araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Comparing the Reliability of Expressed Prostatic Secretion (EPS) and Post Massage Urine (PMU) for the Prediction of Prostate Cancer Biopsy Outcome

Summary: This randomized pilot phase I trial studies the best way, either expressed prostatic secretion (EPS) or post massage urine (PMU) biomarkers, of predicting biopsy results in patients undergoing prostate biopsy. Studying samples of urine in the laboratory may help doctors detect prostate cancer. It is not yet known whether EPS or PMU biomarkers are more effective in predicting prostate biopsy results

Detailed description: OBJECTIVES:
  I. To determine which non-invasive test for prostate cancer, EPS or PMU, is a better predictor of prostate cancer biopsy result. (Part I)
  II. To determine whether standardized testing for transmembrane protease, serine 2 (TMPRSS2):ERG Types III and VI is superior to testing for TMPRSS2:ERG Type III in predicting prostate biopsy outcome. (Part I)
  III. To expand the sample size utilizing the best TMPRSS2:ERG test and the best specimen type as determined in objective I and II in order to estimate with reasonable accuracy the positive predictive value (PPV) and negative predictive value (NPV) for each test. (Part II)
  IV. To expand the biomarker set, to include Prostate Cancer Antigen 3 (PCA3)-ribonucleic acid (RNA), d-glyceraldehyde-3-phosphate dehydrogenase (GADPH)-RNA, prostate-specific antigen (PSA)-RNA, and deoxyribonucleic acid (DNA) methylation levels at glutathione s-transferase pi (GSTP1), adenomatous polyposis coli (APC), retinoic acid receptor beta (RARB), Mitochondrial DNA (MT-DNA) Deletions and ras association (RalGDS/AF-6) domain family 1 (RASSF1), so as to develop an extensive data set for use in multivariate analysis. (Part II)
  V. Use multivariate analysis to determine which combination of molecular markers offers the greatest improvements in our ability to predict biopsy outcome over current baseline predictors (Serum PSA and digital rectal examination [DRE]). (Part II)
  VI. Estimate PPV and NPVs from this analysis and compare them to the standard assay's performance. (Part II)
  OUTLINE: Patients are randomized to 1 of 2 treatment arms. ARM I: Patients receive digital rectal palpation and then void a spontaneous urine sample for PMU analysis. Patients then undergo a prostate biopsy.
  ARM II: Patients receive DRE with prostatic massage for 30-60 seconds and are then milked at the urethra to provide a collection of EPS. Patients then undergo a prostate biopsy.

Eligibility: Inclusion Criteria:
  -  All men who will be undergoing transrectal ultrasound of the prostate (TRUSP) with biopsy in the department of Urology or participating urology clinics for the evaluation of prostate cancer
  Exclusion Criteria:
  -  Men with a previous diagnosis of prostate cancer
  -  Men without a prior diagnosis of prostate cancer but who have previously undergone a biopsy for a suspicious DRE or PSA
  -  Men with a prior diagnosis of cancer < 5 years ago, excluding basal cell carcinoma and/or squamous cell carcinoma

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Brentuximab Vedotin in Patients With CD30-positive Nonlymphomatous Malignancies

Summary: This is an open-label, multicenter, phase 2 clinical trial to evaluate the antitumor activity of brentuximab vedotin as a single agent in patients with CD30-positive nonlymphomatous malignancies.


Eligibility: Inclusion Criteria:
  -  Histologically-confirmed by central review CD30-positive nonlymphomatous malignancy
  -  Have failed, refused, or have been deemed ineligible for standard therapy
  -  Measurable disease
  -  Eastern Cooperative Oncology Group (ECOG) Performance Status score of 0 or 1 or a Karnofsky or Lansky Performance Status score greater than or equal to 70
  Exclusion Criteria:
  -  Primary diagnosis of lymphoma or central nervous system (CNS) malignancy
  -  History of another primary invasive malignancy that has not been definitively treated or in remission for at least 3 years
  -  Evidence of active cerebral/meningeal disease

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Phase 1 Study of MLN0264 in Adult Patients With Advanced Gastrointestinal Malignancies Expressing Guanylyl Cyclase C

Summary: This is an Open-Label, Multicenter, Dose Escalation, First-in-Human Study of MLN0264 in Adult Patients With Advanced Gastrointestinal Malignancies Expressing Guanylyl Cyclase C.


Eligibility: Inclusion Criteria:
  -  Voluntary consent form
  -  Diagnosis of GI malignancy with a GCC protein expressing tumor
  -  Male or female patients 18 years or older with measurable disease as defined by Response Evaluation Criteria in Solid Tumors (RECIST)
  -  Female patients who are post menopausal, surgically sterile, or agree to practice 2 effective methods of contraception or agree to abstain from heterosexual intercourse
  -  Male patients who agree to practice effective barrier contraception or agree to abstain from heterosexual intercourse
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1
  -  Adequate bone marrow, hepatic and renal function as specified in the protocol
  Exclusion Criteria:
  -  Female patients who are lactating or have a positive serum pregnancy test during the screening period
  -  Any serious medical or psychiatric illness that could interfere with the completion of treatment
  -  Major surgery or treatment with investigational drug before the first dose
  -  Serious infection within 14 days before the first dose of study drug
  -  Known HIV, inflammatory bowel disease, viral hepatitis or cerebral/meningeal brain metastases
  -  Patients with cardiovascular conditions specified in protocols
  -  Patients with history of another primary malignancy not in remission for at least 3 years
  Please note that there are additional inclusion and exclusion criteria. The study center will determine if you meet all of the criteria.
  Site personnel will explain the trial in detail and answer any question you may have if you do qualify for the study. You can then decide whether or not you wish to participate. If you do not qualify for the trial, site personnel will explain the reasons.

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Reduced Planning Target Volume (PTV) Margins for the Treatment of Prostate Cancer Using the Calypso 4D Localization System

Summary: This prospective study evaluates the clinical utility of a novel real-time localization system allowing for smaller volumes of normal tissue to be included in radiation field and determines dosimetric parameters and adverse effect profiles of radiation therapy using this technology. Subjects will have beacon transponders implanted into the prostate to more precisely localize the position of the organ during radiation therapy. Hypothesis: 1. Treatment with highly targeted radiation therapy can be delivered in a daily treatment time consistent with routine clinical practice. 2. Highly targeted radiation therapy with reduced PTV margin will result in a significant decrease in rectal and bladder volume treated.

Detailed description: This study will seek to establish the clinical feasibility of a novel real-time localization and tracking system for use of reduced PTV margins during intensity modulated radiation therapy (IMRT), which will allow treatment of smaller volumes of normal tissue during radiation therapy. Such a reduction in the PTV margins and the exposure of healthy tissue during treatment may allow for several future improvements in prostate radiotherapy including:
  -  decreased acute and chronic adverse effects with similar local tumor control
  -  dose escalation to achieve higher cure rates with similar adverse effects to standard dose treatment
  -  hypofractionation to shorten the time of, and lower the expense of, treatment without increased adverse effects.

Eligibility: Inclusion Criteria:
  -  Histologically confirmed adenocarcinoma of the prostate
  -  Low Risk: T1a, T1b, T1c, T2a; Gleason Score less than 7, PSA less than or equal to 10
  -  Intermediate Risk: T2b, T2c; Gleason Score less than or equal to 7, PSA less than or equal to 15
  -  Ability to comply with study schedule
  -  Age 40 or older
  -  Zubrod PS 0 or 1
  -  Signed informed consent
  Exclusion Criteria:
  -  Node positive or metastatic prostate cancer
  -  Prior treatment of prostate cancer with surgery, chemotherapy, cryotherapy or brachytherapy
  -  History of prior pelvic radiotherapy
  -  History of abdominoperineal resection
  -  History of HIV infection
  -  History of chronic prostatitis or chronic cystitis
  -  History of bleeding disorder or any active anticoagulation (excluding ASA)
  -  PT or INR outside normal range for institution
  -  Active implanted devices such as cardiac pacemakers and automatic defibrillators.
  -  Prosthetic implants in the pelvic region that contain metal or conductive materials (eg., an artificial hip).
  -  Patients with maximum anterior-posterior separation through the torso minus the height of the center of the prostate greater than 17 cm (technical reason for Calypso System, see appendix 8).
  -  Prior history of androgen deprivation therapy has been deleted and these patients are allowed on study.

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Open-Label,Non-Randomized Trial of Cisplatin Chemotherapy in BRCA1-Positive Metastatic Breast Cancer Patients

Summary: Among women with a BRCA1 mutation and breast cancer, choice of chemotherapy is a critical issue. There are emerging data which suggest that mutation carriers may respond differently than non-carriers to particular agents. BRCA1-associated cancers differ from non-hereditary cancers for a range of pathologic and molecular factors, including tumor grade and histologic appearance. Several studies have shown that the response to treatment for women with a BRCA1-associated breast cancer reflects the underlying tumor biology, in particular, the impairment of the DNA damage response and repair pathways, and that it is possible to exploit the sensitivity of BRCA1-associated cancers to DNA damage.
  It is equally important that the investigators evaluate the benefit of cisplatin in women with disseminated breast cancer, including those who have previously been treated with one or more chemotherapy regimens. This study is undertaken to evaluate the efficacy of cisplatin chemotherapy in BRCA1 carriers with metastatic breast cancer. The primary objective is to determine the objective response rate of cisplatin in BRCA1 carriers with metastatic breast cancer. The secondary objectives are to determine 3-year survival and to evaluate the toxicities of cisplatin in BRCA1 carriers with metastatic breast cancer.


Eligibility: Inclusion Criteria:
  -  Female patients aged ≥ 18 years, with measurable (defined by Response Evaluation Criteria in Solid Tumors (RECIST) criteria (14)) metastatic (stage IV) breast cancer, and who are known to carry a BRCA1 mutation, are eligible.
  -  In addition, the following are required:
  -  adequate hematologic
  -  renal, and hepatic function
  -  adequate recovery from recent surgery and/or radiation therapy
  -  recovery from all prior treatment-related toxicities (to grade < 2 according to National Cancer Institute Common Toxicity Criteria, Version3.0, except alopecia)
  -  life expectancy of at least 12 weeks
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1. -
  -  Patients could have received up to four prior chemotherapies for metastatic disease.
  Exclusion Criteria:
  -  Patients with known brain metastases are not eligible.
  -  Patients previously treated with a platinum-based chemotherapy are not eligible.

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: To Investigate the Safety and Tolerability of Aztreonam-Avibactam (ATM-AVI)

Summary: This is a randomised, double-blind, 3-part study designed to investigate the safety and tolerability of ATM-AVI. The study aims to characterise the pharmacokinetics of ATM-AVI, when both drugs are administered alone (ATM or AVI) and in combination (ATM-AVI), following single administration, and following multiple administrations of ATM-AVI in healthy male and female (females of nonchildbearing potential) volunteers both young and elderly.

Detailed description: A Phase I, Randomised, Double-blind, 3-Part Study in Healthy Young and Elderly Subjects to Assess the Safety and Tolerability, and Investigate the Pharmacokinetics of Aztreonam and Avibactam given Alone and in Combination (ATM-AVI)

Eligibility: Inclusion Criteria:
  -  Provision of signed and dated, written informed consent prior to any study specific procedures
  -  Healthy young male and female volunteers aged 18 to 45 years (inclusive) and healthy elderly volunteers aged 65 or older (Part C) with suitable veins for cannulation or repeated venipuncture
  -  Have a body mass index (BMI) between 19 and 30 kg/m2
  -  Be able to understand and willing to comply with study procedures, restrictions, and requirements, as judged by the PI
  Exclusion Criteria:
  -  History of any clinically significant disease or disorder which, in the opinion of the PI, may either put the volunteer at risk because of participation in the study, or influence the results or the volunteer's ability to participate in the study
  -  History or presence of gastrointestinal, hepatic, or renal disease, or any other condition known to interfere with absorption, distribution, metabolism, or excretion of drugs
  -  Known history of severe allergy to betalactam and/or L-arginine
  -  History of severe allergy/hypersensitivity or ongoing clinically important allergy/hypersensitivity, as judged by the PI or history of hypersensitivity to drugs with a similar chemical structure or class to ATM or AVI
  -  Any clinically significant illness, medical/surgical procedure, or trauma within 4 weeks prior to the first administration of IP

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Atomoxetine Treatment for Cognitive Impairment in Parkinson's Disease (ATM-Cog)

Summary: The purpose of this study is to determine the safety and effectiveness of a drug called atomoxetine for the treatment of cognitive impairment for Parkinson 's disease. Atomoxetine (ATM) is an approved drug currently on the market for the treatment of attention deficit. It works to increase the amount of norepinephrine (a chemical in the brain that helps keep us awake and alert) in our brain. ATM has not been approved by the Food and Drug Administration (FDA) to be used in the treatment of PD.


Eligibility: Inclusion Criteria:
  -  Confirmed diagnosis of idiopathic PD according to the United Kingdom Parkinson's Disease Society Brain Bank (UKPDSBB) criteria
  -  Male or female subjects aged between 35 and 75 years, inclusive at the time of consent
  -  Hoehn & Yahr Stage I-IV
  -  Diagnosis of PD mild cognitive impairment (MCI), Montreal Cognitive Assessment (MoCa) score 21-25
  -  Stable concomitant medications for 60 days
  Exclusion Criteria:
  -  Secondary parkinsonism or atypical parkinsonism, Prior Deep Brain Stimulation (DBS) or other brain surgery
  -  PD Dementia; MoCA score <21
  -  Presence of Psychosis, pregnancy, suicidal ideation on the Columbia Suicide Severity Rating Scale (C-SSRS) type 4 or 5 in past 3 months.
  -  Current treatment with anticholinergics, monoamine oxidase (MAO) inhibitors or neuroleptics (including quetiapine)
  -  Serious cardiac abnormalities, Narrow angle glaucoma, Pheochromocytoma, Bipolar Disorder
  -  Liver Function Tests (LFTs) >1.5 X upper limit of normal value

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: ARCHER1050: A Study of Dacomitinib vs. Gefitinib in 1st-Line Treatment Of Advanced NSCLC.

Summary: This is a multinational, multicenter, randomized, open-label, Phase 3 study comparing the efficacy and safety of treatment with dacomitinib (PF-00299804) to treatment with gefitinib in patients with locally advanced or metastatic non-small cell lung cancer, with epidermal growth factor receptor EGFR-activating mutation (s). Analyses of primary objective (Progression Free Survival) will be done as defined in the protocol.

Detailed description: 452 patients were randomized in a 1:1 ratio between dacomitinib (PF-00299804 ) vs. gefitinib.

Eligibility: Inclusion Criteria:
  -  Evidence of histo or cytopathology confirmed, advanced NSCLC (with known histology) with the presence of EGFR-activating mutation (exon 19 deletion or the L858R mutation in exon 21).
  -  It is acceptable for subjects with the presence of the exon 20 T790M mutation together with either EGFR-activating mutation (exon 19 deletion or the L858R mutation in exon 21) to be included in this study
  -  Minimum of 12 months disease free interval between completion of systemic therapy and recurrence of NSCLC
  -  Adequate tissue sample must be available for central analyses.
  -  Adequate renal, hematologic, liver function.
  -  ECOG PS of 0-1.
  -  Radiologically measurable disease.
  Exclusion Criteria:
  -  Any evidence of mixed histology that includes elements of small cell or carcinoid lung cancer.
  -  Any other mutation other than exon 19 deletion or L858R in exon 21, with or without the presence of the exon 20 T790M mutation.
  -  Any history of brain mets or leptomeningeal mets.
  -  Any previous anti-cancer systemic treatment of early, locally advanced, or metastatic NSCLC.
  -  Uncontrolled medical disorders.

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Efficacy and Safety Study of Olaparib in Combination With Paclitaxel to Treat Advanced Gastric Cancer.

Summary: This study is a phase III, multi-centre study of olaparib in combination with paclitaxel, compared with placebo in combination with paclitaxel in patients with advanced gastric cancer who have progressed following first-line therapy. Patients will be from China, Japan , Korea and Taiwan.

Detailed description: A randomized, double-blinded, multicentre phase III study to access the efficacy and safety of olaparib in combination with paclitaxel, compared with placebo in combination with paclitaxel in Asian patients with advanced gastric cancer (including gastro-oesophageal junction) who have progressed following first line therapy.

Eligibility: Inclusion Criteria:
  -  Advanced gastric cancer (including GEJ) that has progressed following first-line therapy.
  -  Patients must be ≥18 years of age. Age ≥20 if Japanese
  -  Provision of tumour sample (from either a resection or biopsy).
  -  At least one lesion (measurable and/or non-measurable) that can be accurately assessed by imaging (CT/MRI) at baseline and following up visits.
  Exclusion Criteria:
  -  More than one prior chemotherapy regimen (except for adjuvant/neoadjuvant chemotherapy with more than 6 month wash out period) for the treatment of gastric cancer in the advanced setting.
  -  Any previous treatment with a Polyadenosine 5'-diphosphoribose [poly-(ADP-ribose)] polymerisation (PARP) inhibitor, including olaparib.
  -  Patients with second primary cancer, except: adequately treated non-melanoma skin cancer, curatively treated in-situ cancer of the cervix, or other solid tumours curatively treated with no evidence of disease for ≥5 years.
  -  Human Epidermalgrowth Factor Receptor-2 (HER2) positive patients.

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Cord Blood Transplantation in Patients With Advanced Lymphoid Malignancies

Summary: Indication: Patients with advanced lymphoid malignancies in the absence of an HLA identical or mismatch donor.
  Objectives: Overall survival at one year. Efficacy >60%, rejection rate <20%. Inclusion criteria: Age: 18-65 years old, no sibling or unrelated donor identified, low grade non-hodgkin lymphoma in third line (who already received at least one autologous transplantation); hodgkin lymphoma in early relapse (<1 year), who received at least one autologous transplantation and sensible to chemotherapy and CLL with 17p deletion or in relapse less than 2 year after a fludarabine nbased regimen or in relapse after one autologous transplantation.
  Stem cell source: Two cord blood units containing both together more than 3x107 frozen nucleated cells/Kg with no more than 2 out of 6 HLA mismatches between them and with the patients.


Eligibility: Inclusion Criteria:
  -  Age: 18-65 years old
  -  no sibling or unrelated donor identified (9/10 or 10/10)
  -  with either one of these advanced lymphoid malignancies
  1. low grade non-hodgkin lymphoma in third line (who already received at least one autologous transplantation)
  2. hodgkin lymphoma in early relapse (<1 year)who received at least one autologous transplantation and sensible to chemotherapy
  3. CLL with 17p deletion or in relapse less than 2 year after a fludarabine nbased regimen or in relapse after one autologous transplantation.
  Exclusion Criteria:
  -  No patient signed consent
  -  Previous allograft
  -  Psychiatric conditions
  -  HIV positive
  -  HVC hepatitis requiring treatment
  -  Previous total body irradiation (TBI)
  -  Any contraindication to TBI
  -  Any contraindication to allograft, such as cardiovascular, respiratory, renla or liver dysfunctions
  -  No Health care insurance

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Prostate Screening Study Using MRI in BRCA Carriers

Summary: Men with a BRCA1 or BRCA2 mutation are at increased risk for early onset, aggressive prostate cancer compared to men in the general population.
  Standard of care screening for men with a BRCA mutation includes PSA testing and digital rectal examination (DRE), the same as with men in the general population.
  This study is being done to assess whether there is value in using MRI as a screening tool to detect prostate cancer at an earlier stage than may otherwise be detected using standard of care screening (PSA, DRE). It is unclear whether MRI has utility as a screening tool in this specific population at high risk for aggressive disease.

Detailed description: To determine the value of using Multispectral 3T MRI (MS3TMRI) for prostate cancer screening in men with a high risk of developing early onset aggressive prostate cancer given known BRCA1 or BRCA2 mutation carrier status, with no prior prostate cancer diagnosis, independent of baseline PSA levels.
  -  Determine the prevalence of prostate cancer in BRCA1 and BRCA2 mutation carriers independent of baseline PSA levels.
  -  To evaluate the accuracy of tumor targeting based on MRI and ultrasound (US) tumor co-localization. To evaluate the sensitivity, specificity, PPV, NPV, and accuracy of an automated computer aided diagnosis method (CAD) applied to MS3TMRI in the prediction of zonal biopsy results for the presence or absence of a significant cancer.

Eligibility: Inclusion Criteria:
  -  Enrolled in the Male Hereditary Cancer Research Program at Sunnybrook Health Sciences Center.
  -  Have positive genetic testing for a pathogenic BRCA1 or BRCA2 mutation.
  -  Clinically eligible for and willing to undergo ultrasound biopsy within 4 weeks after the MRI.
  -  Be 50 years of age or older.
  Exclusion Criteria:
  -  Claustrophobia
  -  Contraindication to MRI
  -  Contraindication to receiving low molecular weight MRI contrast agent
  -  Previously diagnosed with prostate cancer

Relevance to patient case: not relevant