araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 57-year-old male with melanoma; genetic feature: BRAF (V600E), PTEN loss of function

Clinical trial: The Predictive Value of Coexisting TMPRSS2-ERG Gene Fusion and PTEN Deletion in Prostate Cancer Patients With Biochemical Failure Status Post Salvage or Radical Radiation Therapy

Summary: The objective of the study is to evaluate the predictive value of TMPRSS2-ERG gene fusion and PTEN in patients with high risk prostate cancer treated with first line LHRH agonist after biochemical failure.

Detailed description: The objective of the study is to evaluate the predictive value of TMPRSS2-ERG gene fusion and PTEN in patients with high risk prostate cancer treated with first line LHRH agonist after biochemical failure.
  Patients in this study will be treated with standard hormonal treatment. Patients will remain on treatment regardless of rising PSA. PSA, other systemic therapy maybe added and the patients with oligometastasis could be treated with radiation therapy; this would be at the discretion of the treating oncologist.
  The primary endpoint of this study is to determine the predictive value of TMPRSS2-ERG gene fusion and PTEN in hormonal refractory free survival and clinical progression rate in three years. The secondary endpoints are to evaluate the relation between Gleason score and TMPRSS2-ERG gene fusion and PTEN independently and together, the relation between T stage and TMPRSS2-ERG gene fusion and PTEN independently and together, and to determine the association of these markers with overall survival.

Eligibility: Inclusion Criteria:
  -  T3a +
  -  PSA > 20
  -  Gleason 8 or higher
  -  Karnofsky performance status ≥ 70.
  -  Signed study-specific informed consent
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 57-year-old male with melanoma; genetic feature: BRAF (V600E), PTEN loss of function

Clinical trial: Study to Analyze Mutations in V600 BRAF Oncogen in Participants With Metastatic Melanoma

Summary: This is a national, multicenter, cross-sectional epidemiological study in adult Spanish participants diagnosed with advanced or metastatic melanoma.


Eligibility: Inclusion Criteria:
  -  Valid tumor samples from participants diagnosed with Stage IIIc or IV melanoma
  -  Written informed consent granted
  Exclusion Criteria:
  - Do not fulfill one or more inclusion criteria

Relevance to patient case: definitely relevant
Patient case: 57-year-old male with melanoma; genetic feature: BRAF (V600E), PTEN loss of function

Clinical trial: Study of Efficacy and Safety of Dabrafenib and Trametinib Combination Therapy in Japanese Patients With BRAF V600E Stage IV NSCLC

Summary: This is an open-label, multicenter, non-randomized, single arm, phase II study to assess efficacy and safety of the dabrafenib and trametinib combination in Japanese patients with any line, stage IV NSCLC harboring a confirmed BRAF V600E mutation.
  Patients will receive oral dabrafenib twice daily and oral trametinib once daily combination therapy. Patients may continue study treatment until disease progression, unacceptable adverse events, start of a new anti-cancer therapy, consent withdrawal, death, or end of the study. Patients who have met the criteria for disease progression (PD) according to RECIST v1.1 may continue to receive study treatment if the investigator believes the patient is receiving clinical benefit and the patient is willing to continue on study treatment. After discontinuation of study treatment, all patients will be followed for survival until death, lost to follow-up, withdrawal of consent, or end of study.


Eligibility: Inclusion Criteria:
  -  Histologically- or cytologically-confirmed diagnosis of NSCLC stage IV (according to AJCC Staging 7th Edition)
  -  Presence of a BRAF V600E mutation in lung cancer tissue. BRAF V600E mutation tested by local laboratory (e.g. study center laboratory, local laboratory company) with proper quality control and license to operation by local health authority is allowed.
  -  Measurable disease according to RECIST v1.1.
  Exclusion Criteria:
  -  Previous treatment with a BRAF inhibitor (including but not limited to dabrafenib, vemurafenib, encorafenib, and XL281/BMS-908662) or MEK inhibitor (including but not limited to trametinib, cobimetinib, binimetinib, AZD6244, and RDEA119) prior to start of study treatment
  -  Patients with brain metastases are excluded if their brain metastases are:
  -  Symptomatic OR
  -  Treated (surgery, radiation therapy) but not clinically and radiographically stable 3 weeks after local therapy (as assessed by contrast enhanced magnetic resonance imaging [MRI] or computed tomography [CT]), OR
  -  Asymptomatic and untreated but >1 cm in the longest dimension
  -  History of malignancy with confirmed activating RAS mutation at any time.
  -  History of interstitial lung disease or pneumonitis
  -  A history or current evidence of retinal vein occlusion (RVO)
  -  Current evidence of unstable aneurysm or one that needs treatment
  Other protocol-defined inclusion/exclusion may apply.

Relevance to patient case: not relevant
Patient case: 57-year-old male with melanoma; genetic feature: BRAF (V600E), PTEN loss of function

Clinical trial: A Study to Detect V-Raf Murine Sarcoma Viral Oncogene Homolog B1 (BRAF) V600 Mutation on Cell-Free Deoxyribonucleic Acid (cfDNA) From Plasma in Participants With Advanced Melanoma

Summary: This is a single arm, multicenter, open label, and non-randomized clinical study on adult participants with unresectable or metastatic melanoma. The study will be conducted in two phases. Pre-screening phase will assess the BRAF V600 mutation in a new mutation analysis triggered by a mutant plasma cfDNA test result. Treatment phase will assess the clinical outcome for the participants treated with vemurafenib plus cobimetinib. The length of the study will be approximately 36 months.


Eligibility: Inclusion Criteria:
  Pre-screening phase:
  -  Participants with histologically confirmed melanoma, either unresectable Stage IIIc or Stage IV metastatic melanoma, as defined by American Joint Committee on Cancer (AJCC) 7th edition
  -  Documentation of BRAF V600 test result mutation-positive status on melanoma tumor tissue using a validated tissue test
  Treatment Phase:
  -  Eastern cooperative oncology group (ECOG) performance status of 0-2
  -  Adequate hematologic and end organ function obtained within 14 days prior to first dose of study drug treatment
  -  Negative serum pregnancy test prior to commencement of dosing in women of childbearing potential
  -  Absence of any psychological, familial, sociological, or geographical condition that potentially hampers compliance with the study protocol and treatment regimen and follow-up after treatment discontinuation schedule
  -  Female participants of childbearing potential and male participants with partners of childbearing potential must agree to always use 2 effective forms of contraception during the course of this study and for at least 3 months after completion of study therapy
  -  Participants should be able to swallow tablets
  -  Documentation of BRAF mutation positive status in melanoma tissue (archival or new)
  Exclusion Criteria:
  Treatment Phase:
  -  History of prior rapidly accelerated fibrosarcoma (RAF) or mitogen-activated protein kinase (MEK) pathway inhibitor treatment
  -  Palliative radiotherapy within 14 days prior to the first dose of study treatment
  -  Evidence of retinal pathology on ophthalmologic examination
  -  Systemic risk factors for retinal vein occlusion (RVO)
  -  History of clinically significant cardiac dysfunction
  -  Current severe, uncontrolled systemic disease
  -  Pregnancy, lactating or breast feeding
  -  Intake of potent cytochrome P450 3A4 (CYP3A4) enzyme inducer and potent CYP3A4 enzyme inhibitor at least 7 days prior to initiation of and during the study treatment

Relevance to patient case: definitely relevant
Patient case: 57-year-old male with melanoma; genetic feature: BRAF (V600E), 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: 57-year-old male with melanoma; genetic feature: BRAF (V600E), PTEN loss of function

Clinical trial: Accelerated Aging in Middle-Aged Men With Sleep-disordered Breathing.

Summary: Obstructive Sleep Apnea Syndrome (OSAS) regardless of any other associated risk factor can lead to accelerated aging. The study of aging-related Obstructive Sleep Apnea (OSA) is difficult because of associated risk factors (diabetes, hypertension, dyslipidemia, obesity), promoting themselves aging. The investigators propose to compare a group of OSAS patients free of any associated pathology, to subjects matched for age, sex, smoking and body mass index (BMI)


Eligibility: Inclusion Criteria
  Patient:
  -  Men aged 20 to 65 years
  -  Having polysomnography in the Functional Explorations department, Sleep Laboratory, Hospital Henri Mondor, Creteil
  -  With an AHI > 5 / h
  Healthy volunteers:
  -  Men aged 20 to 65 years
  -  With an AHI ≤ 5 / h
  Exclusion Criteria
  All subjects:
  -  Known cardiovascular risk: hypertension treated, diabetes treated, dyslipidemia treated,
  -  Known cardiovascular disease associated (heart failure, rhythm disorder ...)
  -  Known respiratory diseases
  -  Known neoplastic pathology, known chronic inflammatory disease
  -  Psychiatric pathology treated
  -  Medication
  -  Not affiliated to the French social health care system
  -  Major protected person
  -  Private person of liberty
  -  People in emergency situation
  -  Patient refusing to participate in the study

Relevance to patient case: not relevant
Patient case: 57-year-old male with melanoma; genetic feature: BRAF (V600E), PTEN loss of function

Clinical trial: Biomarker-Integrated Umbrella, Advanced Gastric Cancer

Summary: In-depth understanding of molecular characteristics of gastric cancer enabled us to realize personalized medicine with targeted agents in gastric cancer treatment.The investigators initiated open-label, randomized, controlled phase II, multi-arm trial comparing targeted therapy based on tumor molecular profiling with standard paclitaxel therapy as second line treatment.


Eligibility: Inclusion Criteria:
  1. Histologically or cytologically confirmed locally advanced or metastatic gastric cancer and gastroesophageal junction cancer
  2. Eastern Cooperative Oncology Group performance status of 0 to 1
  3. Male or female; ≥ 19 years of age
  4. On or progression after 1st line palliative chemotherapy
  5. Subjects with evaluable lesion (using RECIST 1.1 criteria)
  6. Subjects who meet the following criteria:
  -  Absolute neutrophil count ≥ 1000 /µL
  -  Platelet count ≥ 75,000/ µL
  -  Serum creatinine < 1.5 x upper limit of normal or Creatinine clearance ≥60 mL/min
  -  aspartate aminotransferase and alanine transaminase 3 x upper limit of normal
  Exclusion Criteria:
  -  Evidence of any other significant clinical disorder or laboratory finding that makes it undesirable for the patient to participate in the study

Relevance to patient case: not relevant
Patient case: 57-year-old male with melanoma; genetic feature: BRAF (V600E), 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: definitely relevant
Patient case: 57-year-old male with melanoma; genetic feature: BRAF (V600E), 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
Patient case: 57-year-old male with melanoma; genetic feature: BRAF (V600E), PTEN loss of function

Clinical trial: Exercise Duration Models, in Middle-aged Men

Summary: Duration of exercise is an important factor among the medical guides for weight loss. However, there is still little knowledge about other its models in middle-aged and older men. The present study aimed to determine the effects of the interval training on weight loss and lipid profile, and to compare its efficiency with the continuous training.

Detailed description: Participants included sedentary men (age 45-75 years) with overweight or obesity (n= 82). They were randomly divided into two groups including continuous exercise, and interval exercise. The weight assessment parameters including change in weight and body composition, blood sample tests were performed pre- and three month post-intervention.

Eligibility: Inclusion Criteria:
  -  Sedentary lifestyle
  -  Good Health
  -  Weight stability
  Exclusion Criteria:
  Abnormality or history of Disease

Relevance to patient case: not relevant
Patient case: 57-year-old male with melanoma; genetic feature: BRAF (V600E), PTEN loss of function

Clinical trial: Risk Stratification Among Individuals Who Have Many Moles on Their Skin

Summary: The investigators are doing this study to improve our ability to identify which people with many moles on their skin are most likely to develop skin melanoma. The investigators hope to identify features of moles that are associated with melanoma risk. The investigators hope to use this information to customize and tailor melanoma screening to the individual patient based on a better estimate of their individual risk.


Eligibility: Inclusion Criteria:
  -  Patients ≥ 18 years of age
  -  High-risk nevus phenotype (≥ 50 nevi and ≥ 1 atypical nevus)
  -  First presented to MSKCC for cutaneous melanoma-related care within the past 12 months
  -  Cases: recent diagnosis (≤ 12 months) of unequivocal invasive cutaneous melanomas (AJCC Stages I-IV) confirmed by MSKCC pathology
  -  Cases: completion of surgical treatment of primary melanoma
  -  Ability to sign informed consent
  Exclusion Criteria:
  -  Known germline high-penetrance melanoma predisposition mutation (that is, CDKN2A and CDK4)
  -  Cases: history of invasive cutaneous melanoma (AJCC Stages I-IV) not confirmed by MSKCC pathology, history of acrolentiginous type of cutaneous melanoma
  -  Cases: history of systemic adjuvant therapy or treatment of metastatic melanoma, including: MEK inhibitors (trametinib, cobimetinib, etc.), BRAF inhibitors (vemurafenib, dabrafenib, etc.), and immunotherapy (pembrolizumab, nivolumab, atezolizumab, ipilimumab, etc.). Controls: history of Stage 0-IV melanoma confirmed by MSKCC pathology
  -  History of limb amputation or other condition (e.g., tattoos, burns) per investigator discretion that would modify nevus phenotype
  -  Physical inability to undergo total body photography or reflectance confocal microscopy imaging (that is, remain relatively still for durations of 3-5 minutes)
  -  Known hypersensitivity to adhesive rings used for reflectance confocal microscopy
  -  Inability to give informed consent
  -  Have skin afflicted with anther skin condition (for example, psoriasis) that would affect ability to characterize nevus phenotype (per investigator discretion)
  -  Familial cutaneous melanoma history (families with at least one invasive melanoma and two or more other diagnoses of invasive melanoma or pancreatic cancer among first- or second-degree relatives on the same side of the family). We will confirm melanoma family history via medical record documentation, whenever possible, as recommended by previous studies that disproved about half of the reported family histories of melanoma among first-degree relatives in case-control studies.

Relevance to patient case: not relevant
Patient case: 67-year-old male with melanoma; genetic feature: BRAF (V600E), NRAS (Q61R)

Clinical trial: Diagnostic Study to Predict the Risk of Developing Metastatic Cancer in Patients With Stage I or Stage II Melanoma

Summary: RATIONALE: Diagnostic procedures that analyze surgically-removed tumor tissue and lymph node samples may help doctors identify patients with melanoma who are at risk for developing metastatic cancer.
  PURPOSE: This clinical trial is studying tumor tissue and lymph node samples to see how well they work in predicting the development of metastatic cancer in patients with stage I or stage II melanoma.

Detailed description: OBJECTIVES:
  -  Correlate degree of melastatin gene expression with risk of developing local regional metastases in patients with primary stage I or II melanoma.
  -  Correlate melastatin expression prospectively with event-free survival of these patients.
  OUTLINE: This is a multicenter study.
  Melastatin mRNA expression is determined by in situ hybridization using tissue from primary tumor and lymph nodes. Tissue is also examined by immunohistochemical staining using antibodies to S-100 and MART-1. Patients do not receive the results of these tests nor do the results influence individual therapy.
  Patients are followed every 4 months for 3.5 years.
  PROJECTED ACCRUAL: A total of 300 patients will be accrued for this study within 3.5 years.

Eligibility: 1. Histologically documented primary AJCC stage I or II melanoma. Evidence of ulceration, vertical growth phase, regression, lymphocytic infiltration, vascular invasion, microscopic satellitosis, and mitotic rate shall be noted.
  2. Patients planning to undergo a sentinel lymph node biopsy, or an elective lymph node dissection of an anatomic draining region from the index primary melanoma.
  3. ≥18 years of age
  4. Patients must be registered prior to planned surgery. The surgery must be performed within 45 days following registration.
  5. No concurrent active malignancy other than carcinoma in situ of the cervix and basal cell carcinoma of the skin, or history of any other primary malignancy including previously primary melanoma.
  6. Tissue blocks: one of primary tumor tissue taken from region of greatest Breslow thickness. Note: If blocks cannot be sent due to institutional policy, slides may be substituted for the locks per the protocol.

Relevance to patient case: not relevant