araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: A Phase 1 Dose Escalation Study of the Safety, Tolerability, and Pharmacokinetics of Ipilimumab in Chinese Subjects With Select Advanced Solid Tumors

Summary: The purpose of this study is to determine whether ipilimumab is effective in the treatment of select advanced (unresectable, metastatic, or recurrent) solid tumors in Chinese subjects.


Eligibility: For more information regarding BMS clinical trial participation, please visit www.BMSStudyConnect.com.
  Inclusion Criteria:
  -  Subjects with the following advanced solid tumors; metastatic or recurrent
  -  Must have measurable/non-measurable lesion per Response Evaluation Criteria in Solid Tumors (RECIST v1.1) criteria.
  -  Subjects have ability to comply with treatment, procedures and pharmacokinetics (PK) sample collection and the required study follow-up
  -  Chinese women and men, ages 18 years or older
  Exclusion Criteria:
  -  Subjects with brain metastases are excluded unless clinically stable for more than 4 weeks at the time of randomization as determined by the investigator
  -  Subjects with ocular melanoma are excluded
  -  Any other malignancy from which the subject has been free of disease for less than two years, with the exception of adequately treated and cured basal or squamous cell skin cancer, superficial bladder cancer, or carcinoma in situ of the cervix
  -  History of, or currently active, autoimmune diseases, including but not limited to inflammatory bowel disease, rheumatoid arthritis, autoimmune hepatitis, systemic sclerosis (scleroderma and variants), systemic lupus erythematosus, autoimmune vasculitis, autoimmune neuropathies (eg, Guillain-Barre syndrome). Vitiligo is not excluded
  -  Any current or history of immunodeficiency, splenectomy, or splenic radiation

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Phase 1/1b Study to Evaluate the Safety and Tolerability of CPI-444 Alone and in Combination With Atezolizumab in Advanced Cancers

Summary: This is a phase 1/1b open-label, multicenter, dose-selection study of CPI-444, an oral small molecule targeting the adenosine-A2A receptor on T-lymphocytes and other cells of the immune system. This trial will study the safety, tolerability, and anti-tumor activity of CPI-444 as a single agent and in combination with atezolizumab, a PD-L1 inhibitor against various solid tumors. CPI-444 blocks adenosine from binding to the A2A receptor. Adenosine suppresses the anti-tumor activity of T cells and other immune cells.

Detailed description: This is a phase 1/1b open-label, multicenter, dose-selection study of CPI-444, an oral small molecule targeting the adenosine-A2A receptor on T-lymphocytes and other cells of the immune system. This trial will study the safety, tolerability, and anti-tumor activity of CPI-444 as a single agent and in combination with atezolizumab, an intravenous PD-L1 inhibitor. CPI-444 blocks adenosine from binding to the A2A receptor. Adenosine suppresses the anti-tumor activity of T cells and other immune cells.

Eligibility: Inclusion Criteria
  1. Eastern Cooperative Oncology Group (ECOG) Performance Status 0-1.
  2. Documented incurable cancer with one of the following histologies: non-small cell lung cancer, malignant melanoma, renal cell cancer, triple negative breast cancer, colorectal cancer with microsatellite instability (MSI), and bladder cancer.
  3. At least 1 measurable lesion per Response Evaluation Criteria in Solid Tumors (RECIST 1.1).
  4. At least 1 but not more than 5 prior systemic therapies for advanced/recurrent or progressing disease.
  Exclusion Criteria
  1. History of severe hypersensitivity reaction to monoclonal antibodies.
  2. Any active autoimmune disease or a documented history of serious autoimmune disease within the past 5 years requiring immunosuppressive therapy.
  3. History of idiopathic pulmonary fibrosis, organizing pneumonia, drug-induced pneumonitis, idiopathic pneumonitis, or clinical symptoms of active pneumonitis.
  4. The use of any investigational medication or device in the 30 days prior to screening and throughout the study is prohibited.
  5. If a patient is currently receiving denosumab, this must be discontinued prior to enrollment. Substitution with biphosphonates are acceptable.

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Employment and Quality of Life in Patients With Malignant Melanoma

Summary: Within the first year after diagnosis, data on employment and quality of life will be collected and evaluated in patients with malignant melanoma


Eligibility: Inclusion Criteria:
  -  first diagnosis of malignant melanoma stage 0 to stage IIIC within the last 6 weeks
  -  written informed consent
  Exclusion Criteria:
  -  diagnosis of malignant melanoma stage IV
  -  inability to follow the protocol

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Biomarkers for the Activity of Immune Checkpoint Inhibitor Therapy in Patients With Advanced Melanoma

Summary: 1. Screen and recruitment: patients will be screened based on their prior history and intention to initiate treatment with an immune checkpoint inhibitor.
  2. Study phase:
  -  Collection of baseline demographic data, prior disease history, nature of ICI therapy, outcome data of ICI therapy (treatment disposition, toxicity, tumor response and survival).
  -  Collection of blood samples will be performed every 3 to 4 weeks for the first year on ICI therapy and every 6 to 12 weeks thereafter until the end of ICI therapy, disease progression, death or loss to follow-up. Collection of blood samples will be aligned with the visits necessary for the administration of the ICI therapy.
  -  Collection of archival melanoma metastasis tissues will be performed on a continuous basis and be triggered by availability of such tissue following therapeutic resections of melanoma metastases.
  3. Follow-up phase

Detailed description: 1. Screen and recruitment: patients will be screened based on their prior history and intention to initiate treatment with an immune checkpoint inhibitor. This screening of candidate patients by the investigators will be non-interventional. Patients that are considered eligible candidates will be invited to participate in this study and to Page 3/18 provide written informed consent.
  2. Study phase:
  -  Collection of baseline demographic data, prior disease history, nature of ICI therapy, outcome data of ICI therapy (treatment disposition, toxicity, tumor response and survival).
  -  Collection of blood samples will be performed every 3 to 4 weeks for the first year on ICI therapy and every 6 to 12 weeks thereafter until the end of ICI therapy, disease progression, death or loss to follow-up. Collection of blood samples will be aligned with the visits necessary for the administration of the ICI therapy.
  -  Collection of archival melanoma metastasis tissues will be performed on a continuous basis and be triggered by availability of such tissue following therapeutic resections of melanoma metastases.
  3. Follow-up phase: patients who stop treatment with the immune checkpoint inhibitor will be followed-up for

Eligibility: Inclusion Criteria:
  1. Histologically confirmed malignant melanoma;
  2. AJCC Stage IIIC or IV melanoma with evaluable disease;
  3. Treatment with an immune checkpoint inhibitor;
  4. Willing and able to give written informed consent;
  5. Accessible for treatment and follow-up;
  Exclusion Criteria:
  -  non

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Improvement of Metabolic Health After Thylakoid Supplementation

Summary: Objective:
  The purpose of this study was to investigate the possible effects of green-plant thylakoid supplementation to a restricted diet intervention study in overweight to obese men.
  Methods:
  Overweight-obese men (BMI 25 - 35) were treated to a 30 E% restricted diet for one month, followed by one month of stabilization. Then they were divided in two treatment arms of one month each; one thylakoid-enriched diet (n=10) and one control diet (n=10). Body measurements and blood samples were taken throughout the study.

Detailed description: Twenty healthy, non-vegetarian, non-smoking Caucasian men were included in the study. Inclusion criteria: men aged 40 to 70 years with a BMI of 25 to 35. Exclusion criteria: Metabolic disturbances, bariatric surgery, recent diet, food allergies or treatment with antibiotics. The study protocol was approved by the Ethical Committee of Lund University, Sweden (#2006/361).
  The trial consisted of three periods: 1) diet-restriction period (one month) 2) stabilizing period (one month) 3) diet-restriction period with supplementation of thylakoids or placebo (one month). The two weight-losing periods included strict diet recommendation with -30 energy % (E%), and macronutrient composition: 55-65 E% carbohydrates, 10-15 E% protein and 25-35 E% fat. Sixty minutes of low intensive exercise per day was also required.
  During the stabilizing month participants were instructed to eat a healthy diet to be able to keep their achieved weight-loss.
  Day 0, 28, 56 and 84 the participants arrived after 12-hour fasting for blood sampling and anthropometric measurements. The blood samples were analyzed for plasma-glucose, insulin, HbA1c, inflammation markers, cholecystokinin, ghrelin, total cholesterol, LDL-cholesterol, HDL-cholesterol, and triacylglycerol.

Eligibility: Inclusion Criteria:
  -  Healthy, overweight, non-vegetarian, non-smoking
  Exclusion Criteria:
  -  Medication for metabolic disturbances, previous bariatric surgery, diabetes, had been on diet or treated with antibiotics during last 3 months, food-allergies

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Comparison Between Hemitrapeziectomy and Total Trapeziectomy With Ligament Reconstruction and Tendon Interposition in Trapeziometacarpal Osteoarthritis II-III Eaton-Littler

Summary: 1. Introduction:
  Investigators think that surgery with preservation of healthy joints (hemitrapeziectomy) in trapeziometacarpal osteoarthritis without affecting sapho-trapezo-trapezoid joints, is better for scaphoid stability by preventing its collapse and thus preserving the stability of the carpus.
  2. Objectives and Hypothesis:
  Ligamentoplasty with partial trapeziectomy in grades II-III Eaton presents better results in the pollicis-lateral pinch (key pinch) strength than ligamentoplasty with total trapeziectomy.
  Main Objective:
  To demonstrate using the dynamometer that the postoperative key pinch strength higher using ligamentoplasty with partial trapeziectomy in grades II-III Eaton.
  Secondary objectives:
  To measure the collapse of the first column of thumb using calibrated radiographic analysis. Pain (E.V.A Scale). Range of motion (measured with goniometer). Quality of life (DISABILITIES OF THE ARM, SHOULDER AND HAND questionnaire).
  3. Methodology:
  It is a single-center randomized trial, parallel-group, in which two types of surgical techniques (TT - TP) will be compared. Patients will be randomized in this two techniques will be followed for one year, in routine clinical practice.


Eligibility: Inclusion Criteria:
  -  Patients with Osteoarthritis in the trapeziometacarpal joint determined by the classification of Eaton-Littler (stages II-III) with trapeziometacarpal joint pain, loss of function, that were included in surgical waiting list and have accepted under informed consent, including the study.
  Exclusion Criteria:
  -  Patients with osteoarthritis Eaton-Littler (stage IV).
  -  Patients with huge affection of trapezium subchondral cysts and poor quality of trabecular bone.
  -  Cognitive impairment.
  -  Old fracture with impairment of the same extremity.
  -  Rheumatic active illness.
  -  Patients who withdraw their informed consent, or in case of impossibility of opinion by clinical status, whose legal guardians or close relatives to withdraw their informed consent to participate in the study.
  -  Patients who for any reason not related to the indication needed discontinue study participation or impossible to carry out assessments under more than two follow-up visits.
  -  Patients in whom it is considered that participation in the clinical study can be a prejudice, the physician responsible for patient care opinion.

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Impact of Obstructive SAS on Metastatic Potential of Cutaneous Melanoma

Summary: Hypothesis: to address if diagnosis of obstructive sleep apnea before or during the extending check-up is a risk factor toward metastasis for melanoma stage ≥ tIIaN0M0 Study design: Adult patients with a Breslow's Thickness ≥ 1mm coming to the surgery consultation will have a nocturnal oximetry for screening of obstructive sleep apnea. Patients having an abnormal nocturnal oximetry will be explored by polysomnography in order to detect sleep apnea syndrome. Patients with sleep apnea will be treated.
  Standard dermatologic follow-up over a 3 years period with thoraco-abdominal-pelvic and cerebral CT-scan and a lymph-node ultrasound every 6 months will be performed.

Detailed description: Melanoma is a cutaneous cancer due to a proliferation of melanocytes. For metastatic cases the prognostic is poor (18% survival at 5 years). Few factors predict metastasis. Sleep Apnea Syndrome is involved in mechanism of carcinogenesis and aggressiveness markers of malignant cutaneous melanoma.
  Hypothesis: to address if diagnosis of obstructive sleep apnea before or during the extending check-up is a risk factor toward metastasis for melanoma stage ≥ tIIaN0M0 Study design: Adult patients with a Breslow's Thickness ≥ 1mm coming to the surgery consultation will have a nocturnal oximetry for screening of obstructive sleep apnea. Patients having an abnormal nocturnal oximetry will be explored by polysomnography in order to detect sleep apnea syndrome. Patients with sleep apnea will be treated.
  Standard dermatologic follow-up over a 3 years period with thoraco-abdominal-pelvic and cerebral CT-scan and a lymph-node ultrasound every 6 months will be performed.
  Sample size: based on previous data from the investigators showing that 25% of patients with a Breslow's Thickness ≥ 1mm will have node or visceral metastasis. For an alpha threshold of 5% and a study power of 80%, with 5% of dropouts, with the hypothesis that 40% of apnea syndrome patients will metastasis versus 20% in the control group the study should include 83 patients in each group.
  Statistical analysis: an intermediate analysis after 80 included patients will be performed. Peto method will be followed, results will be considered significant with a p≤0.001 and the study will be stopped.
  Normality of data will be checked by Kurtosis and Skewness tests, variance equality will be tested with the Leven test. The significance level will be set at 5%.

Eligibility: Inclusion Criteria:
  -  adults hospitalized in the dermatological unit for the initial consult for a melanoma with a Breslow's Thickness ≥ 1mm
  Exclusion Criteria:
  -  pregnant women
  -  Institutionalized patient
  -  patients with metastasis in the lymph node or any organ at the time of the first consult
  -  patients with another neoplasia requiring treatment other than surgery in the last 5 years
  -  patients with creatinine above 200µmol/ml or clearance below 30ml/min

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Optimized Caloric-proteic Nutrition in Septic and Septic Shock Patients

Summary: In this pilot randomized prospective controlled trial the investigators intend to compare the use of a nutritional therapy based on caloric intake determined by indirect calorimetry and high protein intake with nutritional regimen based on 25 Kcal / kg / day and protein intake usually recommended for critically ill patients (1.4 to 1.5 grams / kg / day of protein).


Eligibility: Inclusion Criteria:
  -  Patients admitted to the ICU with sepsis and septic shock according to 3rd International Sepsis Consensus Conference Definitions for sepsis and septic shock
  -  Mechanically ventilated
  -  Expected length of stay in ICU ≥ 4 days
  -  Written informed consent obtained from authorized surrogates
  Exclusion Criteria:
  -  Pregnancy
  -  Requirement for inspired oxygen content (FIO2) > 0.60
  -  High output bronchopleural fistula

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Non-Surgical Management of Attenuated and Deleterious (Classical) Familial Adenomatous Polyposis: A Long-term Surveillance Program

Summary: The primary objective of this chart review study is to evaluate the outcomes of subjects with Attenuated Familial Adenomatous Polyposis (AFAP) and Deleterious Familial Adenomatous Polyposis (FAP) who have not undergone surgical resection of the colon.
  A secondary objective of this study is to compare 1) the colonoscopic and pathology histories including history of ampullary adenoma in the duodenum over family generations, 2) the use of chemopreventive medications, and 3) clinical features of subjects who pursued prophylactic surgical resection of the colon with those that have elected to continue routine colonoscopic surveillance in an effort to better characterize factors (e.g. polyp burden, ampullary adenoma and level of dysplasia, etc) which may influence management decisions.

Detailed description: The UTMDACC family history database will be queried for the presence of cases meeting the above criteria (attenuated Familial Adenomatous Polyposis (FAP), classical AFP [i.e. identifiable APC mutation], and/or a compatible family history or personal adenoma burden of > 50 adenomas).
  The data related to the patients with attenuated FAP and classical AFP who underwent endoscopic surveillance or surgery will be collected through chart review and all data is retrospective as of February 15, 2016.
  The University of Texas MD Anderson Cancer Center (UTMDACC) medical record number for these cases will be used to identify the patient in ClinicStation: 1) records of endoscopy procedures, 2) operative reports, and 3) associated clinic notes will be reviewed for: a) whether the above evaluation criteria have been met, b) age, c) gender, d) age at initial colonoscopy, e) total number of colonoscopies, f) number of adenomas identified, g) cancer diagnoses, h) chemopreventive medications, i) type of surgery, j) number of hospitalizations, k) length of hospital stay, l) identification of an underlying APC mutation, and ll) family history information. The UT MDACC family history database will also be reviewed for updated family history information including ampullary adenomas and outcomes of genetic testing for identified cases.

Eligibility: Inclusion Criteria:
  1. Participants with either a genetic diagnosis of AFAP/FAP (i.e. an identifiable APC gene mutation), and/or a compatible family history and pathology including history of ampullary adenoma in the duodenum over family generations, or personal adenoma burden of > 50 adenomas are to be included.
  Exclusion Criteria:
  1. Participants who do not have with Attenuated Familial Adenomatous Polyposis (AFAP) and Deleterious Familial Adenomatous Polyposis (FAP).

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Evaluation Interest of the Circulating Tumor DNA Dosage in Patient With Hepatic Metastatic Uveal Melanoma Candidate to Complete Resection (ct DNA R0)

Summary: Prospective, open labelled, monocentric trial to evaluation of the circulating tumor DNA rate in the blood, before and after curative resection of hepatic metastasis of uveal melanoma (HMUM) and during post-surgery follow-up

Detailed description: The ct DNA R0 study is a prospective, open labelled, monocentric trial. The aim is to evaluate the circulating tumor DNA rate in the blood, before and after curative resection of hepatic metastasis of uveal melanoma (HMUM) and during post-surgery follow-up.
  The patient will have a blood sample before and after the surgery and during the post-surgery follow-up. The patient will have a maximum of 10 blood samples during the 2 years of his follow-up of the study.

Eligibility: Inclusion Criteria:
  1. Aged 18 years old or more
  2. Patient with hepatic injury of metastatic uveal melanoma eligible for curative surgery (R0).
  3. No other distant metastasis (CT thoracic -abdomino -pelvic, bone scan).Measurable metastatic disease (echography, CT and/or MRI, FDG-PET, (fluoro- D-glucose integrated with computed tomography)).
  4. Patient able to stand a blood collection.
  5. Patient explanation given and consent information signed or by legal representative.
  Exclusion Criteria:
  6. Patient without social protection / insurance..
  7. Patient with hepatic metastasis unresectable by surgery
  8. Patient with extra-hepatic metastasis.
  9. Person deprived of liberty or under guardianship
  10. Inability to submit to medical monitoring of the trial for reasons of geography, social or psychological.

Relevance to patient case: not relevant
Patient case: 47-year-old male with melanoma; genetic feature: APC loss of function

Clinical trial: Intestinal Stem Cells Characterization

Summary: A monocentric pilot studying intestinal organoids from endoscopic biopsies of IBD (Crohn and ulcerative colitis), FAP patients and healthy controls. Investigate the morphological characteristics of organoids, the expression of genes and proteins of the Wnt/APC/beta-catenin pathway within both ISC.

Detailed description: Intestinal organoids are 3D mini-guts produced in vitro based on intestinal stem cell (ISC) capabilities. These organoids contain all of the intestinal epithelial cells. The renewal of the two kinds of ISCs, which are present at the bottom of intestinal crypts, is controlled by Wnt/APC/beta-catenin pathway. Mutations of genes involved in this pathway are found in intestinal polyposes like familial adenomatous polyposis (FAP, APC gene).
  This model is of interest to study early pathophysiological events occurring within intestinal epithelium, in the context of FAP and inflammatory bowel diseases (IBD). An excessive proliferation or an abnormal healing is found in FAP and IBD respectively. Investigators hypothesized that it could specifically involved one of the 2 ISCs. Columnar basal cells (CBC) and ISC located at the +4 position from the bottom of the crypt (ISC+4) can both differentiate into absorptive or secretory intestinal epithelial cells. However, CBC and ISC+4 could have different metabolic, migratory functions, or stress survival.
  Investigators designed a monocentric pilot study to develop intestinal organoids from endoscopic biopsies of IBD (Crohn and ulcerative colitis), FAP patients and healthy controls. Investigators plan to investigate the morphological characteristics of organoids, the expression of genes and proteins of the Wnt/APC/beta-catenin pathway within both ISC. Will also be studied the expression of key genes of tumor initiation (PTEN, BMPR1A, p53 and KRAS) and inflammatory parameters (cytokines and lipid mediators).
  The results of this study could improve the understanding of intestine renewal. Later on, the development of new drugs could beneficiate to IBD and FAP patients.

Eligibility: Inclusion Criteria: patient must have a coloscopy for intestinal pain -
  Exclusion Criteria: cancer

Relevance to patient case: not relevant