araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Deformable Registration of Multi-parametric MRI to Intra-operative Transrectal Ultrasound for Prostate Brachytherapy

Summary: Objective:
  To focus the high dose radiation to the gross tumor in the prostate while maintaining adequate dose for control of microscopic disease elsewhere in the prostate.
  In order to test the incorporation of the robust MRI and TRUS fusion algorithm in the clinical setting the investigators planned a study of Focused therapy with a primary endpoint of accurate localization of the high risk region. This is a pilot study of dose painted permanent I-125 seed implant to verify absence of tumor cells outside a high risk region using multi-parametric MRI and deformable TRUS registration. The high risk region will be dose painted to 160 Gy and the rest of the prostate will receive the normal prescription dose.

Detailed description: Primary end-point:
  Feasibility of dose painting will be determined by the absence of tumor outside the high-risk region on an intra-operative trans-perineal biopsy.
  Frozen sections will not be obtained, however on receipt of the final pathology 2-4 weeks after the procedure 2 possible scenarios arise:
  1. There is no evidence of cancer: this confirms the accuracy of the TRUS MRI registration.
  2. There is evidence of tumor on the stereotactic biopsy: In this case a regular dosimetric check (this is performed in the Standard of care procedure and is known as post-operative dosimetry) will be performed to determine whether adequate dose was delivered. If not, as the involved needle position was recorded in the treatment plan and labeled with co-ordinates, the regular possibility of accurately adding radioactive seeds is possible.

Eligibility: Inclusion Criteria:
  -  Men suitable for monotherapy with permanent Iodine 125 implant
  -  Age > 50 yrs
  -  PS 0-2 (WHO)
  -  Histologic diagnosis of prostate adenocarcinoma made on transrectal guided prostate biopsy with no fewer than 12 cores taken
  -  No more than 50% of cores involved (summary)
  -  MRI of Prostate with Diffusion Weighted Imaging and Dynamic Contrast Enhancement with demonstrable lesion compatible with biopsy result
  -  Gleason sum no greater than 3+4 =7 in any core
  -  Clinical T stage no higher than T T (tumor) 2A
  -  Prostate volume ≤60 cc
  -  Serum prostate-specific antigen (PSA) no higher than 15 ng/mL
  -  No prior history of malignancy except non-melanoma skin cancer
  -  Must be suitable for general or spinal anesthesia
  Exclusion Criteria:
  Have anesthesia surgical assignment category IV or greater
  -  Cannot cease anti-coagulant therapy
  -  Had a malignancy, other than prostate or skin cancer (except malignant melanoma), within 5 years
  -  urethral stricture
  -  Prior prostate cancer therapies

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Sulphate Accumulation in Prostate

Summary: This study evaluates whether a broccoli intervention (≥ 4 weeks) will result in differences in tissue sulphate levels in men scheduled for prostate biopsies. Comparisons will be made between participants randomised to the broccoli-rich diet and those randomised to the non-intervention arm.

Detailed description: Epidemiological studies provide evidence for a negative correlation between prostate cancer and intake of cruciferous vegetables such as broccoli. Preliminary data from ongoing intervention trials carried out at the IFR suggest that dietary changes can directly influence the metabolic profile of prostate tissue. The most significant result observed to date is that of sulphate accumulation within the prostate. The additional sulphate is likely to drive synthesis of 3'-phosphoadenosine-5'-phosphosulfate, a universal sulphate donor, a process which would consume energy from ATP. A significant rise in levels of both ADP and phosphate has also been observed in prostate tissue from these studies, supporting the potential depletion of cellular ATP. Interestingly, the data indicate that the extent of ADP accumulation is negatively correlated with prostate cancer progression.
  The investigators now propose to undertake a two arm parallel un-blinded study to test the hypothesis that a short-term intervention with broccoli soups will lead to the accumulation of sulphate and ADP in prostate tissue. A potential increase in glutathione metabolites indicating a change in redox status, and therefore functional status, of specific genes involved in tumour suppression (PTEN) will also be investigated.
  Furthermore, the investigators aim to determine whether the accumulation of sulphate and ADP is specific to the prostate gland through the metabolic analyses of both prostate and non-prostate tissues.

Eligibility: Inclusion Criteria:
  -  Males
  -  Scheduled for TPB as part of routine investigation or staging for prostate cancer
  -  Aged 18-80 years
  -  BMI between 19.5 and 35 kg/m2
  -  Smokers and non-smokers
  Exclusion Criteria:
  -  Those regularly taking 5α-reductase inhibitors or testosterone replacement medicines
  -  Those on warfarin treatment
  -  Those diagnosed with diabetes
  -  Those diagnosed with or suspected to be high-risk for human immunodeficiency virus (HIV) and/or hepatitis
  -  Those allergic to any of the ingredients of the broccoli soups
  -  Those taking dietary supplements or herbal remedies which may affect the study outcome. Please note that some supplements may not affect the study and this will be assessed on an individual basis
  -  Those that are unable to understand English or give informed consent
  -  Parallel participation in another research project that involves dietary intervention
  -  Any person related to or living with any member of the study team

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN 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: 68-year-old male with melanoma; genetic feature: PTEN 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
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: The Effect of Medical Exercise Therapy on Pain, Function and Physical Activity in Patients With Knee Osteoarthritis

Summary: The aim of the project is to investigate effects of medical exercise therapy (MET) on patients with knee osteoarthritis. MET is a common physical therapy intervention, and the project aim to strengthen the evidence of this intervention. An experimental cohort design is chosen, and 20 participants will be followed for 6 months. Assessments will be clinical tests, questionnaires and accelerometer measurements before, during, and after a 3 month period of exercise (3 days per week) with a physical therapist. The project will answer if a 3 month physical therapy intervention using MET causes changes in pain level, function and activity level for patients with knee osteoarthritis. In addition, it will investigate whether a single global endurance workout for 30 minutes will have an effect on pain level for these patients


Eligibility: Inclusion Criteria:
  -  x-ray verified knee osteoarthritis (Kellegren & Lawrence grade I-III)
  -  Loss of function and withstanding pain >3 months
  Exclusion Criteria:
  -  physical therapy treatment during the last 3 months
  -  knee injury
  -  inflammatory arthritis
  -  symptoms from the hip joints greater than the knee pain
  -  planned knee surgery the next 6 months
  -  heart and lung disorders or other health issues affecting the ability to complete the intervention

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: A Study of the Anti-PD1 Antibody PDR001, in Combination With Dabrafenib and Trametinib in Advanced Melanoma

Summary: To evaluate the safety and efficacy of the combination of an anti-PD-1 antibody (PDR001), a BRAF inhibitor (dabrafenib) and a MEK inhibitor (trametinib) in unresectable or metastatic BRAF V600 mutant melanoma


Eligibility: Inclusion criteria Part 1: Safety run-in
  -  Histologically confirmed, unresectable or metastatic melanoma with BRAF V600 mutation
  -  Aspartate transaminase (AST) < 2.5× ULN and Alanine transaminase (ALT) < 2.5× ULN
  -  ECOG performance status ≤ 1
  Part 2: Biomarker cohort
  -  Histologically confirmed, unresectable or metastatic melanoma with BRAF V600 mutation
  -  At least two cutaneous or subcutaneous or nodal lesions for tumor sample collection
  -  ECOG performance status ≤ 2
  Part 3: Double-blind, randomized, placebo-controlled part
  -  Histologically confirmed, unresectable or metastatic melanoma with BRAF V600 mutation
  -  ECOG performance status ≤ 2
  Exclusion Criteria:
  Part 1: Safety run-in
  -  Subjects with uveal or mucosal melanoma
  -  Any history of CNS metastases
  -  Prior systemic anti-cancer treatment for unresectable or metastatic melanoma
  -  Prior loco-regional treatment for unresectable or metastatic melanoma in the last 6 month
  -  Prior neoadjuvant and/or adjuvant therapy for melanoma completed less than 6 months
  -  Radiation therapy within 4 weeks prior to start of study treatment
  -  Active, known, suspected or a documented history of autoimmune disease
  Parts 2 & 3: Biomarker cohort & double-blind, randomized, placebo-controlled part
  -  Subjects with uveal or mucosal melanoma
  -  Clinically active cerebral melanoma metastasis
  -  Prior systemic anti-cancer treatment for unresectable or metastatic melanoma
  -  Prior loco-regional treatment for unresectable or metastatic melanoma in the last 6 month
  -  Prior neoadjuvant and/or adjuvant therapy for melanoma completed less than 6 months
  -  Radiation therapy within 4 weeks prior to start of study treatment
  -  Active, known, suspected or a documented history of autoimmune disease
  Other protocol-defined Inclusion/Exclusion may apply.

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: A Study of PLX3397 in Patients With Unresectable or Metastatic KIT-mutated Melanoma

Summary: The purpose of this Phase I/II study is to evaluate safety, pharmacokinetics, and preliminary efficacy of the investigational drug PLX3397 in subjects with unresectable or metastatic KIT-mutated melanoma.


Eligibility: Inclusion Criteria:
  -  Age ≥ 18 years
  -  Unresectable stage III or stage IV melanoma which is histologically confirmed at the treating institution with KIT mutation(s) not known to be resistant to PLX3397
  -  Presence of measurable lesions by Response Evaluation Criteria in Solid Tumors
  -  Eastern Cooperative Oncology Group (ECOG) performance Status (PS) 0-2
  -  Life expectancy ≥ 3 months
  -  Adequate organ and bone marrow function
  -  Women of child-bearing potential must have a negative serum pregnancy test at Screening and must agree to use an effective form of contraception from the time of the negative pregnancy test up to 3 months after the last dose of study drug. Women of non-child-bearing potential must have been postmenopausal for ≥ 1 year or surgically sterile.
  -  Fertile men must agree to use an effective method of birth control during the study and for up to 3 months after the last dose of study drug.
  -  Willingness and ability to provide written informed consent prior to any study-related procedures and to comply with all study requirements
  Exclusion Criteria:
  -  Prior treatment with a KIT inhibitor for melanoma
  -  Presence of NRAS or BRAF mutation
  -  Exposure to any investigational drug within 28 days or unresolved adverse effects from previous therapy
  -  Symptomatic brain metastases.
  -  Active secondary malignancy unless the malignancy is not expected to interfere with the evaluation of safety and is approved by the Sponsor
  -  Concomitant treatment with other anti-neoplastic agents (hormonal therapy acceptable)
  -  Uncontrolled intercurrent or infectious illness
  -  Major surgical procedure or significant traumatic injury within 14 days of initiating study drug or anticipation of the need for major surgery during the study
  -  Previous radiotherapy to 25% or more of the bone marrow and/or radiation therapy within 28 days prior to study entry
  -  Inability to swallow capsules, or refractory nausea and vomiting, malabsorption, an external biliary shunt, or significant bowel resection that would preclude adequate absorption
  -  Congestive heart failure (CHF) New York (NY) Heart Association class III or IV; unstable coronary artery disease (myocardial infarction [MI] more than 6 months prior to study entry is permitted); or serious cardiac arrhythmia
  -  Baseline QTcF ≥ 450 msec (for males) or ≥ 470 msec (for females) at Screening
  -  Active or chronic infection with human immunodeficiency virus (HIV), hepatitis C virus (HCV), or hepatitis B virus (HBV)
  -  Known chronic liver disease
  -  Women who are breast-feeding or pregnant

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Lysosomal Movement and Anabolic Resistance

Summary: Age-associated loss of muscle mass, termed sarcopenia, is strongly associated with functional impairment and physical disability in the elderly. Maintenance or growth of muscle mass is mainly driven by increased muscle protein synthesis (i.e. the generation of new muscle protein) in response to exercise and feeding. However, several investigations have shown that elderly individuals have a blunted protein synthetic response following protein intake. This inability of the elderly to properly respond to growth stimuli has been termed anabolic resistance and plays a significant role in the development of sarcopenia. However, the precise mechanisms underpinning anabolic resistance are unknown.
  It is well established that muscle protein synthesis at the molecular level is regulated by a cellular protein complex called mTORC1. When exposed to a growth stimulus, mTORC1 has been shown to associate with lysosomes, i.e. the intracellular organelles responsible for the breakdown of cellular proteins, and subsequently moving towards the cell periphery.
  This movement of lysosome-associated mTORC1 within the cell is believed to be vital for the activation of protein synthesis, as inhibition of lysosomal movement blunts mTORC1 activation in response to amino acids. Thus, dysregulation of lysosomal movement in ageing muscle may represent an underlying mechanism in the development of anabolic resistance. However, this area of research is unexplored in the context of human skeletal muscle. The investigators hypothesize that dysregulation of lysosomal movement plays a central role in the development of age-associated skeletal muscle anabolic resistance.


Eligibility: Inclusion Criteria:
  Be a non-smoking male within the specified age range for each group (young; 18-35 yrs, old; 65-75 yrs)
  Have a BMI (body mass index, body weight/height in m2) between 18 and 25 kg/m2, which is considered a normal body mass index.
  Be in good general health: no cardiovascular diseases or metabolic diseases.
  Exclusion Criteria:
  Health problems such as: heart disease , metabolic disease such as phenylketonuria, rheumatoid arthritis, uncontrolled hypertension, poor lung function, or any health condition that might put the participant at risk when participating in this study.
  Generalized neuromuscular disease (such as Parkinson's disease or motorneuron disease).
  Involvement in regular structured resistance exercise training at the time of the study.
  Consumption of any analgesic drugs, anti-inflammatory drugs, or medication that is known to affect protein metabolism (beta-blockers, corticosteroids, NSAIDs).
  Participants who have undergone muscle biopsy testing or isotope infusion procedures within the last 5 years.
  Allergic to lidocaine

Relevance to patient case: not relevant
Patient case: 68-year-old male with melanoma; genetic feature: PTEN loss of function

Clinical trial: Study of 1cm Versus 2cm Margins for the Surgical Treatment of cT2N0M0 Melanoma

Summary: This is a randomized non-blinded pilot study for patients with melanoma staging cT2N0M0 who are candidates for surgical resection. The primary objective is to determine the feasibility of randomizing participants with cT2N0M0 malignant melanoma to surgical treatment with 1cm versus 2cm margins. Study will try to determine overall survival for cT2N0M0 malignant melanoma after surgical treatment with 1cm versus 2cm margins.

Detailed description: After randomization, participants will undergo surgery with wide local excision with either 1cm or 2cm margins. The margin will be based upon the previous biopsy site or area of pigmentation. The skin and subcutaneous tissue (down to fascia) will be resected. Closure considerations may require removal of additional tissue for non-oncologic purposes. As per standard of care, sentinel lymph node biopsy will be performed using a dual tracer technique (technetium radiolabeled sulfur colloid and isosulfan blue) with or without lymphoscintigraphy.

Eligibility: Inclusion Criteria:
  -  Biopsy proven T2 malignant melanoma.
  -  Eastern Cooperative Oncology Group (ECOG) score of 0-2.
  Exclusion Criteria:
  -  Visible additional disease that suggests a greater than T2 malignant melanoma
  -  Unable to tolerate general anesthesia
  -  Evidence of distant metastatic disease
  -  Melanoma located on face or digits

Relevance to patient case: not relevant