamin B12, and Iron.
  -  Other serious medical conditions such as neurological, liver, kidney, auto- immune or systemic disease.
  -  History of gastrointestinal surgery or planned gastrointestinal surgery in the future.
  -  Tobacco, alcohol, or illicit drug abuse
  -  Planned surgery during the potential study participation time
  -  Inability to swallow study medication

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

Clinical trial: Protein and RNA Expression Patterns in Predicting Response to Treatment in Patients With Lung Cancer

Summary: RATIONALE: Studying samples of tumor tissue and blood in the laboratory from patients with cancer may help doctors learn more about changes that occur in genetic material (DNA and RNA) and may also identify protein expression patterns related to cancer. It may also help doctors predict how patients will respond to treatment.
  PURPOSE: This research study evaluates changes in DNA, RNA, and proteins with the goal of predicting response to treatment in patients with lung cancer.

Detailed description: OBJECTIVES:
  -  To determine protein and/or RNA expression patterns capable of predicting tumor response to therapy in tumor tissue samples from patients with lung cancer or suspected of having lung cancer.
  -  To characterize the genes and proteins found to be predictive of response in order to help elucidate the molecular biology underlying cancer chemosensitivity.
  -  To evaluate DNA mutations found within the lung cancer sample which may be predictive of response or resistance to certain therapeutic agents.
  OUTLINE: Patients undergo collection of tumor tissue by percutaneous fine needle aspiration, core biopsy, thoracentesis, or during any medically indicated procedure involving removal of lung cancer tissue. Tissue samples are analyzed by a variety of techniques, including DNA sequencing, RNA sequencing and expression levels, protein assessment [by immunohistochemistry, western blot, Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-MS]). The goal of these studies is to identify of gene mutations, gene expression levels, and proteins predictive of treatment response. Blood samples are also collected to obtain normal DNA for analysis.
  After completion of study, patients will be followed until their death.

Eligibility: Inclusion criteria
  -  Diagnosis of suspected lung cancer or lung cancer
  Exclusion criteria
  -  Inability to undergo therapy

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

Clinical trial: DNA Analysis of Tumor Tissue Samples From Patients With Human Papilloma Virus-Associated Cancer of the Oropharynx

Summary: RATIONALE: Studying samples of tumor tissue in the laboratory from patients with cancer may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer.
  PURPOSE: This laboratory study is looking at the DNA in tumor tissue samples from patients with human papilloma virus-associated cancer of the oropharynx.

Detailed description: OBJECTIVES:
  -  Analyze PIK3CA expression and mutation and p110α amplification and expression in tumor tissue samples from patients with human papilloma virus positive (HPV+) and human papilloma virus negative (HPV-) squamous cell carcinoma (SCC) of the oropharynx.
  -  Determine proliferation and survival after PI3K inhibition in HPV(+) and HPV(-) oropharyngeal SCC cell lines and in HPV E6 and E7 expressing cells.
  -  Determine proliferation and survival after PI3K inhibition in short-term cultures of tumor tissue samples from patients with HPV(+) and HPV(-) primary SCC of the oropharynx.
  OUTLINE: Previously collected tumor tissue samples are analyzed for HPV DNA by PCR amplification and direct sequencing of PCR products; expression of E6 protein and relative expression of PIK3CA by qRT-PCR; amplification of PIK3CA by Southern blotting; mutation of PIK3CA; expression of p110α, phospho-AKT, total AKT, and FOXO1 by polyacrylamide gel electrophoresis (PAGE) and immunoblotting; and the effect of PI3K inhibition on cell cycle and apoptosis by flow cytometry. Pharmacological studies are performed on oropharyngeal squamous cell carcinoma cell lines and short-term cultures and HPV E6 and E7 expressing cells using LY 294002 in vitro to analyze response to PI3K inhibition. Results of response to PI3K inhibition will be correlated with HPV status, PIK3CA expression, amplification, and mutation, and p110α expression.
  PROJECTED ACCRUAL: A total of 20 HPV(+) and 20 HPV(-) tumor tissue specimens from patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Undergoing operative procedures for biopsy and/or resection of squamous cell carcinoma (SCC) of the oropharynx
  -  Tumor tissue sample available from the Head and Neck Tissue Repository and Clinical Database of Vanderbilt University
  -  No tumors with human papilloma virus (HPV) DNA sequences but no expression of E6
  PATIENT CHARACTERISTICS:
  -  See Disease Characteristics
  PRIOR CONCURRENT THERAPY:
  -  Not specified

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

Clinical trial: Biomarkers in Predicting Response to Treatment in Patients With Newly Diagnosed Stage III or Stage IV Head and Neck Cancer Treated With Carboplatin, Paclitaxel, and Radiation Therapy

Summary: RATIONALE: Studying samples of tumor tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer. It may also help doctors predict how patients will respond to treatment.
  PURPOSE: This research study is looking at biomarkers in predicting response to treatment in patients with newly diagnosed stage III or stage IV head and neck cancer treated with carboplatin, paclitaxel, and radiation therapy.

Detailed description: OBJECTIVES:
  -  Determine if gene expression patterns that correlate with treatment response and survival can be identified using DNA microarrays in patients with newly diagnosed head and neck squamous cell carcinoma (HNSCC) treated with carboplatin, paclitaxel, and radiotherapy.
  -  Determine if protein expression patterns that correlate with treatment response and survival in HNSCC can be identified using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOFMS).
  -  Determine if the molecular signature of human papilloma virus-16 infection can be determined using DNA microarray and MALDI-TOFMS and correlate with gene and protein expression, treatment response, and survival.
  OUTLINE: Tumor tissue samples are analyzed by DNA microarray analysis and validated by quantitative reverse transcription-polymerase chain reaction (PCR). Protein and gene expression patterns are analyzed by laser desorption ionization-time-of-flight mass spectrometry, high performance liquid chromatography, liquid chromatography-tandem mass spectrometry, and PCR. Samples are also analyzed by tissue microarray and immunohistochemistry.

Eligibility: DISEASE CHARACTERISTICS:
  -  Newly diagnosed head and neck squamous cell carcinoma
  -  Stage III-IV disease
  -  Scheduled for pan-endoscopy
  -  Tumor tissue available from patients treated with carboplatin, paclitaxel, and radiotherapy on protocol VU-VICC-HN-0356
  PATIENT CHARACTERISTICS:
  -  Able to speak English
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

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

Clinical trial: Gene and Protein Expression Patterns in Predicting Response to Cetuximab in Patients With Recurrent and/or Metastatic Head and Neck Cancer

Summary: RATIONALE: Studying samples of tumor tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer. It may also help doctors predict how will patients respond to treatment.
  PURPOSE: This research study is looking at gene and protein expression patterns in predicting response to cetuximab in patients with recurrent and/or metastatic head and neck cancer.

Detailed description: OBJECTIVES:
  -  To identify 100 patients from the Head and Neck Tumor Tissue Repository and Clinical Database treated with cetuximab monotherapy or cetuximab-containing combination therapy as a standard of care for recurrent and/or metastatic head and neck squamous cell carcinoma at Vanderbilt University Medical Center.
  -  To assay the diversity of gene and protein expression patterns seen in these patients.
  -  To identify predictive patterns associated with treatment response and survival of these patients by correlating the laboratory data with clinical data.
  OUTLINE: Tumor tissue specimens and clinical data are obtained from the Head and Neck Tumor Tissue Repository and Clinical Database protocol VU-VICC-HN-0356. Specimens are analyzed for patterns of gene and protein expression predictive of cetuximab treatment response and survival by DNA microarray, tissue microarray, reverse transcriptase-PCR, and mass spectroscopy.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of recurrent and/or metastatic head and neck squamous cell carcinoma
  -  Enrolled on the Head and Neck Tissue Repository and Clinical Database protocol VU-VICC-HN-0356
  -  Previously treated with cetuximab monotherapy or cetuximab-based combination therapy
  -  Sufficient biological material available for analysis
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

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

Clinical trial: Biomarkers in Stored Tumor Samples From Younger Patients With Liver Cancer

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

Detailed description: OBJECTIVES:
  -  To characterize, at a molecular level, archived samples of tissue from young patients with fibrolamellar carcinoma and hepatocellular carcinoma in non-cirrhotic livers matched for age and sex.
  -  To perform genomic analysis on these tissue samples using array comparative genomic hybridization.
  -  To perform targeted gene mutation analysis on these samples by PCR.
  -  To perform proteomic profiling on fixed tissues in these samples by various proteomic methods, including IHC and mass spectrometry.
  -  To look for association between molecular aberrations and clinicopathologic features in these samples.
  OUTLINE: Archived tissue samples are collected from the pathology department at Vanderbilt University Medical Center and from the Mayo Clinic in Rochester, Minnesota. Tissue samples are analyzed by genomic analysis using array comparative genomic hybridization, target gene mutation analysis by PCR, and proteomic profiling on fixed tissues using various proteomic methods, including IHC and mass spectrometry. Samples are also examined for association between molecular aberrations and clinicopathologic features found in each disease.
  Clinical patient data (i.e., age, sex, race, date of diagnosis, risk factors, histology, surgical staging, follow-ups, date of death, and adjuvant therapy) are also collected.

Eligibility: Inclusion Criteria:
  DISEASE CHARACTERISTICS:
  -  Diagnosis of fibrolamellar carcinoma or hepatocellular carcinoma in a non-cirrhotic liver
  -  Archived tumor specimens available for analysis from Vanderbilt University or Mayo Clinic
  Exclusion Criteria:
  -  Not specified
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

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

Clinical trial: Protein Expression in Tumor Tissue Samples From Patients With Cancer of the Oropharynx

Summary: RATIONALE: Studying the proteins expressed in samples of tumor tissue from patients with cancer may help doctors identify and learn more about biomarkers related to cancer. It may also help doctors plan better treatment for patients with cancer of the oropharynx.
  PURPOSE: This laboratory study is looking at protein expression in tumor tissue samples from patients with cancer of the oropharynx.

Detailed description: OBJECTIVES:
  -  To investigate if some of the differences in gene expression are also reflected at the protein level.
  -  To determine whether differences in gene expression that are also reflected at the protein level can be used to develop markers for early detection and disease surveillance.
  -  To identify targets for therapy.
  OUTLINE: Archived tumor tissue samples are analyzed for expression of standard immunohistological markers (e.g., p16, p53, and Ki-67) as well as expression of genes identified in a previous gene expression study. Protein expression data are tested for clinical and demographic correlates and compared with gene expression data.

Eligibility: Inclusion Criteria:
  -  Diagnosis of squamous cell carcinoma of the oropharynx
  -  Tumor tissue samples available from Vanderbilt Head and Neck Tumor Repository and Vanderbilt Pathology archives
  Exclusion Criteria:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

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

Clinical trial: SWOG-9023, DNA Analysis of Tumor Tissue From Patients With Metastatic Kidney Cancer

Summary: RATIONALE: DNA analysis of tumor tissue may help doctors predict how well patients will respond to treatment.
  PURPOSE: This laboratory study is analyzing the DNA in tumor tissue from patients with metastatic kidney cancer.

Detailed description: OBJECTIVES:
  -  Determine if cytogenetic abnormalities can predict clinical outcome, in terms of response to treatment and survival, in patients with metastatic renal cell carcinoma registered to the nephrectomy arm (arm I) of SWOG-8949.
  -  Correlate cytogenetic abnormalities and DNA content analysis (DNA index and S-phase fraction) with clinical outcome.
  OUTLINE: This is a partially prospective, partially retrospective, multicenter, companion study.
  Paraffin-embedded tumor tissue specimens from patients enrolled in SWOG-8949 are evaluated by cytogenetic analysis (e.g., presence of trisomy and loss of Y chromosome) and flow cytometric analysis (e.g., presence of nondiploid cells and presence of abnormal proliferation index).
  PROJECTED ACCRUAL: A total of 80 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of renal cell carcinoma
  -  Any T, any N, M1 disease as specified in SWOG-8949
  -  Eligible for and registered on the nephrectomy arm* (arm I) of SWOG-8949 NOTE: *Patients must be registered on this study before undergoing nephrectomy on SWOG-8949
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

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

Clinical trial: Collecting and Storing Blood Samples From Patients With Cancer

Summary: RATIONALE: Collecting and storing samples of blood from patients with cancer to test in the laboratory may help the study of cancer in the future.
  PURPOSE: This research study is collecting and storing blood samples from patients with cancer.

Detailed description: OBJECTIVES:
  -  To establish a repository for long-term storage of DNA obtained from patients treated at the Cancer Institute of New Jersey.
  -  To establish a mechanism whereby investigators can analyze correlations between genetic polymorphisms and clinical outcomes (e.g., response to treatment).
  OUTLINE: Additional blood samples are collected for banking from patients while they are scheduled for routine blood draw as a part of their normal care. Samples are stored in a secure place under the control of the Cancer Institute of New Jersey Tissue Retrieval service. The samples may be used for DNA, RNA, or protein extraction and analyses, as well as generation of cell lines.
  Demographic data (ethnicity, race, age, and sex), diagnosis, family history, and previous treatments (chemotherapy, radiation, and surgery) are recorded on the case report form and kept in a secure location in the Office of Human Research Services (OHRS).
  Patients may have their samples removed and destroyed at any time.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically or cytologically confirmed malignancy or bone marrow disorder (i.e., myelodysplasia, myeloproliferative syndrome, or aplastic anemia)
  -  Must be undergoing treatment or planning to undergo treatment at the Cancer Institute of New Jersey
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

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

Clinical trial: Transition From Hospital to Home in Solid Organ Transplant (SOT)

Summary: The aim of this study is to determine the influences of discharge teaching and care coordination on how ready a parent is to take their child home from the hospital after a solid organ (kidney, heart and liver) transplant. This study will also look into how the parent handles coping, utilization of healthcare resources, and parent adjustment 3 weeks after discharge from the hospital.

Detailed description: Parents of children that have received a heart, kidney or liver transplant will be asked to participate in this protocol. Involvement in this study involves completion of questionnaires prior to the child being discharged from the hospital. Three weeks after discharge, there will also be a follow-up phone call to complete more questionnaires.
  Readiness for hospital discharge is a under-investigated topic in pediatric solid organ transplant patients, despite the increasing number of pediatric patients undergoing transplant surgery. Results from this study will be used to develop an intervention program to promote readiness for hospital discharge in parents of children who receive a solid organ transplant.

Eligibility: Inclusion Criteria:
  -  parents of children who have undergo a heart, kidney, or liver transplant
  -  English Speaking
  -  Parents are 18 years of age or older
  Exclusion Criteria:
  -  parents with significant cognitive or communication impairment that would not allow them to complete the questionnaires
  -  parent whose child is receiving their 2nd or 3rd organ transplant

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

Clinical trial: Genetic Modifiers for 22q11.2 Syndrome

Summary: The purpose of the project is the determination of how the deletion of DNA from chromosome 22 at the q11.2 band causes the phenotypes observed in velo-cardio-facial syndrome (VCFS). In other words, the purpose remains genotype-to-phenotype matching. Current methods includes the use of whole genome chips and microarray analysis. Blood samples are collected for DNA from every patient who consents from the VCFS Center at Upstate Medical University. They are examined for phenotypic features consistent with our typical clinical evaluation. The information from these examinations will be entered anonymously into a database. Genomic information is then matched to clinical phenotype with appropriate statistical method applied.


Eligibility: Inclusion Criteria:
  -  FISH confirmed diagnosis of 22q11.2 deletion syndrome
  Exclusion Criteria:
  -  none

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

Clinical trial: Omentectomy and Metabolic Syndrome

Summary: The aim of the present study was to evaluate the additional effect of sudden visceral fat reduction by omentectomy on Metabolic Syndrome, acute phase reactants and inflammatory mediators in patients with morbid obesity undergoing Laparoscopic Roux-en-Y Gastric Bypass.

Detailed description: Although weight loss controls Metabolic Syndrome and reduces the level of inflammatory markers in patients with Morbid Obesity, patients may enjoy the benefit achieving metabolic control before significant weight loss occurs.

Eligibility: Inclusion Criteria:
  -  BMI > 35 Kg/m2
  -  Metabolic syndrome diagnosed
  Exclusion Criteria:
  -  Type 1 diabetes
  -  Uncontrolled type 2 diabetes
  -  Cirrhosis or active hepatitis
  -  Pregnancy
  -  Recent MI or stroke

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

Clinical trial: Trends in Intellectual Development in Down Syndrome

Summary: Previous foreign studies revealed that the IQ in Down syndrome (DS) declines with age, but not any investigation of domestic data in Taiwan was available. Individuals with DS are characterized by limited verbal development, and in this article, authors look into the diverging verbal-nonverbal abilities in the DS phenotype.

Detailed description: The present study investigated this by analysis the test results of development /intelligence scales. To compare initial cross-sectional data with longitudinal follow-up, about 12 people with DS were included.

Eligibility: Inclusion Criteria:
  -  Down syndrome with psychological test results
  Exclusion Criteria:
  -  Comorbidity of severe Autism or visual/auditory impairment

Relevance to patient case: not relevant